tag:blogger.com,1999:blog-17928966378147213502024-03-18T05:07:07.094-05:00Synthetic DaisiesScientific Synthesis, focusing on computation and complexity.Bradly Aliceahttp://www.blogger.com/profile/06482487682656113637noreply@blogger.comBlogger452125tag:blogger.com,1999:blog-1792896637814721350.post-79708194434641333802024-02-11T15:01:00.003-06:002024-02-12T08:47:24.614-06:00Charles Darwin meets Rube Goldberg: a tale of biological convolutedness<div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhhI_8ozlTIZ9FI0MT7usD7XIEtJ93CePlvvnI-f1BTaGIf8KsavVoEkv98G1uYcKPxVls2PMrLJ4K6LjDaAYjF6JVsnrn2T-fVxrjEmxlT6b1PHULNjVzAaFpt6HHNiw16TdI1QRXyVkv6WbWlmyU7wjdG4-3yQ9_AM2j_zQHjBrwwnSpHewA8z9_tAw0/s1344/charles-darwin-building-a-rube-goldberg-machine%20(1).jpg" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="768" data-original-width="1344" height="366" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhhI_8ozlTIZ9FI0MT7usD7XIEtJ93CePlvvnI-f1BTaGIf8KsavVoEkv98G1uYcKPxVls2PMrLJ4K6LjDaAYjF6JVsnrn2T-fVxrjEmxlT6b1PHULNjVzAaFpt6HHNiw16TdI1QRXyVkv6WbWlmyU7wjdG4-3yQ9_AM2j_zQHjBrwwnSpHewA8z9_tAw0/w640-h366/charles-darwin-building-a-rube-goldberg-machine%20(1).jpg" width="640" /></a></div><br /><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgAAlIC_eTLklMxaVfnJ-QY3C4Z3f0jvAQvN6rOrk6aXF8IhLSaZM5jSU85KfI0MFanDvfXR9fRP0dphHeL5MhqjwxH099iKRaiwMExTuaLhtmz-nnvJnClNP9BScnpIGh_Aj3EQkOlY8FKvgLghc86e7RvdnA6UZSkHuRlnl9vCNfir_tM8FzZlG-FNGU/s1344/charles-darwin-building-a-rube-goldberg-machine%20(4).jpg" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="768" data-original-width="1344" height="366" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgAAlIC_eTLklMxaVfnJ-QY3C4Z3f0jvAQvN6rOrk6aXF8IhLSaZM5jSU85KfI0MFanDvfXR9fRP0dphHeL5MhqjwxH099iKRaiwMExTuaLhtmz-nnvJnClNP9BScnpIGh_Aj3EQkOlY8FKvgLghc86e7RvdnA6UZSkHuRlnl9vCNfir_tM8FzZlG-FNGU/w640-h366/charles-darwin-building-a-rube-goldberg-machine%20(4).jpg" width="640" /></a></div><p style="text-align: center;">Charles Darwin studying a Rube Goldberg Machine (<a href="https://www.bing.com/ck/a?!&&p=680756bd2841c4a0JmltdHM9MTcwNzUyMzIwMCZpZ3VpZD0xZmVlN2UwMi1iZTBhLTY2ZmEtMmJhZS02ZGUzYmZkOTY3MDgmaW5zaWQ9NTI4Mw&ptn=3&ver=2&hsh=3&fclid=1fee7e02-be0a-66fa-2bae-6de3bfd96708&psq=freepik+generative+AI&u=a1aHR0cHM6Ly93d3cuZnJlZXBpay5jb20vZnJlZS1waG90b3MtdmVjdG9ycy9nZW5lcmF0aXZlLWFp&ntb=1">Freepik Generative AI, text-to-image</a>)</p><p style="text-align: justify;">For this Darwin Day post (2024), I will discuss the paper <i><a href="https://arxiv.org/abs/1104.3559">Machinery of Biocomplexity</a></i> [1]. This paper introduces the notion of <a href="https://en.wikipedia.org/wiki/Rube_Goldberg_machine">Rube Goldberg machines</a> as a way to explore biological complexity and non-optimal function. This concept was first highlighted on Synthetic Daises in 2009 [2], while an earlier version of the paper was discussed on Synthetic Daisies in 2013 [3]. The paper was revised in 2014 to include a number of more advanced computational concepts, after a talk to the <a href="http://dyn.phys.northwestern.edu/pdf/netfrontier2013.pdf">Network Frontiers Workshop</a> at Northwestern University in 2013 [4]. </p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj14KvFDw5YfhPu6IOs0yd7IowoHRJf7-Ui2iLRkpNVSUaKOWyKag5lSdMwnSzURqT2OQqnTCCb-eGa6_ujjkm3Q49G4nMnj1IYBdGTLIDd_QQ_PoL0_e-JkE7mA0k5jPajSY5PpMVoQgmAI05xLUQPYRjT3-bwXjMIwBmRZ7lRbJiz6h9HDNT8AAg_dXI/s575/transformations-in-boxes-arrows.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="298" data-original-width="575" height="332" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj14KvFDw5YfhPu6IOs0yd7IowoHRJf7-Ui2iLRkpNVSUaKOWyKag5lSdMwnSzURqT2OQqnTCCb-eGa6_ujjkm3Q49G4nMnj1IYBdGTLIDd_QQ_PoL0_e-JkE7mA0k5jPajSY5PpMVoQgmAI05xLUQPYRjT3-bwXjMIwBmRZ7lRbJiz6h9HDNT8AAg_dXI/w640-h332/transformations-in-boxes-arrows.png" width="640" /></a></div><p style="text-align: center;">Figure 1. Block and arrow model of a biological RGM (bRGM) that captures the non-optimal changes resulting from greater complexity. Mutation/Co-option removes the connection between A and B, then establishes a new set of connection with D. Inversion (bottom) flips the direction of connections between C-B and C-A, while also removing the output. This results in the addition of E and D which reestablishes the output in a circuitous manner.</p><p style="text-align: justify;">Biological Rube Goldberg Machines (bRGNs) are defined as a computational abstraction of convoluted, non-optimal mechanisms. Non-optimal biological systems are represented using flexible Markovian box and arrow models that can be mutated and expanded given functional imperatives [5]. Non-optimality is captured through the principle of "maximum intermediate steps": biological systems such as neural pathways, metabolic reactions, and serial interactions do not evolve to the shortest route but is constrained (and perhaps even converge to) the largest number of steps. This results in a set of biological traits that functionally emerge as a biological process. Figure 1B shows an example where maximal steps represents a balance between the path of least resistance and exploration given constraints on possible interconnections [6]. The paths from A-E, E-B, and C-D are the paths of least resistance given the constraints of structure and function. In the sense that optimality is a practical outcome of physiological function, a great degree of intermediacy can preserve unconventional pathways that are utilized only spontaneously.</p><p style="text-align: justify;">This can be seen in a wide variety of biological systems and is a consequence of evolution. Evolutionary exaptation, the evolution of alternative functions, and serial innovation all result in systems with a large number of steps from input to output. But sometimes convolution is the evolutionary imperative in and of itself. As fitness criteria change over evolutionary time, traces of these historical trajectories can be observed in redundant pathways and other results of subsequent evolutionary neutrality. One example from the paper involves a multiscale model (genotype-to-phenotype) that exploits both tree depth and lateral connectivity to maximize innovation in the production of a phenotype (Figure 2). While our models are based on connections between discrete states, bRGMs can also provide insight into the evolution of looser collections of single traits and even networks, where the sequence of function is bidirectional and hard to follow in stepwise fashion.</p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjYxWFkpoGcFn3EyKjDElZjjUrfXCDVpALoLRyLuAvscAN7aFcce9HJe7OXwFXYJC-0wzI8zCbkqJHWkL9Cw8kzXLNxoTWz4c9gzECOcRXvl0fRKlNKr75vtxwAL5AW6pDjrzWRtZh1h4BEDN1tZtkB4QLbG5aJoSoLOJihUZmiBCd5pA5usfSxxBrz1y4/s645/Figure%202.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="425" data-original-width="645" height="422" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjYxWFkpoGcFn3EyKjDElZjjUrfXCDVpALoLRyLuAvscAN7aFcce9HJe7OXwFXYJC-0wzI8zCbkqJHWkL9Cw8kzXLNxoTWz4c9gzECOcRXvl0fRKlNKr75vtxwAL5AW6pDjrzWRtZh1h4BEDN1tZtkB4QLbG5aJoSoLOJihUZmiBCd5pA5usfSxxBrz1y4/w640-h422/Figure%202.png" width="640" /></a></div><p style="text-align: center;">Figure 2. A hypothetical biological RGM representing a multi-scale relationship. Each set of elements (A-F) represents the number of elements at each scale (actual and potential connections are shown with bold and thin lines, respectively). Examples of convolutedness incorporate both loops (as with E5,1 and E5,5) and the depth of the entire network.</p><p style="text-align: justify;">The paper also features extensions of the basic bRGM, including massively convoluted architectures and microfluidic implementations. In the former, interconnected networks represent systems that are not only maximal in terms of size or length, but also massively topologically complex [7]. One example of this is cortical folding and the resulting neuronal connectivity in Mammalian brains. The latter example is based on fluid dynamics and combinatorial architectures that are more in line with discrete bRGMs (Figure 3). </p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgwzK0dWD17DW3FDsrPER6Fx-jYD8FTiaipGt3mUdecDvMw1QMSOzXOP36altgGwTFmnhqfL9STjPqQEw9u50Mq_lo9WkfzdgTK5zGk6URKNjdhsURamnKG1al5IS3cZg2MUQwt0QHuf60DBh6EQ4ZH-vbhFASa6h9Dlns2wIiLN8rWuOnSrLMUFpsCB-U/s597/microfluidic-model-mimic-biological-fluid-dynamics.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="288" data-original-width="597" height="308" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgwzK0dWD17DW3FDsrPER6Fx-jYD8FTiaipGt3mUdecDvMw1QMSOzXOP36altgGwTFmnhqfL9STjPqQEw9u50Mq_lo9WkfzdgTK5zGk6URKNjdhsURamnKG1al5IS3cZg2MUQwt0QHuf60DBh6EQ4ZH-vbhFASa6h9Dlns2wIiLN8rWuOnSrLMUFpsCB-U/w640-h308/microfluidic-model-mimic-biological-fluid-dynamics.png" width="640" /></a></div><div style="text-align: center;">Figure 3. A microfluidic-inspired bRGM model that mimics the complexity of biological fluid dynamics (e.g. blood vessel networks). G1, G2, and G3 represent iterations of the system.</div><p><br /></p><p><b>References:</b></p><p style="text-align: justify;">[1] Alicea, B. (2014). <a href="https://arxiv.org/abs/1104.3559">The "Machinery" of Biocomplexity: understanding non-optimal architectures in biological systems</a>. <i>arXiv</i>, 1104.3559.</p><p style="text-align: justify;">[2] Non-razors, unite! January 30, 2009. <a href="https://syntheticdaisies.blogspot.com/2009/01/non-razors-unite.html">https://syntheticdaisies.blogspot.com/2009/01/non-razors-unite.html</a></p><p style="text-align: justify;">[3] Maps, Models, and Concepts: July Edition. <i>Synthetic Daises</i> blog. July 13, 2013. <a href="https://syntheticdaisies.blogspot.com/2013/07/maps-models-and-concepts-july-edition.html">https://syntheticdaisies.blogspot.com/2013/07/maps-models-and-concepts-july-edition.html</a></p><p style="text-align: justify;">[4] Inspired by a visit to the Network's Frontier.... <i>Synthetic Daises</i> blog. December 16, 2013. <a href="https://syntheticdaisies.blogspot.com/2013/12/fireside-science-inspired-by-visit-to.html">https://syntheticdaisies.blogspot.com/2013/12/fireside-science-inspired-by-visit-to.html</a></p><div>[5] when dealing with a large number of steps or in a polygenic context, these types of models can also resemble renormalization groups. For more on renormalization group, please see: Wilson, K.G. (1975). <a href="https://www.sciencedirect.com/science/article/pii/0001870875901498">Renormalization group methods</a>. <i>Advances in Mathematics</i>, 16(2), 170-186.</div><div><br /></div><div>[6] this balance is as predicted by Constructive Neutral Evolution (CNE). For a relevant paper, please see: Gray et.al (2010). <a href="https://www.science.org/doi/10.1126/science.1198594">Irremediable Complexity?</a> <i>Science</i>, 330(6006), 920-921.</div><div><br /></div><div>[7] in the paper, this is referred to as Spaghettification, a term borrowed from the physics of gravitation. See this reference for an interesting implementation of this in soft materials: Bonamassa et.al (2024). <a href="https://arxiv.org/abs/2401.02579">Bundling by volume exclusion in non-equilibrium spaghetti</a>. <i>arXiv</i>, 2401.02579.</div>Bradly Aliceahttp://www.blogger.com/profile/06482487682656113637noreply@blogger.com0tag:blogger.com,1999:blog-1792896637814721350.post-20069355568146602442023-08-24T09:54:00.000-05:002023-08-24T09:54:00.174-05:00Saturday Morning NeuroSim Discussion Thread: Physical Computing<p> <img alt="" class="bg mc md c" height="184" loading="eager" role="presentation" src="https://miro.medium.com/v2/resize:fit:700/1*0wDFdbfI7VxTnsV5yYbFig.png" style="background-color: white; box-sizing: inherit; color: rgba(0, 0, 0, 0.8); font-family: medium-content-sans-serif-font, -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, Oxygen, Ubuntu, Cantarell, "Open Sans", "Helvetica Neue", sans-serif; height: auto; max-width: 100%; vertical-align: middle; width: 680px;" width="700" /></p><figure class="ls lt lu lv lw lx lp lq paragraph-image" style="background-color: white; box-sizing: inherit; clear: both; color: rgba(0, 0, 0, 0.8); font-family: medium-content-sans-serif-font, -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, Oxygen, Ubuntu, Cantarell, "Open Sans", "Helvetica Neue", sans-serif; margin: 40px auto 0px;"><figcaption class="me mf mg lp lq mh mi be b bf z dv" data-selectable-paragraph="" style="box-sizing: inherit; color: #6b6b6b; font-family: sohne, "Helvetica Neue", Helvetica, Arial, sans-serif; font-size: 14px; line-height: 20px; margin-left: auto; margin-right: auto; margin-top: 10px; max-width: 728px; text-align: center;">From the “Macy Conference Redux” feature form our July 1 meeting</figcaption></figure><p class="pw-post-body-paragraph mj mk fo ml b mm mn mo mp mq mr ms mt mu mv mw mx my mz na nb nc nd ne nf ng fh bj" data-selectable-paragraph="" id="0fcd" style="background-color: white; box-sizing: inherit; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;">Over the past three years, the <a class="af nh" href="https://representational-brains-phenotypes.weebly.com/saturday-morning-neurosim.html" rel="noopener ugc nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;" target="_blank">Saturday Morning NeuroSim</a> group has met weekly on Saturdays (mornings in North America). The Saturday Morning format continues in the tradition of Saturday Morning Physics and covers a wide variety of topics.</p><p class="pw-post-body-paragraph mj mk fo ml b mm mn mo mp mq mr ms mt mu mv mw mx my mz na nb nc nd ne nf ng fh bj" data-selectable-paragraph="" id="f8c0" style="background-color: white; box-sizing: inherit; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;">One recent lecture/discussion thread is on Physical Computation. Our approach to the topic begins with the debate around the role of computation in Cognitive Science and the Neurosciences. And so we begin in Week 1 with a discussion of the connections between computation, information processing, and the brain, largely focusing on the work of <a class="af nh" href="https://en.wikipedia.org/wiki/Gualtiero_Piccinini" rel="noopener ugc nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;" target="_blank">Gualtiero Piccinini</a> and <a class="af nh" href="https://coreymaley.net/" rel="noopener ugc nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;" target="_blank">Corey Maley</a>. A starting point for this session is their <a class="af nh" href="https://plato.stanford.edu/" rel="noopener ugc nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;" target="_blank">Stanford Encyclopedia of Philosophy</a> article on “<a class="af nh" href="https://plato.stanford.edu/entries/computation-physicalsystems/" rel="noopener ugc nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;" target="_blank">Computation in Physical Systems</a>”. Many current assumptions about computation in the brain stem from the <a class="af nh" href="https://en.wikipedia.org/wiki/Church%E2%80%93Turing_thesis" rel="noopener ugc nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;" target="_blank">Church-Turing thesis</a>, which often leads to a poor fit between model and experiment. Piccinini and Maley propose that the <a class="af nh" href="https://en.wikipedia.org/wiki/Church%E2%80%93Turing%E2%80%93Deutsch_principle" rel="noopener ugc nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;" target="_blank">Church-Turing-Deutsch</a> thesis is preferable when talking about systems that perform non-digital computations. Amanda Nelson pointed out the it makes sese to think of evolved biological systems (brains) as instances of analogue computers. Another interesting point from the session is the distinction between the digital (<a class="af nh" href="https://en.wikipedia.org/wiki/Von_Neumann_architecture" rel="noopener ugc nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;" target="_blank">Von Neumann</a>) computers and alternatives such as “physical” or “analog” computation, which would be picked up on in the next session.</p><figure class="nj nk nl nm nn lx lp lq paragraph-image" style="background-color: white; box-sizing: inherit; clear: both; color: rgba(0, 0, 0, 0.8); font-family: medium-content-sans-serif-font, -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, Oxygen, Ubuntu, Cantarell, "Open Sans", "Helvetica Neue", sans-serif; margin: 56px auto 0px;"><div class="ly lz eb ma bg mb" role="button" style="box-sizing: inherit; cursor: zoom-in; position: relative; transition: transform 300ms cubic-bezier(0.2, 0, 0.2, 1) 0s; width: 680px; z-index: auto;" tabindex="0"><div class="lp lq ni" style="box-sizing: inherit; margin-left: auto; margin-right: auto; max-width: 4480px;"><picture style="box-sizing: inherit;"><source sizes="(min-resolution: 4dppx) and (max-width: 700px) 50vw, (-webkit-min-device-pixel-ratio: 4) and (max-width: 700px) 50vw, (min-resolution: 3dppx) and (max-width: 700px) 67vw, (-webkit-min-device-pixel-ratio: 3) and (max-width: 700px) 65vw, (min-resolution: 2.5dppx) and (max-width: 700px) 80vw, (-webkit-min-device-pixel-ratio: 2.5) and (max-width: 700px) 80vw, (min-resolution: 2dppx) and (max-width: 700px) 100vw, (-webkit-min-device-pixel-ratio: 2) and (max-width: 700px) 100vw, 700px" srcset="https://miro.medium.com/v2/resize:fit:640/format:webp/1*gaMKaP6oqmgaMsiTJ6Slkg.png 640w, https://miro.medium.com/v2/resize:fit:720/format:webp/1*gaMKaP6oqmgaMsiTJ6Slkg.png 720w, https://miro.medium.com/v2/resize:fit:750/format:webp/1*gaMKaP6oqmgaMsiTJ6Slkg.png 750w, https://miro.medium.com/v2/resize:fit:786/format:webp/1*gaMKaP6oqmgaMsiTJ6Slkg.png 786w, https://miro.medium.com/v2/resize:fit:828/format:webp/1*gaMKaP6oqmgaMsiTJ6Slkg.png 828w, https://miro.medium.com/v2/resize:fit:1100/format:webp/1*gaMKaP6oqmgaMsiTJ6Slkg.png 1100w, https://miro.medium.com/v2/resize:fit:1400/format:webp/1*gaMKaP6oqmgaMsiTJ6Slkg.png 1400w" style="box-sizing: inherit;" type="image/webp"></source><source data-testid="og" sizes="(min-resolution: 4dppx) and (max-width: 700px) 50vw, (-webkit-min-device-pixel-ratio: 4) and (max-width: 700px) 50vw, (min-resolution: 3dppx) and (max-width: 700px) 67vw, (-webkit-min-device-pixel-ratio: 3) and (max-width: 700px) 65vw, (min-resolution: 2.5dppx) and (max-width: 700px) 80vw, (-webkit-min-device-pixel-ratio: 2.5) and (max-width: 700px) 80vw, (min-resolution: 2dppx) and (max-width: 700px) 100vw, (-webkit-min-device-pixel-ratio: 2) and (max-width: 700px) 100vw, 700px" srcset="https://miro.medium.com/v2/resize:fit:640/1*gaMKaP6oqmgaMsiTJ6Slkg.png 640w, https://miro.medium.com/v2/resize:fit:720/1*gaMKaP6oqmgaMsiTJ6Slkg.png 720w, https://miro.medium.com/v2/resize:fit:750/1*gaMKaP6oqmgaMsiTJ6Slkg.png 750w, https://miro.medium.com/v2/resize:fit:786/1*gaMKaP6oqmgaMsiTJ6Slkg.png 786w, https://miro.medium.com/v2/resize:fit:828/1*gaMKaP6oqmgaMsiTJ6Slkg.png 828w, https://miro.medium.com/v2/resize:fit:1100/1*gaMKaP6oqmgaMsiTJ6Slkg.png 1100w, https://miro.medium.com/v2/resize:fit:1400/1*gaMKaP6oqmgaMsiTJ6Slkg.png 1400w" style="box-sizing: inherit;"></source><img alt="" class="bg mc md c" height="394" loading="lazy" role="presentation" src="https://miro.medium.com/v2/resize:fit:700/1*gaMKaP6oqmgaMsiTJ6Slkg.png" style="box-sizing: inherit; height: auto; max-width: 100%; vertical-align: middle; width: 680px;" width="700" /></picture></div></div></figure><figure class="nj nk nl nm nn lx lp lq paragraph-image" style="background-color: white; box-sizing: inherit; clear: both; color: rgba(0, 0, 0, 0.8); font-family: medium-content-sans-serif-font, -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, Oxygen, Ubuntu, Cantarell, "Open Sans", "Helvetica Neue", sans-serif; margin: 56px auto 0px;"><div class="ly lz eb ma bg mb" role="button" style="box-sizing: inherit; cursor: zoom-in; position: relative; transition: transform 300ms cubic-bezier(0.2, 0, 0.2, 1) 0s; width: 680px; z-index: auto;" tabindex="0"><div class="lp lq ni" style="box-sizing: inherit; margin-left: auto; margin-right: auto; max-width: 4480px;"><picture style="box-sizing: inherit;"><source sizes="(min-resolution: 4dppx) and (max-width: 700px) 50vw, (-webkit-min-device-pixel-ratio: 4) and (max-width: 700px) 50vw, (min-resolution: 3dppx) and (max-width: 700px) 67vw, (-webkit-min-device-pixel-ratio: 3) and (max-width: 700px) 65vw, (min-resolution: 2.5dppx) and (max-width: 700px) 80vw, (-webkit-min-device-pixel-ratio: 2.5) and (max-width: 700px) 80vw, (min-resolution: 2dppx) and (max-width: 700px) 100vw, (-webkit-min-device-pixel-ratio: 2) and (max-width: 700px) 100vw, 700px" srcset="https://miro.medium.com/v2/resize:fit:640/format:webp/1*v_1scLJzaSpiqCeuiendhw.png 640w, https://miro.medium.com/v2/resize:fit:720/format:webp/1*v_1scLJzaSpiqCeuiendhw.png 720w, https://miro.medium.com/v2/resize:fit:750/format:webp/1*v_1scLJzaSpiqCeuiendhw.png 750w, https://miro.medium.com/v2/resize:fit:786/format:webp/1*v_1scLJzaSpiqCeuiendhw.png 786w, https://miro.medium.com/v2/resize:fit:828/format:webp/1*v_1scLJzaSpiqCeuiendhw.png 828w, https://miro.medium.com/v2/resize:fit:1100/format:webp/1*v_1scLJzaSpiqCeuiendhw.png 1100w, https://miro.medium.com/v2/resize:fit:1400/format:webp/1*v_1scLJzaSpiqCeuiendhw.png 1400w" style="box-sizing: inherit;" type="image/webp"></source><source data-testid="og" sizes="(min-resolution: 4dppx) and (max-width: 700px) 50vw, (-webkit-min-device-pixel-ratio: 4) and (max-width: 700px) 50vw, (min-resolution: 3dppx) and (max-width: 700px) 67vw, (-webkit-min-device-pixel-ratio: 3) and (max-width: 700px) 65vw, (min-resolution: 2.5dppx) and (max-width: 700px) 80vw, (-webkit-min-device-pixel-ratio: 2.5) and (max-width: 700px) 80vw, (min-resolution: 2dppx) and (max-width: 700px) 100vw, (-webkit-min-device-pixel-ratio: 2) and (max-width: 700px) 100vw, 700px" srcset="https://miro.medium.com/v2/resize:fit:640/1*v_1scLJzaSpiqCeuiendhw.png 640w, https://miro.medium.com/v2/resize:fit:720/1*v_1scLJzaSpiqCeuiendhw.png 720w, https://miro.medium.com/v2/resize:fit:750/1*v_1scLJzaSpiqCeuiendhw.png 750w, https://miro.medium.com/v2/resize:fit:786/1*v_1scLJzaSpiqCeuiendhw.png 786w, https://miro.medium.com/v2/resize:fit:828/1*v_1scLJzaSpiqCeuiendhw.png 828w, https://miro.medium.com/v2/resize:fit:1100/1*v_1scLJzaSpiqCeuiendhw.png 1100w, https://miro.medium.com/v2/resize:fit:1400/1*v_1scLJzaSpiqCeuiendhw.png 1400w" style="box-sizing: inherit;"></source><img alt="" class="bg mc md c" height="394" loading="lazy" role="presentation" src="https://miro.medium.com/v2/resize:fit:700/1*v_1scLJzaSpiqCeuiendhw.png" style="box-sizing: inherit; height: auto; max-width: 100%; vertical-align: middle; width: 680px;" width="700" /></picture></div></div></figure><figure class="nj nk nl nm nn lx lp lq paragraph-image" style="background-color: white; box-sizing: inherit; clear: both; color: rgba(0, 0, 0, 0.8); font-family: medium-content-sans-serif-font, -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, Oxygen, Ubuntu, Cantarell, "Open Sans", "Helvetica Neue", sans-serif; margin: 56px auto 0px;"><div class="ly lz eb ma bg mb" role="button" style="box-sizing: inherit; cursor: zoom-in; position: relative; transition: transform 300ms cubic-bezier(0.2, 0, 0.2, 1) 0s; width: 680px; z-index: auto;" tabindex="0"><div class="lp lq ni" style="box-sizing: inherit; margin-left: auto; margin-right: auto; max-width: 4480px;"><picture style="box-sizing: inherit;"><source sizes="(min-resolution: 4dppx) and (max-width: 700px) 50vw, (-webkit-min-device-pixel-ratio: 4) and (max-width: 700px) 50vw, (min-resolution: 3dppx) and (max-width: 700px) 67vw, (-webkit-min-device-pixel-ratio: 3) and (max-width: 700px) 65vw, (min-resolution: 2.5dppx) and (max-width: 700px) 80vw, (-webkit-min-device-pixel-ratio: 2.5) and (max-width: 700px) 80vw, (min-resolution: 2dppx) and (max-width: 700px) 100vw, (-webkit-min-device-pixel-ratio: 2) and (max-width: 700px) 100vw, 700px" srcset="https://miro.medium.com/v2/resize:fit:640/format:webp/1*_l6KWUc_gwZQvBQnUpFA5A.png 640w, https://miro.medium.com/v2/resize:fit:720/format:webp/1*_l6KWUc_gwZQvBQnUpFA5A.png 720w, https://miro.medium.com/v2/resize:fit:750/format:webp/1*_l6KWUc_gwZQvBQnUpFA5A.png 750w, https://miro.medium.com/v2/resize:fit:786/format:webp/1*_l6KWUc_gwZQvBQnUpFA5A.png 786w, https://miro.medium.com/v2/resize:fit:828/format:webp/1*_l6KWUc_gwZQvBQnUpFA5A.png 828w, https://miro.medium.com/v2/resize:fit:1100/format:webp/1*_l6KWUc_gwZQvBQnUpFA5A.png 1100w, https://miro.medium.com/v2/resize:fit:1400/format:webp/1*_l6KWUc_gwZQvBQnUpFA5A.png 1400w" style="box-sizing: inherit;" type="image/webp"></source><source data-testid="og" sizes="(min-resolution: 4dppx) and (max-width: 700px) 50vw, (-webkit-min-device-pixel-ratio: 4) and (max-width: 700px) 50vw, (min-resolution: 3dppx) and (max-width: 700px) 67vw, (-webkit-min-device-pixel-ratio: 3) and (max-width: 700px) 65vw, (min-resolution: 2.5dppx) and (max-width: 700px) 80vw, (-webkit-min-device-pixel-ratio: 2.5) and (max-width: 700px) 80vw, (min-resolution: 2dppx) and (max-width: 700px) 100vw, (-webkit-min-device-pixel-ratio: 2) and (max-width: 700px) 100vw, 700px" srcset="https://miro.medium.com/v2/resize:fit:640/1*_l6KWUc_gwZQvBQnUpFA5A.png 640w, https://miro.medium.com/v2/resize:fit:720/1*_l6KWUc_gwZQvBQnUpFA5A.png 720w, https://miro.medium.com/v2/resize:fit:750/1*_l6KWUc_gwZQvBQnUpFA5A.png 750w, https://miro.medium.com/v2/resize:fit:786/1*_l6KWUc_gwZQvBQnUpFA5A.png 786w, https://miro.medium.com/v2/resize:fit:828/1*_l6KWUc_gwZQvBQnUpFA5A.png 828w, https://miro.medium.com/v2/resize:fit:1100/1*_l6KWUc_gwZQvBQnUpFA5A.png 1100w, https://miro.medium.com/v2/resize:fit:1400/1*_l6KWUc_gwZQvBQnUpFA5A.png 1400w" style="box-sizing: inherit;"></source><img alt="" class="bg mc md c" height="394" loading="lazy" role="presentation" src="https://miro.medium.com/v2/resize:fit:700/1*_l6KWUc_gwZQvBQnUpFA5A.png" style="box-sizing: inherit; height: auto; max-width: 100%; vertical-align: middle; width: 680px;" width="700" /></picture></div></div></figure><p class="pw-post-body-paragraph mj mk fo ml b mm mn mo mp mq mr ms mt mu mv mw mx my mz na nb nc nd ne nf ng fh bj" data-selectable-paragraph="" id="42f2" style="background-color: white; box-sizing: inherit; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;"><a class="af nh" href="https://youtu.be/B3TgewI3MF0?t=1366" rel="noopener ugc nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;" target="_blank">Physical Computation Session I</a> from June 24 (roughly one hour in length).</p><p class="pw-post-body-paragraph mj mk fo ml b mm mn mo mp mq mr ms mt mu mv mw mx my mz na nb nc nd ne nf ng fh bj" data-selectable-paragraph="" id="ac49" style="background-color: white; box-sizing: inherit; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;">The second session focused on physical computation, and led us to discuss the idea of pancomputationalism. While pancomputationalism is the fundamental assumption behind the phrase “the brain is a computer” [1], we we also introduced to pancomputationalism in ferrofluidic systems and mycelial networks. We discussed the works of <a class="af nh" href="https://en.wikipedia.org/wiki/Richard_Feynman" rel="noopener ugc nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;" target="_blank">Richard Feynman</a> (<a class="af nh" href="https://books.google.com/books/about/Feynman_Lectures_On_Computation.html?id=x9ZiDwAAQBAJ" rel="noopener ugc nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;" target="_blank">Feynman Lectures on Computation</a>) and <a class="af nh" href="https://en.wikipedia.org/wiki/Edward_Fredkin" rel="noopener ugc nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;" target="_blank">Edward Fredkin</a> (<a class="af nh" href="https://en.wikipedia.org/wiki/Digital_physics" rel="noopener ugc nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;" target="_blank">Digital Physics</a>), which helped us form an epistemic framework for computation in nature [2]. We also discussed <a class="af nh" href="https://en.wikipedia.org/wiki/Andrew_Adamatzky" rel="noopener ugc nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;" target="_blank">Andy Adamatsky’s</a> work on unconventional computation, particularly his work on <a class="af nh" href="https://books.google.com/books/about/Reaction_Diffusion_Automata_Phenomenolog.html?id=KKZiKkPyHfkC" rel="noopener ugc nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;" target="_blank">Reaction-Diffusion (R-D) Automata</a>, that while discrete in nature has <a class="af nh" href="https://www.youtube.com/watch?v=_a_xV05ILLI" rel="noopener ugc nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;" target="_blank">connections to excitable (e.g neural) systems via the Fitzhugh-Nagumo</a> model.</p><figure class="nj nk nl nm nn lx lp lq paragraph-image" style="background-color: white; box-sizing: inherit; clear: both; color: rgba(0, 0, 0, 0.8); font-family: medium-content-sans-serif-font, -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, Oxygen, Ubuntu, Cantarell, "Open Sans", "Helvetica Neue", sans-serif; margin: 56px auto 0px;"><div class="ly lz eb ma bg mb" role="button" style="box-sizing: inherit; cursor: zoom-in; position: relative; transition: transform 300ms cubic-bezier(0.2, 0, 0.2, 1) 0s; width: 680px; z-index: auto;" tabindex="0"><div class="lp lq ni" style="box-sizing: inherit; margin-left: auto; margin-right: auto; max-width: 4480px;"><picture style="box-sizing: inherit;"><source sizes="(min-resolution: 4dppx) and (max-width: 700px) 50vw, (-webkit-min-device-pixel-ratio: 4) and (max-width: 700px) 50vw, (min-resolution: 3dppx) and (max-width: 700px) 67vw, (-webkit-min-device-pixel-ratio: 3) and (max-width: 700px) 65vw, (min-resolution: 2.5dppx) and (max-width: 700px) 80vw, (-webkit-min-device-pixel-ratio: 2.5) and (max-width: 700px) 80vw, (min-resolution: 2dppx) and (max-width: 700px) 100vw, (-webkit-min-device-pixel-ratio: 2) and (max-width: 700px) 100vw, 700px" srcset="https://miro.medium.com/v2/resize:fit:640/format:webp/1*0_wAnd5iPqhj1WWDv0tIrg.png 640w, https://miro.medium.com/v2/resize:fit:720/format:webp/1*0_wAnd5iPqhj1WWDv0tIrg.png 720w, https://miro.medium.com/v2/resize:fit:750/format:webp/1*0_wAnd5iPqhj1WWDv0tIrg.png 750w, https://miro.medium.com/v2/resize:fit:786/format:webp/1*0_wAnd5iPqhj1WWDv0tIrg.png 786w, https://miro.medium.com/v2/resize:fit:828/format:webp/1*0_wAnd5iPqhj1WWDv0tIrg.png 828w, https://miro.medium.com/v2/resize:fit:1100/format:webp/1*0_wAnd5iPqhj1WWDv0tIrg.png 1100w, https://miro.medium.com/v2/resize:fit:1400/format:webp/1*0_wAnd5iPqhj1WWDv0tIrg.png 1400w" style="box-sizing: inherit;" type="image/webp"></source><source data-testid="og" sizes="(min-resolution: 4dppx) and (max-width: 700px) 50vw, (-webkit-min-device-pixel-ratio: 4) and (max-width: 700px) 50vw, (min-resolution: 3dppx) and (max-width: 700px) 67vw, (-webkit-min-device-pixel-ratio: 3) and (max-width: 700px) 65vw, (min-resolution: 2.5dppx) and (max-width: 700px) 80vw, (-webkit-min-device-pixel-ratio: 2.5) and (max-width: 700px) 80vw, (min-resolution: 2dppx) and (max-width: 700px) 100vw, (-webkit-min-device-pixel-ratio: 2) and (max-width: 700px) 100vw, 700px" srcset="https://miro.medium.com/v2/resize:fit:640/1*0_wAnd5iPqhj1WWDv0tIrg.png 640w, https://miro.medium.com/v2/resize:fit:720/1*0_wAnd5iPqhj1WWDv0tIrg.png 720w, https://miro.medium.com/v2/resize:fit:750/1*0_wAnd5iPqhj1WWDv0tIrg.png 750w, https://miro.medium.com/v2/resize:fit:786/1*0_wAnd5iPqhj1WWDv0tIrg.png 786w, https://miro.medium.com/v2/resize:fit:828/1*0_wAnd5iPqhj1WWDv0tIrg.png 828w, https://miro.medium.com/v2/resize:fit:1100/1*0_wAnd5iPqhj1WWDv0tIrg.png 1100w, https://miro.medium.com/v2/resize:fit:1400/1*0_wAnd5iPqhj1WWDv0tIrg.png 1400w" style="box-sizing: inherit;"></source><img alt="" class="bg mc md c" height="394" loading="lazy" role="presentation" src="https://miro.medium.com/v2/resize:fit:700/1*0_wAnd5iPqhj1WWDv0tIrg.png" style="box-sizing: inherit; height: auto; max-width: 100%; vertical-align: middle; width: 680px;" width="700" /></picture></div></div></figure><figure class="nj nk nl nm nn lx lp lq paragraph-image" style="background-color: white; box-sizing: inherit; clear: both; color: rgba(0, 0, 0, 0.8); font-family: medium-content-sans-serif-font, -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, Oxygen, Ubuntu, Cantarell, "Open Sans", "Helvetica Neue", sans-serif; margin: 56px auto 0px;"><div class="ly lz eb ma bg mb" role="button" style="box-sizing: inherit; cursor: zoom-in; position: relative; transition: transform 300ms cubic-bezier(0.2, 0, 0.2, 1) 0s; width: 680px; z-index: auto;" tabindex="0"><div class="lp lq ni" style="box-sizing: inherit; margin-left: auto; margin-right: auto; max-width: 4480px;"><picture style="box-sizing: inherit;"><source sizes="(min-resolution: 4dppx) and (max-width: 700px) 50vw, (-webkit-min-device-pixel-ratio: 4) and (max-width: 700px) 50vw, (min-resolution: 3dppx) and (max-width: 700px) 67vw, (-webkit-min-device-pixel-ratio: 3) and (max-width: 700px) 65vw, (min-resolution: 2.5dppx) and (max-width: 700px) 80vw, (-webkit-min-device-pixel-ratio: 2.5) and (max-width: 700px) 80vw, (min-resolution: 2dppx) and (max-width: 700px) 100vw, (-webkit-min-device-pixel-ratio: 2) and (max-width: 700px) 100vw, 700px" srcset="https://miro.medium.com/v2/resize:fit:640/format:webp/1*_-4qOQf1mSTbyDfelHs7qw.png 640w, https://miro.medium.com/v2/resize:fit:720/format:webp/1*_-4qOQf1mSTbyDfelHs7qw.png 720w, https://miro.medium.com/v2/resize:fit:750/format:webp/1*_-4qOQf1mSTbyDfelHs7qw.png 750w, https://miro.medium.com/v2/resize:fit:786/format:webp/1*_-4qOQf1mSTbyDfelHs7qw.png 786w, https://miro.medium.com/v2/resize:fit:828/format:webp/1*_-4qOQf1mSTbyDfelHs7qw.png 828w, https://miro.medium.com/v2/resize:fit:1100/format:webp/1*_-4qOQf1mSTbyDfelHs7qw.png 1100w, https://miro.medium.com/v2/resize:fit:1400/format:webp/1*_-4qOQf1mSTbyDfelHs7qw.png 1400w" style="box-sizing: inherit;" type="image/webp"></source><source data-testid="og" sizes="(min-resolution: 4dppx) and (max-width: 700px) 50vw, (-webkit-min-device-pixel-ratio: 4) and (max-width: 700px) 50vw, (min-resolution: 3dppx) and (max-width: 700px) 67vw, (-webkit-min-device-pixel-ratio: 3) and (max-width: 700px) 65vw, (min-resolution: 2.5dppx) and (max-width: 700px) 80vw, (-webkit-min-device-pixel-ratio: 2.5) and (max-width: 700px) 80vw, (min-resolution: 2dppx) and (max-width: 700px) 100vw, (-webkit-min-device-pixel-ratio: 2) and (max-width: 700px) 100vw, 700px" srcset="https://miro.medium.com/v2/resize:fit:640/1*_-4qOQf1mSTbyDfelHs7qw.png 640w, https://miro.medium.com/v2/resize:fit:720/1*_-4qOQf1mSTbyDfelHs7qw.png 720w, https://miro.medium.com/v2/resize:fit:750/1*_-4qOQf1mSTbyDfelHs7qw.png 750w, https://miro.medium.com/v2/resize:fit:786/1*_-4qOQf1mSTbyDfelHs7qw.png 786w, https://miro.medium.com/v2/resize:fit:828/1*_-4qOQf1mSTbyDfelHs7qw.png 828w, https://miro.medium.com/v2/resize:fit:1100/1*_-4qOQf1mSTbyDfelHs7qw.png 1100w, https://miro.medium.com/v2/resize:fit:1400/1*_-4qOQf1mSTbyDfelHs7qw.png 1400w" style="box-sizing: inherit;"></source><img alt="" class="bg mc md c" height="394" loading="lazy" role="presentation" src="https://miro.medium.com/v2/resize:fit:700/1*_-4qOQf1mSTbyDfelHs7qw.png" style="box-sizing: inherit; height: auto; max-width: 100%; vertical-align: middle; width: 680px;" width="700" /></picture></div></div></figure><figure class="nj nk nl nm nn lx lp lq paragraph-image" style="background-color: white; box-sizing: inherit; clear: both; color: rgba(0, 0, 0, 0.8); font-family: medium-content-sans-serif-font, -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, Oxygen, Ubuntu, Cantarell, "Open Sans", "Helvetica Neue", sans-serif; margin: 56px auto 0px;"><div class="ly lz eb ma bg mb" role="button" style="box-sizing: inherit; cursor: zoom-in; position: relative; transition: transform 300ms cubic-bezier(0.2, 0, 0.2, 1) 0s; width: 680px; z-index: auto;" tabindex="0"><div class="lp lq ni" style="box-sizing: inherit; margin-left: auto; margin-right: auto; max-width: 4480px;"><picture style="box-sizing: inherit;"><source sizes="(min-resolution: 4dppx) and (max-width: 700px) 50vw, (-webkit-min-device-pixel-ratio: 4) and (max-width: 700px) 50vw, (min-resolution: 3dppx) and (max-width: 700px) 67vw, (-webkit-min-device-pixel-ratio: 3) and (max-width: 700px) 65vw, (min-resolution: 2.5dppx) and (max-width: 700px) 80vw, (-webkit-min-device-pixel-ratio: 2.5) and (max-width: 700px) 80vw, (min-resolution: 2dppx) and (max-width: 700px) 100vw, (-webkit-min-device-pixel-ratio: 2) and (max-width: 700px) 100vw, 700px" srcset="https://miro.medium.com/v2/resize:fit:640/format:webp/1*WgP-FWDKpmCbt8o64g-sDw.png 640w, https://miro.medium.com/v2/resize:fit:720/format:webp/1*WgP-FWDKpmCbt8o64g-sDw.png 720w, https://miro.medium.com/v2/resize:fit:750/format:webp/1*WgP-FWDKpmCbt8o64g-sDw.png 750w, https://miro.medium.com/v2/resize:fit:786/format:webp/1*WgP-FWDKpmCbt8o64g-sDw.png 786w, https://miro.medium.com/v2/resize:fit:828/format:webp/1*WgP-FWDKpmCbt8o64g-sDw.png 828w, https://miro.medium.com/v2/resize:fit:1100/format:webp/1*WgP-FWDKpmCbt8o64g-sDw.png 1100w, https://miro.medium.com/v2/resize:fit:1400/format:webp/1*WgP-FWDKpmCbt8o64g-sDw.png 1400w" style="box-sizing: inherit;" type="image/webp"></source><source data-testid="og" sizes="(min-resolution: 4dppx) and (max-width: 700px) 50vw, (-webkit-min-device-pixel-ratio: 4) and (max-width: 700px) 50vw, (min-resolution: 3dppx) and (max-width: 700px) 67vw, (-webkit-min-device-pixel-ratio: 3) and (max-width: 700px) 65vw, (min-resolution: 2.5dppx) and (max-width: 700px) 80vw, (-webkit-min-device-pixel-ratio: 2.5) and (max-width: 700px) 80vw, (min-resolution: 2dppx) and (max-width: 700px) 100vw, (-webkit-min-device-pixel-ratio: 2) and (max-width: 700px) 100vw, 700px" srcset="https://miro.medium.com/v2/resize:fit:640/1*WgP-FWDKpmCbt8o64g-sDw.png 640w, https://miro.medium.com/v2/resize:fit:720/1*WgP-FWDKpmCbt8o64g-sDw.png 720w, https://miro.medium.com/v2/resize:fit:750/1*WgP-FWDKpmCbt8o64g-sDw.png 750w, https://miro.medium.com/v2/resize:fit:786/1*WgP-FWDKpmCbt8o64g-sDw.png 786w, https://miro.medium.com/v2/resize:fit:828/1*WgP-FWDKpmCbt8o64g-sDw.png 828w, https://miro.medium.com/v2/resize:fit:1100/1*WgP-FWDKpmCbt8o64g-sDw.png 1100w, https://miro.medium.com/v2/resize:fit:1400/1*WgP-FWDKpmCbt8o64g-sDw.png 1400w" style="box-sizing: inherit;"></source><img alt="" class="bg mc md c" height="394" loading="lazy" role="presentation" src="https://miro.medium.com/v2/resize:fit:700/1*WgP-FWDKpmCbt8o64g-sDw.png" style="box-sizing: inherit; height: auto; max-width: 100%; vertical-align: middle; width: 680px;" width="700" /></picture></div></div></figure><p class="pw-post-body-paragraph mj mk fo ml b mm mn mo mp mq mr ms mt mu mv mw mx my mz na nb nc nd ne nf ng fh bj" data-selectable-paragraph="" id="6a87" style="background-color: white; box-sizing: inherit; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;"><a class="af nh" href="https://youtu.be/coiFubGAHw0?t=3156" rel="noopener ugc nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;" target="_blank">Physical Computation Session II</a> from July 1 (roughly one hour in length)</p><p class="pw-post-body-paragraph mj mk fo ml b mm mn mo mp mq mr ms mt mu mv mw mx my mz na nb nc nd ne nf ng fh bj" data-selectable-paragraph="" id="50a4" style="background-color: white; box-sizing: inherit; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;">After taking a break from the topic, our July 15 meeting featured an alternative viewpoint on pancomputationalism. This was made manifest in a shorter discussion on physical computation, with views from <a class="af nh" href="https://en.wikipedia.org/wiki/Tommaso_Toffoli" rel="noopener ugc nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;" target="_blank">Tomasso Toffoli</a> and Stephen Wolfram. We covered Toffoli’s paper “<a class="af nh" href="https://citeseerx.ist.psu.edu/document?repid=rep1&type=pdf&doi=74e7f87968f5390b3bf7413f2e638935afef8e06" rel="noopener ugc nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;" target="_blank">Action, or the funcgability of computation</a>”, which connects physical entropy, information, action, and the amount of computation performed by a system. This paper is of great interest to the group in light of our work and discussions on 4E (embodied, embedded, enactive, and extended) cognition [3]. Toffoli makes some provocative arguments herein, including the notion of computation as “units of action”. A concrete example of this is a 10-speed bicycle, which is not only not a conventional computer, but also has linkages to perception and action. Amanda Nelson found the notion of transformation from one unit into another particularly salient to the distinction between analogue and digital computation. The physical basis of all forms of computation can also be better defined by revisiting “A New Kind of Science” [4], in which Wolfram sketches out the essential components and analogies of a computational system with a physical substrate. We can then compare some of the more abstract aspects of a physical computer with neural systems. This is particularly relevant to engineered systems that include select components of biological networks.</p><figure class="nj nk nl nm nn lx lp lq paragraph-image" style="background-color: white; box-sizing: inherit; clear: both; color: rgba(0, 0, 0, 0.8); font-family: medium-content-sans-serif-font, -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, Oxygen, Ubuntu, Cantarell, "Open Sans", "Helvetica Neue", sans-serif; margin: 56px auto 0px;"><div class="ly lz eb ma bg mb" role="button" style="box-sizing: inherit; cursor: zoom-in; position: relative; transition: transform 300ms cubic-bezier(0.2, 0, 0.2, 1) 0s; width: 680px; z-index: auto;" tabindex="0"><div class="lp lq ni" style="box-sizing: inherit; margin-left: auto; margin-right: auto; max-width: 4480px;"><picture style="box-sizing: inherit;"><source sizes="(min-resolution: 4dppx) and (max-width: 700px) 50vw, (-webkit-min-device-pixel-ratio: 4) and (max-width: 700px) 50vw, (min-resolution: 3dppx) and (max-width: 700px) 67vw, (-webkit-min-device-pixel-ratio: 3) and (max-width: 700px) 65vw, (min-resolution: 2.5dppx) and (max-width: 700px) 80vw, (-webkit-min-device-pixel-ratio: 2.5) and (max-width: 700px) 80vw, (min-resolution: 2dppx) and (max-width: 700px) 100vw, (-webkit-min-device-pixel-ratio: 2) and (max-width: 700px) 100vw, 700px" srcset="https://miro.medium.com/v2/resize:fit:640/format:webp/1*uaoC2vIaS2ATMYkSa0IksQ.png 640w, https://miro.medium.com/v2/resize:fit:720/format:webp/1*uaoC2vIaS2ATMYkSa0IksQ.png 720w, https://miro.medium.com/v2/resize:fit:750/format:webp/1*uaoC2vIaS2ATMYkSa0IksQ.png 750w, https://miro.medium.com/v2/resize:fit:786/format:webp/1*uaoC2vIaS2ATMYkSa0IksQ.png 786w, https://miro.medium.com/v2/resize:fit:828/format:webp/1*uaoC2vIaS2ATMYkSa0IksQ.png 828w, https://miro.medium.com/v2/resize:fit:1100/format:webp/1*uaoC2vIaS2ATMYkSa0IksQ.png 1100w, https://miro.medium.com/v2/resize:fit:1400/format:webp/1*uaoC2vIaS2ATMYkSa0IksQ.png 1400w" style="box-sizing: inherit;" type="image/webp"></source><source data-testid="og" sizes="(min-resolution: 4dppx) and (max-width: 700px) 50vw, (-webkit-min-device-pixel-ratio: 4) and (max-width: 700px) 50vw, (min-resolution: 3dppx) and (max-width: 700px) 67vw, (-webkit-min-device-pixel-ratio: 3) and (max-width: 700px) 65vw, (min-resolution: 2.5dppx) and (max-width: 700px) 80vw, (-webkit-min-device-pixel-ratio: 2.5) and (max-width: 700px) 80vw, (min-resolution: 2dppx) and (max-width: 700px) 100vw, (-webkit-min-device-pixel-ratio: 2) and (max-width: 700px) 100vw, 700px" srcset="https://miro.medium.com/v2/resize:fit:640/1*uaoC2vIaS2ATMYkSa0IksQ.png 640w, https://miro.medium.com/v2/resize:fit:720/1*uaoC2vIaS2ATMYkSa0IksQ.png 720w, https://miro.medium.com/v2/resize:fit:750/1*uaoC2vIaS2ATMYkSa0IksQ.png 750w, https://miro.medium.com/v2/resize:fit:786/1*uaoC2vIaS2ATMYkSa0IksQ.png 786w, https://miro.medium.com/v2/resize:fit:828/1*uaoC2vIaS2ATMYkSa0IksQ.png 828w, https://miro.medium.com/v2/resize:fit:1100/1*uaoC2vIaS2ATMYkSa0IksQ.png 1100w, https://miro.medium.com/v2/resize:fit:1400/1*uaoC2vIaS2ATMYkSa0IksQ.png 1400w" style="box-sizing: inherit;"></source><img alt="" class="bg mc md c" height="394" loading="lazy" role="presentation" src="https://miro.medium.com/v2/resize:fit:700/1*uaoC2vIaS2ATMYkSa0IksQ.png" style="box-sizing: inherit; height: auto; max-width: 100%; vertical-align: middle; width: 680px;" width="700" /></picture></div></div></figure><figure class="nj nk nl nm nn lx lp lq paragraph-image" style="background-color: white; box-sizing: inherit; clear: both; color: rgba(0, 0, 0, 0.8); font-family: medium-content-sans-serif-font, -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, Oxygen, Ubuntu, Cantarell, "Open Sans", "Helvetica Neue", sans-serif; margin: 56px auto 0px;"><div class="ly lz eb ma bg mb" role="button" style="box-sizing: inherit; cursor: zoom-in; position: relative; transition: transform 300ms cubic-bezier(0.2, 0, 0.2, 1) 0s; width: 680px; z-index: auto;" tabindex="0"><div class="lp lq no" style="box-sizing: inherit; margin-left: auto; margin-right: auto; max-width: 960px;"><picture style="box-sizing: inherit;"><source sizes="(min-resolution: 4dppx) and (max-width: 700px) 50vw, (-webkit-min-device-pixel-ratio: 4) and (max-width: 700px) 50vw, (min-resolution: 3dppx) and (max-width: 700px) 67vw, (-webkit-min-device-pixel-ratio: 3) and (max-width: 700px) 65vw, (min-resolution: 2.5dppx) and (max-width: 700px) 80vw, (-webkit-min-device-pixel-ratio: 2.5) and (max-width: 700px) 80vw, (min-resolution: 2dppx) and (max-width: 700px) 100vw, (-webkit-min-device-pixel-ratio: 2) and (max-width: 700px) 100vw, 700px" srcset="https://miro.medium.com/v2/resize:fit:640/format:webp/1*OotmVH2l3ApTW2g3FcBsyw.png 640w, https://miro.medium.com/v2/resize:fit:720/format:webp/1*OotmVH2l3ApTW2g3FcBsyw.png 720w, https://miro.medium.com/v2/resize:fit:750/format:webp/1*OotmVH2l3ApTW2g3FcBsyw.png 750w, https://miro.medium.com/v2/resize:fit:786/format:webp/1*OotmVH2l3ApTW2g3FcBsyw.png 786w, https://miro.medium.com/v2/resize:fit:828/format:webp/1*OotmVH2l3ApTW2g3FcBsyw.png 828w, https://miro.medium.com/v2/resize:fit:1100/format:webp/1*OotmVH2l3ApTW2g3FcBsyw.png 1100w, https://miro.medium.com/v2/resize:fit:1400/format:webp/1*OotmVH2l3ApTW2g3FcBsyw.png 1400w" style="box-sizing: inherit;" type="image/webp"></source><source data-testid="og" sizes="(min-resolution: 4dppx) and (max-width: 700px) 50vw, (-webkit-min-device-pixel-ratio: 4) and (max-width: 700px) 50vw, (min-resolution: 3dppx) and (max-width: 700px) 67vw, (-webkit-min-device-pixel-ratio: 3) and (max-width: 700px) 65vw, (min-resolution: 2.5dppx) and (max-width: 700px) 80vw, (-webkit-min-device-pixel-ratio: 2.5) and (max-width: 700px) 80vw, (min-resolution: 2dppx) and (max-width: 700px) 100vw, (-webkit-min-device-pixel-ratio: 2) and (max-width: 700px) 100vw, 700px" srcset="https://miro.medium.com/v2/resize:fit:640/1*OotmVH2l3ApTW2g3FcBsyw.png 640w, https://miro.medium.com/v2/resize:fit:720/1*OotmVH2l3ApTW2g3FcBsyw.png 720w, https://miro.medium.com/v2/resize:fit:750/1*OotmVH2l3ApTW2g3FcBsyw.png 750w, https://miro.medium.com/v2/resize:fit:786/1*OotmVH2l3ApTW2g3FcBsyw.png 786w, https://miro.medium.com/v2/resize:fit:828/1*OotmVH2l3ApTW2g3FcBsyw.png 828w, https://miro.medium.com/v2/resize:fit:1100/1*OotmVH2l3ApTW2g3FcBsyw.png 1100w, https://miro.medium.com/v2/resize:fit:1400/1*OotmVH2l3ApTW2g3FcBsyw.png 1400w" style="box-sizing: inherit;"></source><img alt="" class="bg mc md c" height="394" loading="lazy" role="presentation" src="https://miro.medium.com/v2/resize:fit:700/1*OotmVH2l3ApTW2g3FcBsyw.png" style="box-sizing: inherit; height: auto; max-width: 100%; vertical-align: middle; width: 680px;" width="700" /></picture></div></div></figure><figure class="nj nk nl nm nn lx lp lq paragraph-image" style="background-color: white; box-sizing: inherit; clear: both; color: rgba(0, 0, 0, 0.8); font-family: medium-content-sans-serif-font, -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, Oxygen, Ubuntu, Cantarell, "Open Sans", "Helvetica Neue", sans-serif; margin: 56px auto 0px;"><div class="ly lz eb ma bg mb" role="button" style="box-sizing: inherit; cursor: zoom-in; position: relative; transition: transform 300ms cubic-bezier(0.2, 0, 0.2, 1) 0s; width: 680px; z-index: auto;" tabindex="0"><div class="lp lq ni" style="box-sizing: inherit; margin-left: auto; margin-right: auto; max-width: 4480px;"><picture style="box-sizing: inherit;"><source sizes="(min-resolution: 4dppx) and (max-width: 700px) 50vw, (-webkit-min-device-pixel-ratio: 4) and (max-width: 700px) 50vw, (min-resolution: 3dppx) and (max-width: 700px) 67vw, (-webkit-min-device-pixel-ratio: 3) and (max-width: 700px) 65vw, (min-resolution: 2.5dppx) and (max-width: 700px) 80vw, (-webkit-min-device-pixel-ratio: 2.5) and (max-width: 700px) 80vw, (min-resolution: 2dppx) and (max-width: 700px) 100vw, (-webkit-min-device-pixel-ratio: 2) and (max-width: 700px) 100vw, 700px" srcset="https://miro.medium.com/v2/resize:fit:640/format:webp/1*qGIs8paoniWXxF4vltvgLA.png 640w, https://miro.medium.com/v2/resize:fit:720/format:webp/1*qGIs8paoniWXxF4vltvgLA.png 720w, https://miro.medium.com/v2/resize:fit:750/format:webp/1*qGIs8paoniWXxF4vltvgLA.png 750w, https://miro.medium.com/v2/resize:fit:786/format:webp/1*qGIs8paoniWXxF4vltvgLA.png 786w, https://miro.medium.com/v2/resize:fit:828/format:webp/1*qGIs8paoniWXxF4vltvgLA.png 828w, https://miro.medium.com/v2/resize:fit:1100/format:webp/1*qGIs8paoniWXxF4vltvgLA.png 1100w, https://miro.medium.com/v2/resize:fit:1400/format:webp/1*qGIs8paoniWXxF4vltvgLA.png 1400w" style="box-sizing: inherit;" type="image/webp"></source><source data-testid="og" sizes="(min-resolution: 4dppx) and (max-width: 700px) 50vw, (-webkit-min-device-pixel-ratio: 4) and (max-width: 700px) 50vw, (min-resolution: 3dppx) and (max-width: 700px) 67vw, (-webkit-min-device-pixel-ratio: 3) and (max-width: 700px) 65vw, (min-resolution: 2.5dppx) and (max-width: 700px) 80vw, (-webkit-min-device-pixel-ratio: 2.5) and (max-width: 700px) 80vw, (min-resolution: 2dppx) and (max-width: 700px) 100vw, (-webkit-min-device-pixel-ratio: 2) and (max-width: 700px) 100vw, 700px" srcset="https://miro.medium.com/v2/resize:fit:640/1*qGIs8paoniWXxF4vltvgLA.png 640w, https://miro.medium.com/v2/resize:fit:720/1*qGIs8paoniWXxF4vltvgLA.png 720w, https://miro.medium.com/v2/resize:fit:750/1*qGIs8paoniWXxF4vltvgLA.png 750w, https://miro.medium.com/v2/resize:fit:786/1*qGIs8paoniWXxF4vltvgLA.png 786w, https://miro.medium.com/v2/resize:fit:828/1*qGIs8paoniWXxF4vltvgLA.png 828w, https://miro.medium.com/v2/resize:fit:1100/1*qGIs8paoniWXxF4vltvgLA.png 1100w, https://miro.medium.com/v2/resize:fit:1400/1*qGIs8paoniWXxF4vltvgLA.png 1400w" style="box-sizing: inherit;"></source><img alt="" class="bg mc md c" height="394" loading="lazy" role="presentation" src="https://miro.medium.com/v2/resize:fit:700/1*qGIs8paoniWXxF4vltvgLA.png" style="box-sizing: inherit; height: auto; max-width: 100%; vertical-align: middle; width: 680px;" width="700" /></picture></div></div></figure><p class="pw-post-body-paragraph mj mk fo ml b mm mn mo mp mq mr ms mt mu mv mw mx my mz na nb nc nd ne nf ng fh bj" data-selectable-paragraph="" id="7247" style="background-color: white; box-sizing: inherit; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;"><a class="af nh" href="https://youtu.be/wZnhHhdBb-M?t=7355" rel="noopener ugc nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;" target="_blank">Physical Computation Session III</a> from July 15 (about 15 minutes in length)</p><p class="pw-post-body-paragraph mj mk fo ml b mm mn mo mp mq mr ms mt mu mv mw mx my mz na nb nc nd ne nf ng fh bj" data-selectable-paragraph="" id="8399" style="background-color: white; box-sizing: inherit; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;">The next session followed up on computation in natural systems as well as Wolfram’s notion of universality, particularly in terms of computational models. In particular, Wolfram argues that cellular automata models can characterize universality, which is related to pancomputationalism. Universality suggests that any one computational model can capture system behavior that can be applied across a wide variety of domains. In this sense, context is not important. Rule 30 produces an output that resembles pattern formation in biological phenotypes (the shell of snail species <em class="np" style="box-sizing: inherit;">Conus textile</em>), but can also be used as a pseudo-random number generator [5]. In “<a class="af nh" href="https://arxiv.org/abs/2307.06851" rel="noopener ugc nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;" target="_blank">A Framework for Universality in Physics, Computer Science, and Beyond</a>”, this perspective is extended to understand the connections between computation defined by the Turing machine and a class of model called Spin Models. This provides a framework for universality that is useful form defining computation across the various levels of neural systems, but also gives rise to understanding what is uncomputable. This sessions natural system examples featured computation among bacterial colonies embedded in a colloidal substrate along with computation in granular matter itself. The latter is an example of non-silicon based polycomputation [6].</p><figure class="nj nk nl nm nn lx lp lq paragraph-image" style="background-color: white; box-sizing: inherit; clear: both; color: rgba(0, 0, 0, 0.8); font-family: medium-content-sans-serif-font, -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, Oxygen, Ubuntu, Cantarell, "Open Sans", "Helvetica Neue", sans-serif; margin: 56px auto 0px;"><div class="ly lz eb ma bg mb" role="button" style="box-sizing: inherit; cursor: zoom-in; position: relative; transition: transform 300ms cubic-bezier(0.2, 0, 0.2, 1) 0s; width: 680px; z-index: auto;" tabindex="0"><div class="lp lq ni" style="box-sizing: inherit; margin-left: auto; margin-right: auto; max-width: 4480px;"><picture style="box-sizing: inherit;"><source sizes="(min-resolution: 4dppx) and (max-width: 700px) 50vw, (-webkit-min-device-pixel-ratio: 4) and (max-width: 700px) 50vw, (min-resolution: 3dppx) and (max-width: 700px) 67vw, (-webkit-min-device-pixel-ratio: 3) and (max-width: 700px) 65vw, (min-resolution: 2.5dppx) and (max-width: 700px) 80vw, (-webkit-min-device-pixel-ratio: 2.5) and (max-width: 700px) 80vw, (min-resolution: 2dppx) and (max-width: 700px) 100vw, (-webkit-min-device-pixel-ratio: 2) and (max-width: 700px) 100vw, 700px" srcset="https://miro.medium.com/v2/resize:fit:640/format:webp/1*RnDGHWvppo5zMEWJswVkBg.png 640w, https://miro.medium.com/v2/resize:fit:720/format:webp/1*RnDGHWvppo5zMEWJswVkBg.png 720w, https://miro.medium.com/v2/resize:fit:750/format:webp/1*RnDGHWvppo5zMEWJswVkBg.png 750w, https://miro.medium.com/v2/resize:fit:786/format:webp/1*RnDGHWvppo5zMEWJswVkBg.png 786w, https://miro.medium.com/v2/resize:fit:828/format:webp/1*RnDGHWvppo5zMEWJswVkBg.png 828w, https://miro.medium.com/v2/resize:fit:1100/format:webp/1*RnDGHWvppo5zMEWJswVkBg.png 1100w, https://miro.medium.com/v2/resize:fit:1400/format:webp/1*RnDGHWvppo5zMEWJswVkBg.png 1400w" style="box-sizing: inherit;" type="image/webp"></source><source data-testid="og" sizes="(min-resolution: 4dppx) and (max-width: 700px) 50vw, (-webkit-min-device-pixel-ratio: 4) and (max-width: 700px) 50vw, (min-resolution: 3dppx) and (max-width: 700px) 67vw, (-webkit-min-device-pixel-ratio: 3) and (max-width: 700px) 65vw, (min-resolution: 2.5dppx) and (max-width: 700px) 80vw, (-webkit-min-device-pixel-ratio: 2.5) and (max-width: 700px) 80vw, (min-resolution: 2dppx) and (max-width: 700px) 100vw, (-webkit-min-device-pixel-ratio: 2) and (max-width: 700px) 100vw, 700px" srcset="https://miro.medium.com/v2/resize:fit:640/1*RnDGHWvppo5zMEWJswVkBg.png 640w, https://miro.medium.com/v2/resize:fit:720/1*RnDGHWvppo5zMEWJswVkBg.png 720w, https://miro.medium.com/v2/resize:fit:750/1*RnDGHWvppo5zMEWJswVkBg.png 750w, https://miro.medium.com/v2/resize:fit:786/1*RnDGHWvppo5zMEWJswVkBg.png 786w, https://miro.medium.com/v2/resize:fit:828/1*RnDGHWvppo5zMEWJswVkBg.png 828w, https://miro.medium.com/v2/resize:fit:1100/1*RnDGHWvppo5zMEWJswVkBg.png 1100w, https://miro.medium.com/v2/resize:fit:1400/1*RnDGHWvppo5zMEWJswVkBg.png 1400w" style="box-sizing: inherit;"></source><img alt="" class="bg mc md c" height="394" loading="lazy" role="presentation" src="https://miro.medium.com/v2/resize:fit:700/1*RnDGHWvppo5zMEWJswVkBg.png" style="box-sizing: inherit; height: auto; max-width: 100%; vertical-align: middle; width: 680px;" width="700" /></picture></div></div></figure><figure class="nj nk nl nm nn lx lp lq paragraph-image" style="background-color: white; box-sizing: inherit; clear: both; color: rgba(0, 0, 0, 0.8); font-family: medium-content-sans-serif-font, -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, Oxygen, Ubuntu, Cantarell, "Open Sans", "Helvetica Neue", sans-serif; margin: 56px auto 0px;"><div class="ly lz eb ma bg mb" role="button" style="box-sizing: inherit; cursor: zoom-in; position: relative; transition: transform 300ms cubic-bezier(0.2, 0, 0.2, 1) 0s; width: 680px; z-index: auto;" tabindex="0"><div class="lp lq ni" style="box-sizing: inherit; margin-left: auto; margin-right: auto; max-width: 4480px;"><picture style="box-sizing: inherit;"><source sizes="(min-resolution: 4dppx) and (max-width: 700px) 50vw, (-webkit-min-device-pixel-ratio: 4) and (max-width: 700px) 50vw, (min-resolution: 3dppx) and (max-width: 700px) 67vw, (-webkit-min-device-pixel-ratio: 3) and (max-width: 700px) 65vw, (min-resolution: 2.5dppx) and (max-width: 700px) 80vw, (-webkit-min-device-pixel-ratio: 2.5) and (max-width: 700px) 80vw, (min-resolution: 2dppx) and (max-width: 700px) 100vw, (-webkit-min-device-pixel-ratio: 2) and (max-width: 700px) 100vw, 700px" srcset="https://miro.medium.com/v2/resize:fit:640/format:webp/1*bxWk4vgHGwyALcHTLZnFBw.png 640w, https://miro.medium.com/v2/resize:fit:720/format:webp/1*bxWk4vgHGwyALcHTLZnFBw.png 720w, https://miro.medium.com/v2/resize:fit:750/format:webp/1*bxWk4vgHGwyALcHTLZnFBw.png 750w, https://miro.medium.com/v2/resize:fit:786/format:webp/1*bxWk4vgHGwyALcHTLZnFBw.png 786w, https://miro.medium.com/v2/resize:fit:828/format:webp/1*bxWk4vgHGwyALcHTLZnFBw.png 828w, https://miro.medium.com/v2/resize:fit:1100/format:webp/1*bxWk4vgHGwyALcHTLZnFBw.png 1100w, https://miro.medium.com/v2/resize:fit:1400/format:webp/1*bxWk4vgHGwyALcHTLZnFBw.png 1400w" style="box-sizing: inherit;" type="image/webp"></source><source data-testid="og" sizes="(min-resolution: 4dppx) and (max-width: 700px) 50vw, (-webkit-min-device-pixel-ratio: 4) and (max-width: 700px) 50vw, (min-resolution: 3dppx) and (max-width: 700px) 67vw, (-webkit-min-device-pixel-ratio: 3) and (max-width: 700px) 65vw, (min-resolution: 2.5dppx) and (max-width: 700px) 80vw, (-webkit-min-device-pixel-ratio: 2.5) and (max-width: 700px) 80vw, (min-resolution: 2dppx) and (max-width: 700px) 100vw, (-webkit-min-device-pixel-ratio: 2) and (max-width: 700px) 100vw, 700px" srcset="https://miro.medium.com/v2/resize:fit:640/1*bxWk4vgHGwyALcHTLZnFBw.png 640w, https://miro.medium.com/v2/resize:fit:720/1*bxWk4vgHGwyALcHTLZnFBw.png 720w, https://miro.medium.com/v2/resize:fit:750/1*bxWk4vgHGwyALcHTLZnFBw.png 750w, https://miro.medium.com/v2/resize:fit:786/1*bxWk4vgHGwyALcHTLZnFBw.png 786w, https://miro.medium.com/v2/resize:fit:828/1*bxWk4vgHGwyALcHTLZnFBw.png 828w, https://miro.medium.com/v2/resize:fit:1100/1*bxWk4vgHGwyALcHTLZnFBw.png 1100w, https://miro.medium.com/v2/resize:fit:1400/1*bxWk4vgHGwyALcHTLZnFBw.png 1400w" style="box-sizing: inherit;"></source><img alt="" class="bg mc md c" height="394" loading="lazy" role="presentation" src="https://miro.medium.com/v2/resize:fit:700/1*bxWk4vgHGwyALcHTLZnFBw.png" style="box-sizing: inherit; height: auto; max-width: 100%; vertical-align: middle; width: 680px;" width="700" /></picture></div></div></figure><p class="pw-post-body-paragraph mj mk fo ml b mm mn mo mp mq mr ms mt mu mv mw mx my mz na nb nc nd ne nf ng fh bj" data-selectable-paragraph="" id="d969" style="background-color: white; box-sizing: inherit; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;"><a class="af nh" href="https://youtu.be/rBFMirYYaDQ?t=7678" rel="noopener ugc nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;" target="_blank">Physical Computation Session IV</a> from July 22 (about 12 minutes in length).</p><p class="pw-post-body-paragraph mj mk fo ml b mm mn mo mp mq mr ms mt mu mv mw mx my mz na nb nc nd ne nf ng fh bj" data-selectable-paragraph="" id="741e" style="background-color: white; box-sizing: inherit; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;">After talking a more extended break from the topic, we returned to this discussion four weeks later (August 19). Our sixth (VI) session occurred in our <a class="af nh" href="https://youtu.be/WzfwcJUaqg4?t=4432" rel="noopener ugc nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;" target="_blank">August 19 meeting</a>, and covered three topics: physical computation and topology, morphological computation, and RNA computing/Molecular Biology as universal computer.</p><p class="pw-post-body-paragraph mj mk fo ml b mm mn mo mp mq mr ms mt mu mv mw mx my mz na nb nc nd ne nf ng fh bj" data-selectable-paragraph="" id="9c7d" style="background-color: white; box-sizing: inherit; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;">We have discussed <a class="af nh" href="https://plato.stanford.edu/entries/category-theory/" rel="noopener ugc nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;" target="_blank">category theory</a> before in our discussions on <a class="af nh" href="https://medium.com/orel-group/recent-saturday-morning-neurosim-conversations-4c7090dfd418" rel="noopener" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;">Symbolic Systems</a> and Causality. In this section, we revisited the role of category theory, but this time with reference to Physical Computation. <a class="af nh" href="https://mathstodon.xyz/@johncarlosbaez" rel="noopener ugc nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;" target="_blank">John Carlos Baez</a> and Mike Stay give a tour of category theory’s role in computation via topology. The idea is that category theory forms analogies with computation, which can be expressed on a topological surface/space.</p><p class="pw-post-body-paragraph mj mk fo ml b mm mn mo mp mq mr ms mt mu mv mw mx my mz na nb nc nd ne nf ng fh bj" data-selectable-paragraph="" id="9454" style="background-color: white; box-sizing: inherit; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;"><a class="af nh" href="https://en.wikipedia.org/wiki/Computable_topology" rel="noopener ugc nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;" target="_blank">Computable Topology</a>, Wikipedia.</p><p class="pw-post-body-paragraph mj mk fo ml b mm mn mo mp mq mr ms mt mu mv mw mx my mz na nb nc nd ne nf ng fh bj" data-selectable-paragraph="" id="63ee" style="background-color: white; box-sizing: inherit; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;">Baez, J. and Stay, M. (2009). <a class="af nh" href="https://arxiv.org/abs/0903.0340" rel="noopener ugc nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;" target="_blank">Physics, Topology, Logic and Computation: A Rosetta Stone</a>. <em class="np" style="box-sizing: inherit;">arXiv</em>, 0903.0340.</p><figure class="nj nk nl nm nn lx lp lq paragraph-image" style="background-color: white; box-sizing: inherit; clear: both; color: rgba(0, 0, 0, 0.8); font-family: medium-content-sans-serif-font, -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, Oxygen, Ubuntu, Cantarell, "Open Sans", "Helvetica Neue", sans-serif; margin: 56px auto 0px;"><div class="ly lz eb ma bg mb" role="button" style="box-sizing: inherit; cursor: zoom-in; position: relative; transition: transform 300ms cubic-bezier(0.2, 0, 0.2, 1) 0s; width: 680px; z-index: auto;" tabindex="0"><div class="lp lq nq" style="box-sizing: inherit; margin-left: auto; margin-right: auto; max-width: 1296px;"><picture style="box-sizing: inherit;"><source sizes="(min-resolution: 4dppx) and (max-width: 700px) 50vw, (-webkit-min-device-pixel-ratio: 4) and (max-width: 700px) 50vw, (min-resolution: 3dppx) and (max-width: 700px) 67vw, (-webkit-min-device-pixel-ratio: 3) and (max-width: 700px) 65vw, (min-resolution: 2.5dppx) and (max-width: 700px) 80vw, (-webkit-min-device-pixel-ratio: 2.5) and (max-width: 700px) 80vw, (min-resolution: 2dppx) and (max-width: 700px) 100vw, (-webkit-min-device-pixel-ratio: 2) and (max-width: 700px) 100vw, 700px" srcset="https://miro.medium.com/v2/resize:fit:640/format:webp/1*DgI8XBfmRASHMQHCXQs63g.png 640w, https://miro.medium.com/v2/resize:fit:720/format:webp/1*DgI8XBfmRASHMQHCXQs63g.png 720w, https://miro.medium.com/v2/resize:fit:750/format:webp/1*DgI8XBfmRASHMQHCXQs63g.png 750w, https://miro.medium.com/v2/resize:fit:786/format:webp/1*DgI8XBfmRASHMQHCXQs63g.png 786w, https://miro.medium.com/v2/resize:fit:828/format:webp/1*DgI8XBfmRASHMQHCXQs63g.png 828w, https://miro.medium.com/v2/resize:fit:1100/format:webp/1*DgI8XBfmRASHMQHCXQs63g.png 1100w, https://miro.medium.com/v2/resize:fit:1400/format:webp/1*DgI8XBfmRASHMQHCXQs63g.png 1400w" style="box-sizing: inherit;" type="image/webp"></source><source data-testid="og" sizes="(min-resolution: 4dppx) and (max-width: 700px) 50vw, (-webkit-min-device-pixel-ratio: 4) and (max-width: 700px) 50vw, (min-resolution: 3dppx) and (max-width: 700px) 67vw, (-webkit-min-device-pixel-ratio: 3) and (max-width: 700px) 65vw, (min-resolution: 2.5dppx) and (max-width: 700px) 80vw, (-webkit-min-device-pixel-ratio: 2.5) and (max-width: 700px) 80vw, (min-resolution: 2dppx) and (max-width: 700px) 100vw, (-webkit-min-device-pixel-ratio: 2) and (max-width: 700px) 100vw, 700px" srcset="https://miro.medium.com/v2/resize:fit:640/1*DgI8XBfmRASHMQHCXQs63g.png 640w, https://miro.medium.com/v2/resize:fit:720/1*DgI8XBfmRASHMQHCXQs63g.png 720w, https://miro.medium.com/v2/resize:fit:750/1*DgI8XBfmRASHMQHCXQs63g.png 750w, https://miro.medium.com/v2/resize:fit:786/1*DgI8XBfmRASHMQHCXQs63g.png 786w, https://miro.medium.com/v2/resize:fit:828/1*DgI8XBfmRASHMQHCXQs63g.png 828w, https://miro.medium.com/v2/resize:fit:1100/1*DgI8XBfmRASHMQHCXQs63g.png 1100w, https://miro.medium.com/v2/resize:fit:1400/1*DgI8XBfmRASHMQHCXQs63g.png 1400w" style="box-sizing: inherit;"></source><img alt="" class="bg mc md c" height="811" loading="lazy" role="presentation" src="https://miro.medium.com/v2/resize:fit:700/1*DgI8XBfmRASHMQHCXQs63g.png" style="box-sizing: inherit; height: auto; max-width: 100%; vertical-align: middle; width: 680px;" width="700" /></picture></div></div><figcaption class="me mf mg lp lq mh mi be b bf z dv" data-selectable-paragraph="" style="box-sizing: inherit; color: #6b6b6b; font-family: sohne, "Helvetica Neue", Helvetica, Arial, sans-serif; font-size: 14px; line-height: 20px; margin-left: auto; margin-right: auto; margin-top: 10px; max-width: 728px; text-align: center;">Mapping category theory operators to a topological description.</figcaption></figure><p class="pw-post-body-paragraph mj mk fo ml b mm mn mo mp mq mr ms mt mu mv mw mx my mz na nb nc nd ne nf ng fh bj" data-selectable-paragraph="" id="1884" style="background-color: white; box-sizing: inherit; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;">We aslo covered the role of Morphological Computation by reviewing three papers on this form of physical computation that intersects with digital computational representations. Morphological Computation is the role of the body in the notion of “cognition is computation”. One idea that is critiqued with in these papers is offloading from the brain to the body. Offloading is moving computational capacity from the central nervous system to the periphery. If you grab a ball with your hand, you recognize and send commands to grasp the ball, but you must grasp and otherwise manipulate the object to fully compute the object. Thus, this capacity is said to be offloaded to the hand or peripheral nervous system.</p><p class="pw-post-body-paragraph mj mk fo ml b mm mn mo mp mq mr ms mt mu mv mw mx my mz na nb nc nd ne nf ng fh bj" data-selectable-paragraph="" id="b8f0" style="background-color: white; box-sizing: inherit; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;">Interestingly, offloading and embodiment are integral parts of <a class="af nh" href="https://books.google.com/books/about/The_Oxford_Handbook_of_4E_Cognition.html?id=zB1rDwAAQBAJ" rel="noopener ugc nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;" target="_blank">4E (Embodied, Embedded, Enactive, and Externalized) Cognition</a>, which itself critiques the brain as computation idea. But as an analytical tool, morphological computation is much more utilitarian than Cognitive Science theory, and is concerned with how the robotic bodies and other mechanical systems interact with an intelligent controller. In non-embodied robotics, body dynamics is treated as noise. But in morphological computation, body dynamics play an integral role in the intelligent system and contribute to a dynamical system.</p><p class="pw-post-body-paragraph mj mk fo ml b mm mn mo mp mq mr ms mt mu mv mw mx my mz na nb nc nd ne nf ng fh bj" data-selectable-paragraph="" id="5432" style="background-color: white; box-sizing: inherit; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;">Muller, V.C. and Hoffmann, M. (2017). <a class="af nh" href="https://direct.mit.edu/artl/article/23/1/1/2858/What-Is-Morphological-Computation-On-How-the-Body" rel="noopener ugc nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;" target="_blank">What Is Morphological Computation? On How the Body Contributes to Cognition and Control</a>. <em class="np" style="box-sizing: inherit;">Artificial Life</em>, 23, 1–24.</p><p class="pw-post-body-paragraph mj mk fo ml b mm mn mo mp mq mr ms mt mu mv mw mx my mz na nb nc nd ne nf ng fh bj" data-selectable-paragraph="" id="5a62" style="background-color: white; box-sizing: inherit; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;">Fuchslin, R.M., Dzyakanchuk, A., Flumini, D., Hauser, H., Hunt, K.J., Luchsinger, R.H., Reller, B., Scheidegger, S., and Walker, R. (2013). <a class="af nh" href="https://direct.mit.edu/artl/article/19/1/9/2747/Morphological-Computation-and-Morphological" rel="noopener ugc nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;" target="_blank">Morphological Computation and Morphological Control: Steps Toward a Formal Theory and Applications</a>. <em class="np" style="box-sizing: inherit;">Artificial Life</em>, 19, 9–34.</p><p class="pw-post-body-paragraph mj mk fo ml b mm mn mo mp mq mr ms mt mu mv mw mx my mz na nb nc nd ne nf ng fh bj" data-selectable-paragraph="" id="6e63" style="background-color: white; box-sizing: inherit; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;">Milkowski, M. (2018). <a class="af nh" href="https://www.mdpi.com/1099-4300/20/12/942" rel="noopener ugc nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;" target="_blank">Morphological Computation: Nothing but Physical Computation</a>. <em class="np" style="box-sizing: inherit;">Entropy</em>, 20, 942.</p><figure class="nj nk nl nm nn lx lp lq paragraph-image" style="background-color: white; box-sizing: inherit; clear: both; color: rgba(0, 0, 0, 0.8); font-family: medium-content-sans-serif-font, -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, Oxygen, Ubuntu, Cantarell, "Open Sans", "Helvetica Neue", sans-serif; margin: 56px auto 0px;"><div class="ly lz eb ma bg mb" role="button" style="box-sizing: inherit; cursor: zoom-in; position: relative; transition: transform 300ms cubic-bezier(0.2, 0, 0.2, 1) 0s; width: 680px; z-index: auto;" tabindex="0"><div class="lp lq nr" style="box-sizing: inherit; margin-left: auto; margin-right: auto; max-width: 1422px;"><picture style="box-sizing: inherit;"><source sizes="(min-resolution: 4dppx) and (max-width: 700px) 50vw, (-webkit-min-device-pixel-ratio: 4) and (max-width: 700px) 50vw, (min-resolution: 3dppx) and (max-width: 700px) 67vw, (-webkit-min-device-pixel-ratio: 3) and (max-width: 700px) 65vw, (min-resolution: 2.5dppx) and (max-width: 700px) 80vw, (-webkit-min-device-pixel-ratio: 2.5) and (max-width: 700px) 80vw, (min-resolution: 2dppx) and (max-width: 700px) 100vw, (-webkit-min-device-pixel-ratio: 2) and (max-width: 700px) 100vw, 700px" srcset="https://miro.medium.com/v2/resize:fit:640/format:webp/1*h0ZhwW9bMaWyKpv66JnyiQ.png 640w, https://miro.medium.com/v2/resize:fit:720/format:webp/1*h0ZhwW9bMaWyKpv66JnyiQ.png 720w, https://miro.medium.com/v2/resize:fit:750/format:webp/1*h0ZhwW9bMaWyKpv66JnyiQ.png 750w, https://miro.medium.com/v2/resize:fit:786/format:webp/1*h0ZhwW9bMaWyKpv66JnyiQ.png 786w, https://miro.medium.com/v2/resize:fit:828/format:webp/1*h0ZhwW9bMaWyKpv66JnyiQ.png 828w, https://miro.medium.com/v2/resize:fit:1100/format:webp/1*h0ZhwW9bMaWyKpv66JnyiQ.png 1100w, https://miro.medium.com/v2/resize:fit:1400/format:webp/1*h0ZhwW9bMaWyKpv66JnyiQ.png 1400w" style="box-sizing: inherit;" type="image/webp"></source><source data-testid="og" sizes="(min-resolution: 4dppx) and (max-width: 700px) 50vw, (-webkit-min-device-pixel-ratio: 4) and (max-width: 700px) 50vw, (min-resolution: 3dppx) and (max-width: 700px) 67vw, (-webkit-min-device-pixel-ratio: 3) and (max-width: 700px) 65vw, (min-resolution: 2.5dppx) and (max-width: 700px) 80vw, (-webkit-min-device-pixel-ratio: 2.5) and (max-width: 700px) 80vw, (min-resolution: 2dppx) and (max-width: 700px) 100vw, (-webkit-min-device-pixel-ratio: 2) and (max-width: 700px) 100vw, 700px" srcset="https://miro.medium.com/v2/resize:fit:640/1*h0ZhwW9bMaWyKpv66JnyiQ.png 640w, https://miro.medium.com/v2/resize:fit:720/1*h0ZhwW9bMaWyKpv66JnyiQ.png 720w, https://miro.medium.com/v2/resize:fit:750/1*h0ZhwW9bMaWyKpv66JnyiQ.png 750w, https://miro.medium.com/v2/resize:fit:786/1*h0ZhwW9bMaWyKpv66JnyiQ.png 786w, https://miro.medium.com/v2/resize:fit:828/1*h0ZhwW9bMaWyKpv66JnyiQ.png 828w, https://miro.medium.com/v2/resize:fit:1100/1*h0ZhwW9bMaWyKpv66JnyiQ.png 1100w, https://miro.medium.com/v2/resize:fit:1400/1*h0ZhwW9bMaWyKpv66JnyiQ.png 1400w" style="box-sizing: inherit;"></source><img alt="" class="bg mc md c" height="394" loading="lazy" role="presentation" src="https://miro.medium.com/v2/resize:fit:700/1*h0ZhwW9bMaWyKpv66JnyiQ.png" style="box-sizing: inherit; height: auto; max-width: 100%; vertical-align: middle; width: 680px;" width="700" /></picture></div></div><figcaption class="me mf mg lp lq mh mi be b bf z dv" data-selectable-paragraph="" style="box-sizing: inherit; color: #6b6b6b; font-family: sohne, "Helvetica Neue", Helvetica, Arial, sans-serif; font-size: 14px; line-height: 20px; margin-left: auto; margin-right: auto; margin-top: 10px; max-width: 728px; text-align: center;">The three insights from our morphological computational discussion.</figcaption></figure><p class="pw-post-body-paragraph mj mk fo ml b mm mn mo mp mq mr ms mt mu mv mw mx my mz na nb nc nd ne nf ng fh bj" data-selectable-paragraph="" id="aab7" style="background-color: white; box-sizing: inherit; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;">While these papers do not get too deeply into the role of pancomputation in Morphological Computation, it is implicitly stated and plays a central role in our last topic: RNA computing and Molecular Biology. For more information, see <a class="af nh" href="https://www.youtube.com/watch?v=pcEod3-o_pg" rel="noopener ugc nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;" target="_blank">this talk on YouTube</a> and the paper below. Basically, while the pancomputationalism perspective is missing from biology, the structure and potential function of DNA and RNA provide a route to phycial computation.</p><p class="pw-post-body-paragraph mj mk fo ml b mm mn mo mp mq mr ms mt mu mv mw mx my mz na nb nc nd ne nf ng fh bj" data-selectable-paragraph="" id="f153" style="background-color: white; box-sizing: inherit; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;">Akhlaghpour, H. (2022). <a class="af nh" href="https://www.sciencedirect.com/science/article/abs/pii/S0022519321004045" rel="noopener ugc nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;" target="_blank">An RNA-based theory of natural universal computation</a>. <em class="np" style="box-sizing: inherit;">Journal of Theoretical Biology</em>, 537, 110984.</p><figure class="nj nk nl nm nn lx lp lq paragraph-image" style="background-color: white; box-sizing: inherit; clear: both; color: rgba(0, 0, 0, 0.8); font-family: medium-content-sans-serif-font, -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, Oxygen, Ubuntu, Cantarell, "Open Sans", "Helvetica Neue", sans-serif; margin: 56px auto 0px;"><div class="ly lz eb ma bg mb" role="button" style="box-sizing: inherit; cursor: zoom-in; position: relative; transition: transform 300ms cubic-bezier(0.2, 0, 0.2, 1) 0s; width: 680px; z-index: auto;" tabindex="0"><div class="lp lq ns" style="box-sizing: inherit; margin-left: auto; margin-right: auto; max-width: 1294px;"><picture style="box-sizing: inherit;"><source sizes="(min-resolution: 4dppx) and (max-width: 700px) 50vw, (-webkit-min-device-pixel-ratio: 4) and (max-width: 700px) 50vw, (min-resolution: 3dppx) and (max-width: 700px) 67vw, (-webkit-min-device-pixel-ratio: 3) and (max-width: 700px) 65vw, (min-resolution: 2.5dppx) and (max-width: 700px) 80vw, (-webkit-min-device-pixel-ratio: 2.5) and (max-width: 700px) 80vw, (min-resolution: 2dppx) and (max-width: 700px) 100vw, (-webkit-min-device-pixel-ratio: 2) and (max-width: 700px) 100vw, 700px" srcset="https://miro.medium.com/v2/resize:fit:640/format:webp/1*cqjzqyk5RH3cyv37NhHccw.png 640w, https://miro.medium.com/v2/resize:fit:720/format:webp/1*cqjzqyk5RH3cyv37NhHccw.png 720w, https://miro.medium.com/v2/resize:fit:750/format:webp/1*cqjzqyk5RH3cyv37NhHccw.png 750w, https://miro.medium.com/v2/resize:fit:786/format:webp/1*cqjzqyk5RH3cyv37NhHccw.png 786w, https://miro.medium.com/v2/resize:fit:828/format:webp/1*cqjzqyk5RH3cyv37NhHccw.png 828w, https://miro.medium.com/v2/resize:fit:1100/format:webp/1*cqjzqyk5RH3cyv37NhHccw.png 1100w, https://miro.medium.com/v2/resize:fit:1400/format:webp/1*cqjzqyk5RH3cyv37NhHccw.png 1400w" style="box-sizing: inherit;" type="image/webp"></source><source data-testid="og" sizes="(min-resolution: 4dppx) and (max-width: 700px) 50vw, (-webkit-min-device-pixel-ratio: 4) and (max-width: 700px) 50vw, (min-resolution: 3dppx) and (max-width: 700px) 67vw, (-webkit-min-device-pixel-ratio: 3) and (max-width: 700px) 65vw, (min-resolution: 2.5dppx) and (max-width: 700px) 80vw, (-webkit-min-device-pixel-ratio: 2.5) and (max-width: 700px) 80vw, (min-resolution: 2dppx) and (max-width: 700px) 100vw, (-webkit-min-device-pixel-ratio: 2) and (max-width: 700px) 100vw, 700px" srcset="https://miro.medium.com/v2/resize:fit:640/1*cqjzqyk5RH3cyv37NhHccw.png 640w, https://miro.medium.com/v2/resize:fit:720/1*cqjzqyk5RH3cyv37NhHccw.png 720w, https://miro.medium.com/v2/resize:fit:750/1*cqjzqyk5RH3cyv37NhHccw.png 750w, https://miro.medium.com/v2/resize:fit:786/1*cqjzqyk5RH3cyv37NhHccw.png 786w, https://miro.medium.com/v2/resize:fit:828/1*cqjzqyk5RH3cyv37NhHccw.png 828w, https://miro.medium.com/v2/resize:fit:1100/1*cqjzqyk5RH3cyv37NhHccw.png 1100w, https://miro.medium.com/v2/resize:fit:1400/1*cqjzqyk5RH3cyv37NhHccw.png 1400w" style="box-sizing: inherit;"></source><img alt="" class="bg mc md c" height="399" loading="lazy" role="presentation" src="https://miro.medium.com/v2/resize:fit:700/1*cqjzqyk5RH3cyv37NhHccw.png" style="box-sizing: inherit; height: auto; max-width: 100%; vertical-align: middle; width: 680px;" width="700" /></picture></div></div><figcaption class="me mf mg lp lq mh mi be b bf z dv" data-selectable-paragraph="" style="box-sizing: inherit; color: #6b6b6b; font-family: sohne, "Helvetica Neue", Helvetica, Arial, sans-serif; font-size: 14px; line-height: 20px; margin-left: auto; margin-right: auto; margin-top: 10px; max-width: 728px; text-align: center;">Bringing pancomputationalism into biology? What is its value?</figcaption></figure><p class="pw-post-body-paragraph mj mk fo ml b mm mn mo mp mq mr ms mt mu mv mw mx my mz na nb nc nd ne nf ng fh bj" data-selectable-paragraph="" id="dded" style="background-color: white; box-sizing: inherit; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;">Thanks to Morgan Hough for joining us from Hawaii (4:00 am!) on August 19.</p><p class="pw-post-body-paragraph mj mk fo ml b mm mn mo mp mq mr ms mt mu mv mw mx my mz na nb nc nd ne nf ng fh bj" data-selectable-paragraph="" id="fe2f" style="background-color: white; box-sizing: inherit; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;"><span class="ml fp" style="box-sizing: inherit; font-weight: 700;">References</span></p><p class="pw-post-body-paragraph mj mk fo ml b mm mn mo mp mq mr ms mt mu mv mw mx my mz na nb nc nd ne nf ng fh bj" data-selectable-paragraph="" id="ac55" style="background-color: white; box-sizing: inherit; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;">[1] Richards, B.A. and Lillicrap, T.P. (2022). <a class="af nh" href="https://www.frontiersin.org/articles/10.3389/fcomp.2022.810358/full" rel="noopener ugc nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;" target="_blank">The Brain-Computer Metaphor Debate Is Useless: A Matter of Semantics</a>. <em class="np" style="box-sizing: inherit;">Frontiers in Computational Science</em>, 4, 810358.</p><p class="pw-post-body-paragraph mj mk fo ml b mm mn mo mp mq mr ms mt mu mv mw mx my mz na nb nc nd ne nf ng fh bj" data-selectable-paragraph="" id="3401" style="background-color: white; box-sizing: inherit; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;">Should we just simply “<a class="af nh" href="https://arxiv.org/abs/0709.4024" rel="noopener ugc nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;" target="_blank">shut up and calculate</a>”, or debate some more?</p><p class="pw-post-body-paragraph mj mk fo ml b mm mn mo mp mq mr ms mt mu mv mw mx my mz na nb nc nd ne nf ng fh bj" data-selectable-paragraph="" id="cb16" style="background-color: white; box-sizing: inherit; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;">[2] Fredkin, E. (2003). <a class="af nh" href="http://52.7.130.124/wp-content/uploads/2015/07/intro-to-DP.pdf" rel="noopener ugc nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;" target="_blank">An Introduction to Digital Philosophy</a>. <em class="np" style="box-sizing: inherit;">International Journal of Theoretical Physics</em>, 42(2), 189.</p><p class="pw-post-body-paragraph mj mk fo ml b mm mn mo mp mq mr ms mt mu mv mw mx my mz na nb nc nd ne nf ng fh bj" data-selectable-paragraph="" id="fa19" style="background-color: white; box-sizing: inherit; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;">This work is the Rosetta Stone for many comparisons between modern AI systems and human-like intelligence, at least in terms of computation.</p><p class="pw-post-body-paragraph mj mk fo ml b mm mn mo mp mq mr ms mt mu mv mw mx my mz na nb nc nd ne nf ng fh bj" data-selectable-paragraph="" id="7702" style="background-color: white; box-sizing: inherit; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;">[3] Newen, A., DeBruin, L., and Gallagher, S. (2018). <a class="af nh" href="https://academic.oup.com/edited-volume/28083" rel="noopener ugc nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;" target="_blank">The Oxford Handbook of 4E Cognition</a>. Oxford University Press.</p><p class="pw-post-body-paragraph mj mk fo ml b mm mn mo mp mq mr ms mt mu mv mw mx my mz na nb nc nd ne nf ng fh bj" data-selectable-paragraph="" id="d7c8" style="background-color: white; box-sizing: inherit; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;">[4] Wolfram, S. (2002). <a class="af nh" href="https://www.wolframscience.com/nks/" rel="noopener ugc nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;" target="_blank">A New Kind of Science</a>. Wolfram Media.</p><p class="pw-post-body-paragraph mj mk fo ml b mm mn mo mp mq mr ms mt mu mv mw mx my mz na nb nc nd ne nf ng fh bj" data-selectable-paragraph="" id="1d99" style="background-color: white; box-sizing: inherit; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;">This is a link to the 20th Anniversary edition, with a full set of Cellular Automata rules, defined by number.</p><p class="pw-post-body-paragraph mj mk fo ml b mm mn mo mp mq mr ms mt mu mv mw mx my mz na nb nc nd ne nf ng fh bj" data-selectable-paragraph="" id="b768" style="background-color: white; box-sizing: inherit; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;">[5] Zenil, H. (2016). <a class="af nh" href="https://www.quora.com/How-can-I-generate-random-numbers-using-the-Rule-30-Cellular-Automaton" rel="noopener ugc nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;" target="_blank">How can I generate random numbers using the Rule 30 Cellular Automaton</a>? Quora post.</p><p class="pw-post-body-paragraph mj mk fo ml b mm mn mo mp mq mr ms mt mu mv mw mx my mz na nb nc nd ne nf ng fh bj" data-selectable-paragraph="" id="daba" style="background-color: white; box-sizing: inherit; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;">[6] Bongard, J. and Levin, M. (2023). <a class="af nh" href="https://www.mdpi.com/2313-7673/8/1/110" rel="noopener ugc nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;" target="_blank">There’s Plenty of Room Right Here: Biological Systems as Evolved, Overloaded, Multi-Scale Machines</a>. <em class="np" style="box-sizing: inherit;">Biomimetics</em>, 8(1), 110.</p>Bradly Aliceahttp://www.blogger.com/profile/06482487682656113637noreply@blogger.com0tag:blogger.com,1999:blog-1792896637814721350.post-41092567406876459682023-08-24T09:49:00.001-05:002023-08-24T09:49:10.500-05:00Saturday Morning NeuroSim Discussion Thread: Causality<p><span style="background-color: white; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em;">Over the past three years, the </span><a href="https://representational-brains-phenotypes.weebly.com/saturday-morning-neurosim.html" style="font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em;">Saturday Morning NeuroSim</a><span style="background-color: white; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em;"> group has met weekly on Saturdays (mornings in North America). The Saturday Morning format continues in the tradition of Saturday Morning Physics and covers a wide variety of topics.</span></p><p><span style="background-color: white; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em;">Our discussion thread on causality begins with</span><span style="background-color: white; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em;"> </span><a class="af mn" href="https://youtu.be/oULBtq8wJoU?t=5780" rel="noopener ugc nofollow" style="-webkit-tap-highlight-color: transparent; background-color: white; box-sizing: inherit; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em;" target="_blank">Causality and Circles on May 13</a><span style="background-color: white; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em;">. From a Mastodon post by Yohan John, we considered how spatialized diagrams are confused with temporal sequences in a feedback loop. We also covered three papers in this session.</span></p><div class="ab ca" style="background-color: white; box-sizing: inherit; display: flex; justify-content: center;"><div class="ch bg et eu ev ew" style="box-sizing: inherit; margin: 0px 24px; max-width: 680px; min-width: 0px; width: 680px;"><div class="separator" style="clear: both; color: rgba(0, 0, 0, 0.8); font-family: medium-content-sans-serif-font, -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, Oxygen, Ubuntu, Cantarell, "Open Sans", "Helvetica Neue", sans-serif; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgJmd_1MGbzgi08ijM5hx43bQ0WdT7AgbVjAi0380T9LGti5Hcv8Hp5tK2KCSrF8dwu2LcVYJ6AnBwGcXNoGlaSp7HMIJFCPomjVygUof4ATvt-_rFwQ3f5kw9bAonbNULStLWIO-yn0_PwBbq2pueUvH-arswRimngR0H50MSKzk6rVv2mDZ3i2DCbUdQ/s1854/1_-TMeI9xNJwkn50xd-8sPeA.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="1854" data-original-width="1161" height="640" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgJmd_1MGbzgi08ijM5hx43bQ0WdT7AgbVjAi0380T9LGti5Hcv8Hp5tK2KCSrF8dwu2LcVYJ6AnBwGcXNoGlaSp7HMIJFCPomjVygUof4ATvt-_rFwQ3f5kw9bAonbNULStLWIO-yn0_PwBbq2pueUvH-arswRimngR0H50MSKzk6rVv2mDZ3i2DCbUdQ/w400-h640/1_-TMeI9xNJwkn50xd-8sPeA.jpg" width="400" /></a></div><div style="text-align: center;"><br /></div><p class="pw-post-body-paragraph lp lq fo lr b ls lt lu lv lw lx ly lz ma mb mc md me mf mg mh mi mj mk ml mm fh bj" data-selectable-paragraph="" id="6e60" style="box-sizing: inherit; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;">Vernon, D., Lowe, R., Thill, S., and Ziemke, T. (2015). <a class="af mn" href="https://www.frontiersin.org/articles/10.3389/fpsyg.2015.01660/full" rel="noopener ugc nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;" target="_blank">Embodied cognition and circular causality: on the role of constitutive autonomy in the reciprocal coupling of perception and action</a>. <em class="nd" style="box-sizing: inherit;">Frontiers in Psychology</em>, 6, 1660.</p><p class="pw-post-body-paragraph lp lq fo lr b ls lt lu lv lw lx ly lz ma mb mc md me mf mg mh mi mj mk ml mm fh bj" data-selectable-paragraph="" id="4126" style="box-sizing: inherit; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;">Raginsky, M. (2023). <a class="af mn" href="https://arxiv.org/abs/1110.0718" rel="noopener ugc nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;" target="_blank">Directed Information and Pearl’s Causal Calculus</a>. <em class="nd" style="box-sizing: inherit;">arXiv</em>, 1110.0718.</p><p class="pw-post-body-paragraph lp lq fo lr b ls lt lu lv lw lx ly lz ma mb mc md me mf mg mh mi mj mk ml mm fh bj" data-selectable-paragraph="" id="defd" style="box-sizing: inherit; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;">Laland, K.N., John Odling-Smee, J., Hoppitt, W., and Uller, T. (2013). <a class="af mn" href="https://link.springer.com/article/10.1007/s10539-012-9335-1" rel="noopener ugc nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;" target="_blank">More on how and why: cause and effect in biology revisited</a>. <em class="nd" style="box-sizing: inherit;">Biological Philosophy</em>, 28, 719–745.</p><p class="pw-post-body-paragraph lp lq fo lr b ls lt lu lv lw lx ly lz ma mb mc md me mf mg mh mi mj mk ml mm fh bj" data-selectable-paragraph="" id="f262" style="box-sizing: inherit; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;">Our conversation continued after the last week of Neuromatch Academy, when the NMA curriculum featured causal networks. Our <a class="af mn" href="https://youtu.be/BFcnPJXPBk8?t=2268" rel="noopener ugc nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;" target="_blank">July 29 meeting</a> featured a collection of references on Bayesianism, Probabilistic Graphical Models, methods of integration, time-series applications, and more. Some core readings are given below.</p><p class="pw-post-body-paragraph lp lq fo lr b ls lt lu lv lw lx ly lz ma mb mc md me mf mg mh mi mj mk ml mm fh bj" data-selectable-paragraph="" id="5542" style="box-sizing: inherit; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;">Stanford Encyclopedia of Philosophy: <a class="af mn" href="https://plato.stanford.edu/entries/causal-models" rel="noopener ugc nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;" target="_blank">causal models</a>. This article takes an epistemological approach and provides us with a baseline for structural equation model, graphical probabilistic models, and other statistical formulations of causal relationships.</p><p class="pw-post-body-paragraph lp lq fo lr b ls lt lu lv lw lx ly lz ma mb mc md me mf mg mh mi mj mk ml mm fh bj" data-selectable-paragraph="" id="4f5a" style="box-sizing: inherit; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;">Daphne Koller’s <a class="af mn" href="http://openclassroom.stanford.edu/MainFolder/CoursePage.php?course=ProbabilisticGraphicalModels" rel="noopener ugc nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;" target="_blank">Probabilistic Graphical Models</a> course. Hosted on Stanford University’s Open Classroom platform, this course includes units on representation, inference, learning, and causation. The causation unit covers decision theory, utility functions, influence diagrams, and the notion of perfect information.</p><p class="pw-post-body-paragraph lp lq fo lr b ls lt lu lv lw lx ly lz ma mb mc md me mf mg mh mi mj mk ml mm fh bj" data-selectable-paragraph="" id="c4f0" style="box-sizing: inherit; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;">Pearl, J. (2000). <a class="af mn" href="https://en.wikipedia.org/wiki/Causality_(book)" rel="noopener ugc nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;" target="_blank">Causality</a>. Cambridge Press, Cambridge, UK. This classic book by Judea Pearl builds from a theory of inferred causation, starting at causal diagrams, and continuing through direct effects, indirect effects, confounds, counterfactuals, bounding effects, and probabilities. The book also covers structural models, decision analysis, and Simpson’s Paradox as the basis for methods for detecting causal relationships.</p><p class="pw-post-body-paragraph lp lq fo lr b ls lt lu lv lw lx ly lz ma mb mc md me mf mg mh mi mj mk ml mm fh bj" data-selectable-paragraph="" id="485d" style="box-sizing: inherit; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;">Scholkopf, B. (2019). <a class="af mn" href="https://arxiv.org/abs/1911.10500" rel="noopener ugc nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;" target="_blank">Causality for Machine Learning</a>. <em class="nd" style="box-sizing: inherit;">arXiv</em>, 1911.10500.</p><p class="pw-post-body-paragraph lp lq fo lr b ls lt lu lv lw lx ly lz ma mb mc md me mf mg mh mi mj mk ml mm fh bj" data-selectable-paragraph="" id="2f05" style="box-sizing: inherit; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;">Heckman, J.J. (2005). <a class="af mn" href="https://www.jstor.org/stable/4148843" rel="noopener ugc nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;" target="_blank">The Scientific Model of Causality</a>. <em class="nd" style="box-sizing: inherit;">Sociological Methodology</em>, 35, 1–97. Causality from an econometrics point-of-view. Counterfactuals are a set of possible outcomes generated by determinants. A causal effect is defined by the change in the manipulated factor where amongst a set of factors, in a situation where all but one is held constant.</p><p class="pw-post-body-paragraph lp lq fo lr b ls lt lu lv lw lx ly lz ma mb mc md me mf mg mh mi mj mk ml mm fh bj" data-selectable-paragraph="" id="c1a1" style="box-sizing: inherit; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;">Taskesen, E. (2021). <a class="af mn" href="https://towardsdatascience.com/a-step-by-step-guide-in-detecting-causal-relationships-using-bayesian-structure-learning-in-python-c20c6b31cee5" rel="noopener" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;" target="_blank">A step-by-step guide in detecting causal relationships using Bayesian structure learning in Python</a>. <em class="nd" style="box-sizing: inherit;">Towards Data Science</em>, September 7.</p><p class="pw-post-body-paragraph lp lq fo lr b ls lt lu lv lw lx ly lz ma mb mc md me mf mg mh mi mj mk ml mm fh bj" data-selectable-paragraph="" id="06c0" style="box-sizing: inherit; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;">Which variables have a direct causal effect on a target variable? <span class="lr fp" style="box-sizing: inherit; font-weight: 700;">Hint:</span> association and correlation are not equivalent to causation.</p><p class="pw-post-body-paragraph lp lq fo lr b ls lt lu lv lw lx ly lz ma mb mc md me mf mg mh mi mj mk ml mm fh bj" data-selectable-paragraph="" id="1973" style="box-sizing: inherit; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;">Bayesian Models:</p><p class="pw-post-body-paragraph lp lq fo lr b ls lt lu lv lw lx ly lz ma mb mc md me mf mg mh mi mj mk ml mm fh bj" data-selectable-paragraph="" id="1284" style="box-sizing: inherit; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;">Neuberg, L.G. (2003). Causality: models, reasoning, and inference. <em class="nd" style="box-sizing: inherit;">Econometric Theory</em>, 19, 675–685.</p><p class="pw-post-body-paragraph lp lq fo lr b ls lt lu lv lw lx ly lz ma mb mc md me mf mg mh mi mj mk ml mm fh bj" data-selectable-paragraph="" id="660a" style="box-sizing: inherit; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;">Pearl, J. (2001). Bayesianism and causality, or, why I am only a half-Bayesian. In “Foundations of Bayesianism”, pgs. 19–36. Kluwer Press.</p><p class="pw-post-body-paragraph lp lq fo lr b ls lt lu lv lw lx ly lz ma mb mc md me mf mg mh mi mj mk ml mm fh bj" data-selectable-paragraph="" id="bad2" style="box-sizing: inherit; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;">Methods of Interaction: networks and non-directional graphs, as opposed to directed acyclic graphs (DAGs), require a different set of considerations. The methods below cover highly interacting systems like graphs and how change over time can be properly interpreted as causal.</p><p class="pw-post-body-paragraph lp lq fo lr b ls lt lu lv lw lx ly lz ma mb mc md me mf mg mh mi mj mk ml mm fh bj" data-selectable-paragraph="" id="0cda" style="box-sizing: inherit; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;">Leng, S., Ma, H., Kurths, J., Lai, Y-C., Lin, W., Aihara, K., and Chen, L. (2020). <a class="af mn" href="https://www.nature.com/articles/s41467-020-16238-0" rel="noopener ugc nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;" target="_blank">Partial cross mapping eliminates indirect causal influences</a>. <em class="nd" style="box-sizing: inherit;">Nature Communications</em>, 11, 2632.</p><p class="pw-post-body-paragraph lp lq fo lr b ls lt lu lv lw lx ly lz ma mb mc md me mf mg mh mi mj mk ml mm fh bj" data-selectable-paragraph="" id="85e9" style="box-sizing: inherit; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;">Park, S.H., Ha, S., and Kim, J.K. (2023). <a class="af mn" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10366229" rel="noopener ugc nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;" target="_blank">A general model-based causal inference method overcomes the curse of synchrony and indirect effects</a>. <em class="nd" style="box-sizing: inherit;">Nature Communications</em>, 14, 4287.</p><figure class="mr ms mt mu mv mw mo mp paragraph-image" style="box-sizing: inherit; clear: both; color: rgba(0, 0, 0, 0.8); font-family: medium-content-sans-serif-font, -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, Oxygen, Ubuntu, Cantarell, "Open Sans", "Helvetica Neue", sans-serif; margin: 56px auto 0px;"><div class="mx my eb mz bg na" role="button" style="box-sizing: inherit; cursor: zoom-in; position: relative; transition: transform 300ms cubic-bezier(0.2, 0, 0.2, 1) 0s; width: 680px; z-index: auto;" tabindex="0"><div class="mo mp ne" style="box-sizing: inherit; margin-left: auto; margin-right: auto; max-width: 1920px;"><picture style="box-sizing: inherit;"><source sizes="(min-resolution: 4dppx) and (max-width: 700px) 50vw, (-webkit-min-device-pixel-ratio: 4) and (max-width: 700px) 50vw, (min-resolution: 3dppx) and (max-width: 700px) 67vw, (-webkit-min-device-pixel-ratio: 3) and (max-width: 700px) 65vw, (min-resolution: 2.5dppx) and (max-width: 700px) 80vw, (-webkit-min-device-pixel-ratio: 2.5) and (max-width: 700px) 80vw, (min-resolution: 2dppx) and (max-width: 700px) 100vw, (-webkit-min-device-pixel-ratio: 2) and (max-width: 700px) 100vw, 700px" srcset="https://miro.medium.com/v2/resize:fit:640/format:webp/1*dwmYQUYLL0I7V6Jvgz_szQ.png 640w, https://miro.medium.com/v2/resize:fit:720/format:webp/1*dwmYQUYLL0I7V6Jvgz_szQ.png 720w, https://miro.medium.com/v2/resize:fit:750/format:webp/1*dwmYQUYLL0I7V6Jvgz_szQ.png 750w, https://miro.medium.com/v2/resize:fit:786/format:webp/1*dwmYQUYLL0I7V6Jvgz_szQ.png 786w, https://miro.medium.com/v2/resize:fit:828/format:webp/1*dwmYQUYLL0I7V6Jvgz_szQ.png 828w, https://miro.medium.com/v2/resize:fit:1100/format:webp/1*dwmYQUYLL0I7V6Jvgz_szQ.png 1100w, https://miro.medium.com/v2/resize:fit:1400/format:webp/1*dwmYQUYLL0I7V6Jvgz_szQ.png 1400w" style="box-sizing: inherit;" type="image/webp"></source><source data-testid="og" sizes="(min-resolution: 4dppx) and (max-width: 700px) 50vw, (-webkit-min-device-pixel-ratio: 4) and (max-width: 700px) 50vw, (min-resolution: 3dppx) and (max-width: 700px) 67vw, (-webkit-min-device-pixel-ratio: 3) and (max-width: 700px) 65vw, (min-resolution: 2.5dppx) and (max-width: 700px) 80vw, (-webkit-min-device-pixel-ratio: 2.5) and (max-width: 700px) 80vw, (min-resolution: 2dppx) and (max-width: 700px) 100vw, (-webkit-min-device-pixel-ratio: 2) and (max-width: 700px) 100vw, 700px" srcset="https://miro.medium.com/v2/resize:fit:640/1*dwmYQUYLL0I7V6Jvgz_szQ.png 640w, https://miro.medium.com/v2/resize:fit:720/1*dwmYQUYLL0I7V6Jvgz_szQ.png 720w, https://miro.medium.com/v2/resize:fit:750/1*dwmYQUYLL0I7V6Jvgz_szQ.png 750w, https://miro.medium.com/v2/resize:fit:786/1*dwmYQUYLL0I7V6Jvgz_szQ.png 786w, https://miro.medium.com/v2/resize:fit:828/1*dwmYQUYLL0I7V6Jvgz_szQ.png 828w, https://miro.medium.com/v2/resize:fit:1100/1*dwmYQUYLL0I7V6Jvgz_szQ.png 1100w, https://miro.medium.com/v2/resize:fit:1400/1*dwmYQUYLL0I7V6Jvgz_szQ.png 1400w" style="box-sizing: inherit;"></source><img alt="" class="bg nb nc c" height="352" loading="lazy" role="presentation" src="https://miro.medium.com/v2/resize:fit:700/1*dwmYQUYLL0I7V6Jvgz_szQ.png" style="box-sizing: inherit; height: auto; max-width: 100%; vertical-align: middle; width: 680px;" width="700" /></picture></div></div><figcaption class="nf ng nh mo mp ni nj be b bf z dv" data-selectable-paragraph="" style="box-sizing: inherit; color: #6b6b6b; font-family: sohne, "Helvetica Neue", Helvetica, Arial, sans-serif; font-size: 14px; line-height: 20px; margin-left: auto; margin-right: auto; margin-top: 10px; max-width: 728px; text-align: center;">From the <a class="af mn" href="https://en.wikipedia.org/wiki/Granger_causality" rel="noopener ugc nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;" target="_blank">Granger Causality Wikipedia</a> entry.</figcaption></figure><p class="pw-post-body-paragraph lp lq fo lr b ls lt lu lv lw lx ly lz ma mb mc md me mf mg mh mi mj mk ml mm fh bj" data-selectable-paragraph="" id="6ca9" style="box-sizing: inherit; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;">Time-series using Granger Causality: the first two references apply Granger Causality to time-series datasets. In such cases, the datapoints are dependent with respect to time. Given two time-series <em class="nd" style="box-sizing: inherit;">x</em> and <em class="nd" style="box-sizing: inherit;">y</em>, <em class="nd" style="box-sizing: inherit;">x</em> is the cause of <em class="nd" style="box-sizing: inherit;">y</em> if <em class="nd" style="box-sizing: inherit;">x</em> predicts <em class="nd" style="box-sizing: inherit;">y</em> (lagged with respect to x over a certain time interval) given <em class="nd" style="box-sizing: inherit;">x</em> and prior values of <em class="nd" style="box-sizing: inherit;">y</em>. This is in comparison with simply predicting the current value of <em class="nd" style="box-sizing: inherit;">y</em> given previous values of <em class="nd" style="box-sizing: inherit;">y</em>, which would be the counterfactual case.</p><p class="pw-post-body-paragraph lp lq fo lr b ls lt lu lv lw lx ly lz ma mb mc md me mf mg mh mi mj mk ml mm fh bj" data-selectable-paragraph="" id="73b6" style="box-sizing: inherit; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;">The final paper in the group (Stokes and Purdon) critiques Granger Causality from a Neuroscience perspective.</p><p class="pw-post-body-paragraph lp lq fo lr b ls lt lu lv lw lx ly lz ma mb mc md me mf mg mh mi mj mk ml mm fh bj" data-selectable-paragraph="" id="a3e6" style="box-sizing: inherit; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;">Carlos‐Sandberg, L. and Clack, C.D. (2021). <a class="af mn" href="https://www.nature.com/articles/s41598-021-97741-2" rel="noopener ugc nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;" target="_blank">Incorporation of causality structures to complex network analysis of time‐varying behaviour of multivariate time series</a>. <em class="nd" style="box-sizing: inherit;">Scientifc Reports</em>, 11, 18880.</p><p class="pw-post-body-paragraph lp lq fo lr b ls lt lu lv lw lx ly lz ma mb mc md me mf mg mh mi mj mk ml mm fh bj" data-selectable-paragraph="" id="f053" style="box-sizing: inherit; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;">Runge, J., Nowack, P., Kretschmer, M., Flaxman, S., Sejdinovic, D. (2019). <a class="af mn" href="https://www.science.org/doi/10.1126/sciadv.aau4996" rel="noopener ugc nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;" target="_blank">Detecting and quantifying causal associations in large nonlinear time series datasets</a>. <em class="nd" style="box-sizing: inherit;">Science Advances</em>, 5(11), aau4996.</p><p class="pw-post-body-paragraph lp lq fo lr b ls lt lu lv lw lx ly lz ma mb mc md me mf mg mh mi mj mk ml mm fh bj" data-selectable-paragraph="" id="b48d" style="box-sizing: inherit; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;">Stokes, P.A. and Purdon, P.L. (2017). <a class="af mn" href="https://www.pnas.org/doi/10.1073/pnas.1704663114" rel="noopener ugc nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;" target="_blank">A study of problems encountered in Granger causality analysis from a neuroscience perspective</a>. <em class="nd" style="box-sizing: inherit;">PNAS</em>, 114(34), E7063-E7072.</p><p class="pw-post-body-paragraph lp lq fo lr b ls lt lu lv lw lx ly lz ma mb mc md me mf mg mh mi mj mk ml mm fh bj" data-selectable-paragraph="" id="3532" style="box-sizing: inherit; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;">The <a class="af mn" href="https://youtu.be/IBObGMYjw1c?t=6843" rel="noopener ugc nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;" target="_blank">third session (August 5)</a> was a focus on causality specifically as it is treated in Neuroscience. This session followed up on a Twitter debate by Kording Lab and Earl Miller about the role of causality in neuroscience. The consensus to the question “Why is Neuroscience so into causality?” was that it provides a means to identify mechanisms for function. Causality in neuroscience differs from philosophical discussions about causality in that Neuroscience must infer causality from data, while philosophers (and statisticians) do the work of proving causality.</p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhRpd9jUgBS8k-BQkoPS1FnhEpbwycsKAPspW9aqgXi9ISdgDVwuqBKUceqggKS8z02WR37gVogaBueuBssv0lXiETvytHwMbCribbHbWYhAuZsho2slq6IJcj9NZRtV1uw1F5b1e8rXYVj75UqM-Npn_zVvHnbB1viG_OgCDPIIAcK21Wbmd5fp-f4oeU/s1800/1.webp" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="1800" data-original-width="1350" height="640" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhRpd9jUgBS8k-BQkoPS1FnhEpbwycsKAPspW9aqgXi9ISdgDVwuqBKUceqggKS8z02WR37gVogaBueuBssv0lXiETvytHwMbCribbHbWYhAuZsho2slq6IJcj9NZRtV1uw1F5b1e8rXYVj75UqM-Npn_zVvHnbB1viG_OgCDPIIAcK21Wbmd5fp-f4oeU/w480-h640/1.webp" width="480" /></a></div><br /><div class="separator" style="clear: both; text-align: center;"><br /></div><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjcgYhqtM9sN6TbcPH04p0t3b4rEHa0RBiV2Iclk98gtXnbyClYkhheJypPrGUZA_7-_z6aiianaIE1qmOuFVCeLVHD8PTl2ogd4fMpZKgOoa3c9y28oXrRCA-ga_rZthLQ8U_6_ybLsRB5b9iDfB31M5Fres1f25d7zNfwGjCwJgLXpZjTtnHKG5NEC6s/s1800/2.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="1800" data-original-width="1350" height="640" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjcgYhqtM9sN6TbcPH04p0t3b4rEHa0RBiV2Iclk98gtXnbyClYkhheJypPrGUZA_7-_z6aiianaIE1qmOuFVCeLVHD8PTl2ogd4fMpZKgOoa3c9y28oXrRCA-ga_rZthLQ8U_6_ybLsRB5b9iDfB31M5Fres1f25d7zNfwGjCwJgLXpZjTtnHKG5NEC6s/w480-h640/2.jpg" width="480" /></a></div></div></div><div class="ab ca" style="background-color: white; box-sizing: inherit; color: rgba(0, 0, 0, 0.8); display: flex; font-family: medium-content-sans-serif-font, -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, Oxygen, Ubuntu, Cantarell, "Open Sans", "Helvetica Neue", sans-serif; justify-content: center;"><div class="ch bg et eu ev ew" style="box-sizing: inherit; margin: 0px 24px; max-width: 680px; min-width: 0px; width: 680px;"><p class="pw-post-body-paragraph lp lq fo lr b ls lt lu lv lw lx ly lz ma mb mc md me mf mg mh mi mj mk ml mm fh bj" data-selectable-paragraph="" id="8a9b" style="box-sizing: inherit; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;"><span style="letter-spacing: -0.003em;">One interesting point from Kording Lab is that there is a difference between proximate causes and ultimate causes. In some fields, causality is obvious and so causal methods are not always necessary. But Neuroscience is partially about the behavioral substrate, and so we can turn to Niko Tinbergen’s four questions. The four questions concern 1) how a trait arose in development (proximate, dynamic), 2) how a trait arose in evolution (ultimate, dynamic), 3) what is the mechanism or structure of a trait (proximate, static), and 4) what is the adaptive value or function of a trait (ultimate, static).</span></p><p class="pw-post-body-paragraph lp lq fo lr b ls lt lu lv lw lx ly lz ma mb mc md me mf mg mh mi mj mk ml mm fh bj" data-selectable-paragraph="" id="8467" style="box-sizing: inherit; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;">You can read more about Tinbergen’s four questions and their causal implications in the following papers.</p><p class="pw-post-body-paragraph lp lq fo lr b ls lt lu lv lw lx ly lz ma mb mc md me mf mg mh mi mj mk ml mm fh bj" data-selectable-paragraph="" id="90e0" style="box-sizing: inherit; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;">Beer, C. (2020). <a class="af mn" href="https://www.sciencedirect.com/science/article/pii/S0003347219302507" rel="noopener ugc nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;" target="_blank">Niko Tinbergen and questions of instinct</a>. <em class="nd" style="box-sizing: inherit;">Animal Behaviour</em>, 164, 261–265.</p><p class="pw-post-body-paragraph lp lq fo lr b ls lt lu lv lw lx ly lz ma mb mc md me mf mg mh mi mj mk ml mm fh bj" data-selectable-paragraph="" id="220a" style="box-sizing: inherit; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;">Nesse, R.M. (2019). <a class="af mn" href="https://academic.oup.com/emph/article/2019/1/2/5232207" rel="noopener ugc nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;" target="_blank">Tinbergen’s four questions: two proximate, two evolutionary</a>. <em class="nd" style="box-sizing: inherit;">Evolution, Medicine, and Public Health</em>, 2, doi:10.1093/ emph/eoy035.</p><p class="pw-post-body-paragraph lp lq fo lr b ls lt lu lv lw lx ly lz ma mb mc md me mf mg mh mi mj mk ml mm fh bj" data-selectable-paragraph="" id="53d2" style="box-sizing: inherit; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;">Mayr, E. (1961). <a class="af mn" href="https://www.science.org/doi/10.1126/science.134.3489.1501" rel="noopener ugc nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;" target="_blank">Cause and effect in biology</a>. <em class="nd" style="box-sizing: inherit;">Science</em>, 134, 1501–1506.</p><p class="pw-post-body-paragraph lp lq fo lr b ls lt lu lv lw lx ly lz ma mb mc md me mf mg mh mi mj mk ml mm fh bj" data-selectable-paragraph="" id="264f" style="box-sizing: inherit; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;">The other papers from this session focused on mental representations and causal functional connectivity in the brain, respectively.</p><p class="pw-post-body-paragraph lp lq fo lr b ls lt lu lv lw lx ly lz ma mb mc md me mf mg mh mi mj mk ml mm fh bj" data-selectable-paragraph="" id="d490" style="box-sizing: inherit; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;">Sloman, S.A. and Lagnado, D. (2015). <a class="af mn" href="https://www.annualreviews.org/doi/10.1146/annurev-psych-010814-015135" rel="noopener ugc nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;" target="_blank">Causality in Thought</a>. <em class="nd" style="box-sizing: inherit;">Annual Reviews in Psychology</em>, 66, 223–247.</p><p class="pw-post-body-paragraph lp lq fo lr b ls lt lu lv lw lx ly lz ma mb mc md me mf mg mh mi mj mk ml mm fh bj" data-selectable-paragraph="" id="a6f9" style="box-sizing: inherit; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;">While Bayesian approaches are good for theory-building, they are an incomplete account of what goes on in the cognitive world.</p><p class="pw-post-body-paragraph lp lq fo lr b ls lt lu lv lw lx ly lz ma mb mc md me mf mg mh mi mj mk ml mm fh bj" data-selectable-paragraph="" id="6856" style="box-sizing: inherit; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;">Biswas, R. and Shlizerman, E. (2022). <a class="af mn" href="https://journals.plos.org/ploscompbiol/article?id=10.1371%2Fjournal.pcbi.1010653" rel="noopener ugc nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;" target="_blank">Statistical perspective on functional and causal neural connectomics: The Time-Aware PC algorithm</a>. <em class="nd" style="box-sizing: inherit;">PLoS Computational Biology</em>, 18(11), e1010653.</p><p class="pw-post-body-paragraph lp lq fo lr b ls lt lu lv lw lx ly lz ma mb mc md me mf mg mh mi mj mk ml mm fh bj" data-selectable-paragraph="" id="2733" style="box-sizing: inherit; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;">The <a class="af mn" href="https://youtu.be/WzfwcJUaqg4?t=1510" rel="noopener ugc nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;" target="_blank">fourth session (August 19)</a> picks up on a point covered in the second session, namely how causality can be inferred from network data. This covers related ideas of transitivity, weak interactions, and anti-causal models. Papers for this session include networks in ecology, anticipative and non-anticipative control theory, and anti-causal systems.</p><figure class="mr ms mt mu mv mw mo mp paragraph-image" style="box-sizing: inherit; clear: both; margin: 56px auto 0px;"><div class="mx my eb mz bg na" role="button" style="box-sizing: inherit; cursor: zoom-in; position: relative; transition: transform 300ms cubic-bezier(0.2, 0, 0.2, 1) 0s; width: 680px; z-index: auto;" tabindex="0"><div class="mo mp nx" style="box-sizing: inherit; margin-left: auto; margin-right: auto; max-width: 1422px;"><picture style="box-sizing: inherit;"><source sizes="(min-resolution: 4dppx) and (max-width: 700px) 50vw, (-webkit-min-device-pixel-ratio: 4) and (max-width: 700px) 50vw, (min-resolution: 3dppx) and (max-width: 700px) 67vw, (-webkit-min-device-pixel-ratio: 3) and (max-width: 700px) 65vw, (min-resolution: 2.5dppx) and (max-width: 700px) 80vw, (-webkit-min-device-pixel-ratio: 2.5) and (max-width: 700px) 80vw, (min-resolution: 2dppx) and (max-width: 700px) 100vw, (-webkit-min-device-pixel-ratio: 2) and (max-width: 700px) 100vw, 700px" srcset="https://miro.medium.com/v2/resize:fit:640/format:webp/1*fRBsau5MiAErhQVf4QDcGw.png 640w, https://miro.medium.com/v2/resize:fit:720/format:webp/1*fRBsau5MiAErhQVf4QDcGw.png 720w, https://miro.medium.com/v2/resize:fit:750/format:webp/1*fRBsau5MiAErhQVf4QDcGw.png 750w, https://miro.medium.com/v2/resize:fit:786/format:webp/1*fRBsau5MiAErhQVf4QDcGw.png 786w, https://miro.medium.com/v2/resize:fit:828/format:webp/1*fRBsau5MiAErhQVf4QDcGw.png 828w, https://miro.medium.com/v2/resize:fit:1100/format:webp/1*fRBsau5MiAErhQVf4QDcGw.png 1100w, https://miro.medium.com/v2/resize:fit:1400/format:webp/1*fRBsau5MiAErhQVf4QDcGw.png 1400w" style="box-sizing: inherit;" type="image/webp"></source><source data-testid="og" sizes="(min-resolution: 4dppx) and (max-width: 700px) 50vw, (-webkit-min-device-pixel-ratio: 4) and (max-width: 700px) 50vw, (min-resolution: 3dppx) and (max-width: 700px) 67vw, (-webkit-min-device-pixel-ratio: 3) and (max-width: 700px) 65vw, (min-resolution: 2.5dppx) and (max-width: 700px) 80vw, (-webkit-min-device-pixel-ratio: 2.5) and (max-width: 700px) 80vw, (min-resolution: 2dppx) and (max-width: 700px) 100vw, (-webkit-min-device-pixel-ratio: 2) and (max-width: 700px) 100vw, 700px" srcset="https://miro.medium.com/v2/resize:fit:640/1*fRBsau5MiAErhQVf4QDcGw.png 640w, https://miro.medium.com/v2/resize:fit:720/1*fRBsau5MiAErhQVf4QDcGw.png 720w, https://miro.medium.com/v2/resize:fit:750/1*fRBsau5MiAErhQVf4QDcGw.png 750w, https://miro.medium.com/v2/resize:fit:786/1*fRBsau5MiAErhQVf4QDcGw.png 786w, https://miro.medium.com/v2/resize:fit:828/1*fRBsau5MiAErhQVf4QDcGw.png 828w, https://miro.medium.com/v2/resize:fit:1100/1*fRBsau5MiAErhQVf4QDcGw.png 1100w, https://miro.medium.com/v2/resize:fit:1400/1*fRBsau5MiAErhQVf4QDcGw.png 1400w" style="box-sizing: inherit;"></source><img alt="" class="bg nb nc c" height="394" loading="eager" role="presentation" src="https://miro.medium.com/v2/resize:fit:700/1*fRBsau5MiAErhQVf4QDcGw.png" style="box-sizing: inherit; height: auto; max-width: 100%; vertical-align: middle; width: 680px;" width="700" /></picture></div></div><figcaption class="nf ng nh mo mp ni nj be b bf z dv" data-selectable-paragraph="" style="box-sizing: inherit; color: #6b6b6b; font-family: sohne, "Helvetica Neue", Helvetica, Arial, sans-serif; font-size: 14px; line-height: 20px; margin-left: auto; margin-right: auto; margin-top: 10px; max-width: 728px; text-align: center;">Typology of causal models for past, present, and future events.</figcaption></figure><p class="pw-post-body-paragraph lp lq fo lr b ls lt lu lv lw lx ly lz ma mb mc md me mf mg mh mi mj mk ml mm fh bj" data-selectable-paragraph="" id="f3ac" style="box-sizing: inherit; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;">Naghshtabrizi, P. and Hespanha, J.P. (2006). <a class="af mn" href="https://link.springer.com/chapter/10.1007/11533382_14" rel="noopener ugc nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;" target="_blank">Anticipative and non-anticipative controller design for network control systems</a>. <em class="nd" style="box-sizing: inherit;">Lecture Notes in Control and Information Science</em>, 331.</p><p class="pw-post-body-paragraph lp lq fo lr b ls lt lu lv lw lx ly lz ma mb mc md me mf mg mh mi mj mk ml mm fh bj" data-selectable-paragraph="" id="1be7" style="box-sizing: inherit; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;">Sugihara, G., May, R., Ye, H., Hsieh, C-H., Deyle, E., Fogarty, M., Munch, S. (2012). <a class="af mn" href="https://deepeco.ucsd.edu/wp-content/uploads/2019/10/causalityCCM.pdf" rel="noopener ugc nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;" target="_blank">Detecting Causality in Complex Ecosystems</a>. <em class="nd" style="box-sizing: inherit;">Science</em>, 338, 496–500.</p><p class="pw-post-body-paragraph lp lq fo lr b ls lt lu lv lw lx ly lz ma mb mc md me mf mg mh mi mj mk ml mm fh bj" data-selectable-paragraph="" id="8ff4" style="box-sizing: inherit; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;">Chattopadhyay, I. (2014). <a class="af mn" href="https://arxiv.org/abs/1406.6651" rel="noopener ugc nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;" target="_blank">Causality Networks</a>. <em class="nd" style="box-sizing: inherit;">arXiv</em>, 1406.6651.</p><p class="pw-post-body-paragraph lp lq fo lr b ls lt lu lv lw lx ly lz ma mb mc md me mf mg mh mi mj mk ml mm fh bj" data-selectable-paragraph="" id="1777" style="box-sizing: inherit; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;"><a class="af mn" href="https://en.wikipedia.org/wiki/Anticausal_system" rel="noopener ugc nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;" target="_blank">Anticausal System</a>. <em class="nd" style="box-sizing: inherit;">Wikipedia</em>.</p><p class="pw-post-body-paragraph lp lq fo lr b ls lt lu lv lw lx ly lz ma mb mc md me mf mg mh mi mj mk ml mm fh bj" data-selectable-paragraph="" id="4bbf" style="box-sizing: inherit; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;">McCurdy, T. (2007). <a class="af mn" href="https://www.physicsforums.com/threads/causal-systems-understanding-the-basics.186612/" rel="noopener ugc nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;" target="_blank">Causal Systems: understanding the basics</a>. <em class="nd" style="box-sizing: inherit;">Physics Forums</em>. September 23.</p><figure class="mr ms mt mu mv mw mo mp paragraph-image" style="box-sizing: inherit; clear: both; margin: 56px auto 0px;"><div class="mx my eb mz bg na" role="button" style="box-sizing: inherit; cursor: zoom-in; position: relative; transition: transform 300ms cubic-bezier(0.2, 0, 0.2, 1) 0s; width: 680px; z-index: auto;" tabindex="0"><div class="mo mp ny" style="box-sizing: inherit; margin-left: auto; margin-right: auto; max-width: 1280px;"><picture style="box-sizing: inherit;"><source sizes="(min-resolution: 4dppx) and (max-width: 700px) 50vw, (-webkit-min-device-pixel-ratio: 4) and (max-width: 700px) 50vw, (min-resolution: 3dppx) and (max-width: 700px) 67vw, (-webkit-min-device-pixel-ratio: 3) and (max-width: 700px) 65vw, (min-resolution: 2.5dppx) and (max-width: 700px) 80vw, (-webkit-min-device-pixel-ratio: 2.5) and (max-width: 700px) 80vw, (min-resolution: 2dppx) and (max-width: 700px) 100vw, (-webkit-min-device-pixel-ratio: 2) and (max-width: 700px) 100vw, 700px" srcset="https://miro.medium.com/v2/resize:fit:640/format:webp/1*lUyd_0A5Hyp9yhsokP32xw.png 640w, https://miro.medium.com/v2/resize:fit:720/format:webp/1*lUyd_0A5Hyp9yhsokP32xw.png 720w, https://miro.medium.com/v2/resize:fit:750/format:webp/1*lUyd_0A5Hyp9yhsokP32xw.png 750w, https://miro.medium.com/v2/resize:fit:786/format:webp/1*lUyd_0A5Hyp9yhsokP32xw.png 786w, https://miro.medium.com/v2/resize:fit:828/format:webp/1*lUyd_0A5Hyp9yhsokP32xw.png 828w, https://miro.medium.com/v2/resize:fit:1100/format:webp/1*lUyd_0A5Hyp9yhsokP32xw.png 1100w, https://miro.medium.com/v2/resize:fit:1400/format:webp/1*lUyd_0A5Hyp9yhsokP32xw.png 1400w" style="box-sizing: inherit;" type="image/webp"></source><source data-testid="og" sizes="(min-resolution: 4dppx) and (max-width: 700px) 50vw, (-webkit-min-device-pixel-ratio: 4) and (max-width: 700px) 50vw, (min-resolution: 3dppx) and (max-width: 700px) 67vw, (-webkit-min-device-pixel-ratio: 3) and (max-width: 700px) 65vw, (min-resolution: 2.5dppx) and (max-width: 700px) 80vw, (-webkit-min-device-pixel-ratio: 2.5) and (max-width: 700px) 80vw, (min-resolution: 2dppx) and (max-width: 700px) 100vw, (-webkit-min-device-pixel-ratio: 2) and (max-width: 700px) 100vw, 700px" srcset="https://miro.medium.com/v2/resize:fit:640/1*lUyd_0A5Hyp9yhsokP32xw.png 640w, https://miro.medium.com/v2/resize:fit:720/1*lUyd_0A5Hyp9yhsokP32xw.png 720w, https://miro.medium.com/v2/resize:fit:750/1*lUyd_0A5Hyp9yhsokP32xw.png 750w, https://miro.medium.com/v2/resize:fit:786/1*lUyd_0A5Hyp9yhsokP32xw.png 786w, https://miro.medium.com/v2/resize:fit:828/1*lUyd_0A5Hyp9yhsokP32xw.png 828w, https://miro.medium.com/v2/resize:fit:1100/1*lUyd_0A5Hyp9yhsokP32xw.png 1100w, https://miro.medium.com/v2/resize:fit:1400/1*lUyd_0A5Hyp9yhsokP32xw.png 1400w" style="box-sizing: inherit;"></source><img alt="" class="bg nb nc c" height="467" loading="lazy" role="presentation" src="https://miro.medium.com/v2/resize:fit:700/1*lUyd_0A5Hyp9yhsokP32xw.png" style="box-sizing: inherit; height: auto; max-width: 100%; vertical-align: middle; width: 680px;" width="700" /></picture></div></div><figcaption class="nf ng nh mo mp ni nj be b bf z dv" data-selectable-paragraph="" style="box-sizing: inherit; color: #6b6b6b; font-family: sohne, "Helvetica Neue", Helvetica, Arial, sans-serif; font-size: 14px; line-height: 20px; margin-left: auto; margin-right: auto; margin-top: 10px; max-width: 728px; text-align: center;">From the <a class="af mn" href="https://en.wikipedia.org/wiki/Necessity_and_sufficiency" rel="noopener ugc nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;" target="_blank">Necessity and Sufficiency Wikipedia</a> entry.</figcaption></figure><p class="pw-post-body-paragraph lp lq fo lr b ls lt lu lv lw lx ly lz ma mb mc md me mf mg mh mi mj mk ml mm fh bj" data-selectable-paragraph="" id="44d0" style="box-sizing: inherit; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;">Finally, some fields (cell and molecular biology) have working models of causation that while useful, are not particularly illuminating. In the cell and molecular biology example, the traditional model of necessity and sufficiency (a mechanism being necessary but not sufficient) can be criticized for not being complete with respect to incorporating counterfactuals or multiple potential causes. See this paper for more information:</p><p class="pw-post-body-paragraph lp lq fo lr b ls lt lu lv lw lx ly lz ma mb mc md me mf mg mh mi mj mk ml mm fh bj" data-selectable-paragraph="" id="8072" style="box-sizing: inherit; color: #242424; font-family: source-serif-pro, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 20px; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;">Bizzarri, M., Brash, D.E., Briscoe, J., Grieneisen, V.A., Stern, C.D., and Levin, M. (2019). <a class="af mn" href="https://www.nature.com/articles/s41580-019-0127-1" rel="noopener ugc nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;" target="_blank">A call for a better understanding of causation in cell biology</a>. <em class="nd" style="box-sizing: inherit;">Nature Reviews Molecular Cell Biology</em>, 20, 261–262.</p></div></div>Bradly Aliceahttp://www.blogger.com/profile/06482487682656113637noreply@blogger.com0tag:blogger.com,1999:blog-1792896637814721350.post-85027356614771213612023-05-08T02:08:00.010-05:002023-05-08T02:21:26.382-05:00Google Summer of Code 2023<div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgCzJtNmSzfPatFzp9jm3eUQIDoLHMOJMuGqGlXRCas1Dlh5lJ2v_C9axm3VqrvRSFFnihibVVrUJeW7uat77aFbNI2drq53Gc9seLwa11ym0KkrxGuHxXzravCf_F1RLKQVy6fmmRbPwP8VK1q9IUzPti2mVBok2yzlMPsznwrgHuxUgLkrJjQW9xG/s192/GSoC-icon-192.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="192" data-original-width="192" height="192" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgCzJtNmSzfPatFzp9jm3eUQIDoLHMOJMuGqGlXRCas1Dlh5lJ2v_C9axm3VqrvRSFFnihibVVrUJeW7uat77aFbNI2drq53Gc9seLwa11ym0KkrxGuHxXzravCf_F1RLKQVy6fmmRbPwP8VK1q9IUzPti2mVBok2yzlMPsznwrgHuxUgLkrJjQW9xG/s1600/GSoC-icon-192.png" width="192" /></a></div><p>Welcome to the new Google Summer of Code scholars for 2023! INCF is sponsoring four students for which I (Bradly Alicea) am acting as mentor: two students for the <a href="https://devoworm.weebly.com/">DevoWorm group</a> (via the <a href="https://openworm.org/">OpenWorm Foundation</a> community) and two students for the <a href="https://orthogonal-research.weebly.com/">Orthogonal Research and Education Laboratory</a>. These four students are pursuing three projects.</p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjyXqWht17lqnKm3lykyLiIZbQt6oEYVfnnrGSAPD_iwmHTmDAruW7P66oo0d6gdbA7JBplhTTo8YHR1v8JYpnQ4hDFPFPhxIlJTtZrPydZQCOxVADTQMn3e2jOJn8FK8r9tGNR0sPLoWL8KX3AIOnlIS2KC72lGFJw-KTe-P9qQd_sEsg2aMm93AfV/s474/OIP.jpg" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="268" data-original-width="474" height="113" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjyXqWht17lqnKm3lykyLiIZbQt6oEYVfnnrGSAPD_iwmHTmDAruW7P66oo0d6gdbA7JBplhTTo8YHR1v8JYpnQ4hDFPFPhxIlJTtZrPydZQCOxVADTQMn3e2jOJn8FK8r9tGNR0sPLoWL8KX3AIOnlIS2KC72lGFJw-KTe-P9qQd_sEsg2aMm93AfV/w200-h113/OIP.jpg" width="200" /></a></div><div class="separator" style="clear: both; text-align: center;"><br /></div><p><b>D-GNNs and DevoLearn (sponsored by the DevoWorm group)</b></p><p>Congratulations to Himanshu Chougule and Sushmanth Reddy Mereddy for being accepted to work on the Developmental Graph Neural Networks (D-GNNs) project. Sushmanth has been contributing to the DevoLearn platform for quite some time and will spend this summer working on improving the image segmentation to GNN embedding pipeline. Himanshu was a part of last Summer's GSoC cohort in the Orthogonal Research and Education Laboratory, working on the Open-source Sustainability project. His work resulted in developing Agent-based Model-Reinforcement Learning hybrid models. This year, he will be working on building Topological Data Analytic capabilities into the D-GNN pipeline. </p><p>Mayukh Deb and Jiahang Li are co-mentors for this project.</p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiapfEQWFqbnbqpjn-S9lEPSBGJBnw3VvRTkPyx3G2cT-RRqN9J9urFqEhGCf19cNC4DIoBo_DnoJc5LLb4QMpCSkJ_voNqhrzBdCDSFLdSRqSF512U1lNstjYJj9V_OIBApAw6DHCkI6M7nt5-UEhDcB_wzdYYyw4I605FDwWIYj6bjiFzN6DE3767/s350/38323286.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="350" data-original-width="350" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiapfEQWFqbnbqpjn-S9lEPSBGJBnw3VvRTkPyx3G2cT-RRqN9J9urFqEhGCf19cNC4DIoBo_DnoJc5LLb4QMpCSkJ_voNqhrzBdCDSFLdSRqSF512U1lNstjYJj9V_OIBApAw6DHCkI6M7nt5-UEhDcB_wzdYYyw4I605FDwWIYj6bjiFzN6DE3767/w200-h200/38323286.png" width="200" /></a></div><p><b>Virtual Reality for Research and Open-source Sustainability (sponsored by the Orthogonal Research and Education Lab)</b></p><p>Congratulations to Vrushali Nandurkar and R.V. Rajagopalan for being accepted to work on the projects Virtual Reality for Research and Open-source Sustainability, respectively. Vrushali is enthusiastic about working on creating open-source virtual world assets for scientific research and educational initiatives. R.V. will be working on a continuation of the Open-source Sustainability project, helping to augment the existing models and web interface.</p><p>Jesse Parent is a co-mentor for both projects, while Brian McCorkle is a co-mentor for the Open-source Sustainability project. </p>Bradly Aliceahttp://www.blogger.com/profile/06482487682656113637noreply@blogger.com0tag:blogger.com,1999:blog-1792896637814721350.post-85738335278856890552023-03-03T16:21:00.002-06:002023-04-06T11:01:47.499-05:00Ancient Embryogenesis and Evolutionary Origins<div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiDP4z7YWztesQ55jqA3tKhoT0bX0LBMGRxnfyeYoVfqlIWjZ4-qLVnt5Zj3pXKg_IuD_HmQoFtgcObBtkzc9iF-GXodw_wEMMPM3ve9sqVc8NqR49jUC9vrDGqFAL-BhFF87dZi_Y0GVk7cccoIF7GB79TAWt9F1AEKHRkU5wMcy0XJIbsrs7Npl6o/s768/darwin-embryo.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="768" data-original-width="768" height="320" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiDP4z7YWztesQ55jqA3tKhoT0bX0LBMGRxnfyeYoVfqlIWjZ4-qLVnt5Zj3pXKg_IuD_HmQoFtgcObBtkzc9iF-GXodw_wEMMPM3ve9sqVc8NqR49jUC9vrDGqFAL-BhFF87dZi_Y0GVk7cccoIF7GB79TAWt9F1AEKHRkU5wMcy0XJIbsrs7Npl6o/s320/darwin-embryo.png" width="320" /></a></div><p style="text-align: center;">"Darwin as an Embryo". In this case, <a href="https://evolution.berkeley.edu/the-history-of-evolutionary-thought/1800s/early-evolution-and-development-ernst-haeckel/">Neoteny really does recapitulates Phylogeny</a>! COURTESY: <a href="https://stablediffusionweb.com/">Stable Diffusion</a>.</p><p>For this year's delayed <a href="https://darwinday.org/">Darwin Day</a> post, I will present some of the latest work on ancient embryos which we have been discussing in the <a href="https://www.youtube.com/channel/UChGTq41_rJwmZ1I4j7SezWQ">DevoWorm group meetings</a>. While this is by no means a complete review, we will discuss the earliest fossil evidence for eggs, embryos, and nervous systems (in animals, not plants), in addition to the conditions that lead to their emergence. In short, how did we get to embryos from a universal common ancestor with bacteria and archebacteria, and why do only different types of Eukaryotes (plants, radial symmetrical Metazoans, and bilateral Metazoans) have embryos?</p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgPNF3zQxCcEfcaunOAj1thS-h2NET-VL7iDptCkOJcq1THVH0tvWkuHdZ8ij8mjH7Thyi5kdU07gZqd9ioCAXNIYGyO3517pJPoBkJp2t-bJEBk_a1E-k2IBi8bIutWOQOiGrqt0dgsWQx5NOE5tjj7i5L235nnyuDFYHdAk6X2baUCHKifySzBH0v/s1411/1.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="1411" data-original-width="1200" height="400" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgPNF3zQxCcEfcaunOAj1thS-h2NET-VL7iDptCkOJcq1THVH0tvWkuHdZ8ij8mjH7Thyi5kdU07gZqd9ioCAXNIYGyO3517pJPoBkJp2t-bJEBk_a1E-k2IBi8bIutWOQOiGrqt0dgsWQx5NOE5tjj7i5L235nnyuDFYHdAk6X2baUCHKifySzBH0v/w340-h400/1.png" width="340" /></a></div><p style="text-align: center;">Tree of Life (genome tree) from Hug et.al [1] with three domains. Click to enlarge.</p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhaoAjPHtoJuN8qhOFfEUyU2drrcU_6RYNglHgADgrbm-_8AIQJUFUIUCyY-YIJ-P34w_ibrt-paLKvZfZpJWqc0w4LBpYM6w3FBmqGXN1_8p9zY0uKtnKh2wO-YjfPUiQwR9FLFbCCqp5_78Gl3ve07nm5guqLN8wVrxBjrIYqlsjLi9VzPIoOltX_/s847/2.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="313" data-original-width="847" height="237" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhaoAjPHtoJuN8qhOFfEUyU2drrcU_6RYNglHgADgrbm-_8AIQJUFUIUCyY-YIJ-P34w_ibrt-paLKvZfZpJWqc0w4LBpYM6w3FBmqGXN1_8p9zY0uKtnKh2wO-YjfPUiQwR9FLFbCCqp5_78Gl3ve07nm5guqLN8wVrxBjrIYqlsjLi9VzPIoOltX_/w640-h237/2.png" width="640" /></a></div><div class="separator" style="clear: both; text-align: center;">The ecological states of early Earth. COURTESY: J. Hirshfeld/Wikimedia. Click to enlarge.</div><p style="text-align: left;">We begin in the Cambrian, where the firs bilaterian appeared around 600 million years ago, approximately 70-80 million years before the Cambrian explosion [2]. In between the emergence of bilaterians, several key innovations occurred that suggests the origins of embryos and egg-laying. The first are the presence of fossilized burrows [2] for egg-laying behaviors. By the end of the Cambrian explosion, early pancrustecean arthropod species were possibly subject to life-history tradeoffs related to clutch size [3]. Another key innovation is direct evidence in the form of well-preserved multicellular structures from the period leading up to the Cambrian explosion that show a transition in cell geometry from a 2-cell stage to a cleavage stage [4]. As representative of a variety of ancestral algae species from the Doushantuo formation, these remains have not been connected to any particular adult form. However, they do demonstrate oogenesis and cleavage [2]. Finally, the functional genomics of developmental pattern formation emerged during this time [5]. This includes a ProtoHox cluster in ancestral cnidarians [6], <i>Hox</i> gene duplication [7], and an increase in body size and shape diversity alongside the advent of bilaterian <i>bauplans </i>[8]. Multiple <i>Hox</i> gene families may have served the role of promoting directed locomotion that in turn promoted active exploration of the environment [7].</p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjyRvAxuMIDIDrfYvEyr-IMMvJg1fiPShZeBoV4P-qwP1nuPG87AUdqibYjA9AZzFjtdnhkSdmgHpTFMDWoUWRU_1R3p9UoJEc16XbAPye0NfxWrTg-9R1_33tYupUbXCdLUNwButj3bpX1_uIZ8lAfuik9rftM1rXyULyySZLoDyB4fYSbRE4m-zIX/s668/6.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="244" data-original-width="668" height="146" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjyRvAxuMIDIDrfYvEyr-IMMvJg1fiPShZeBoV4P-qwP1nuPG87AUdqibYjA9AZzFjtdnhkSdmgHpTFMDWoUWRU_1R3p9UoJEc16XbAPye0NfxWrTg-9R1_33tYupUbXCdLUNwButj3bpX1_uIZ8lAfuik9rftM1rXyULyySZLoDyB4fYSbRE4m-zIX/w400-h146/6.png" width="400" /></a></div><p style="text-align: center;">Images of a potential early embryo, including the 2-cell and cleavage stages [from 4]. Click to enlarge.</p><p style="text-align: left;">The Ediacaran (630-540 million years ago) has yielded a large number of potential embryonic forms. In the Ediacaran biota, we find a number of Metazoan remains with no clear phylogenetic position. However, Evans et.al [9] propose that early embryos evolved independently (with several origins) in the bilaterian clade. However, during this time, a number of general trends emerge that enabled modern bilaterian adult forms. As previously discussed, Multicellular structures with distinct cell types, axial polarity, and anatomical segmentation [10, 11] emerged during this time. Left-right symmetry was a related feature of these embryos [11]. So-called polarized elements [12] such as microtubules, flagella, and apical-to-basal orientation were all found soon after the last Eukaryotic common ancestor (LECA). The evolution and diversification of polarity proteins is consistent with this timeline [12]. Other organismal structures such as a gut, sub-specialization of the phenotype, and a nervous system with heads and appendages are also features of note. We will talk about the emergence of nervous systems later on.</p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiImY7hltKAtTeXuvInT5A8M3f9OmuStGmp3yIYzVxGiZhZ9HtXUsljdMmbhkUm1k7UTIksG0S0uhFpSdDNBwDb7mTeSnbVQwIPpLbbJJqyI2H2CcpKqBdOfy2r_rezROH4MFcZkivP42e31dmuJvpY8BGeHsaYGfiAHwMxAgNRBxEAsdBuF6Ea3q0R/s860/7.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="574" data-original-width="860" height="268" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiImY7hltKAtTeXuvInT5A8M3f9OmuStGmp3yIYzVxGiZhZ9HtXUsljdMmbhkUm1k7UTIksG0S0uhFpSdDNBwDb7mTeSnbVQwIPpLbbJJqyI2H2CcpKqBdOfy2r_rezROH4MFcZkivP42e31dmuJvpY8BGeHsaYGfiAHwMxAgNRBxEAsdBuF6Ea3q0R/w400-h268/7.png" width="400" /></a></div><p style="text-align: center;">Scenario for the origins of development in bilaterians from [9]. Click to enlarge.</p><div class="separator" style="clear: both; text-align: left;"><i style="text-align: center;">Bicellum brasieri </i><span style="text-align: center;">is a 10<sup>9</sup> year old fossil holozoan that might provide the very earliest examples of modern embryos and embryogenesis [13]. </span>Microfossils of <i>Bicellum</i> demonstrate morphogenesis in the form of cell-cell adhesion for different cell types, as well as differential layers of cells (driven by adhesion) which may be the precursors of tissue differentiation. This can be compared to the Doushantuo embryos from Precambrian China [14], and Caveasphera from 609 million years ago [15], which are perhaps the direct ancestors of Metazoan embryonic forms. These are the first examples of development proceeding within an enclosed space, enabled by cell adhesion similar to what is observed during gastrulation in modern embryos. Caveasphera in particular shows evidence of anatomical polarization (particularly polar aggregation), cell division events, and ingression [15]. This is informative but is not diagnostic of the Urmetazoan condition [16].</div><div class="separator" style="clear: both; text-align: left;"><br /></div><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjr8h6LtnYxpj0wNr4DtSdCrWGazoTzpw8JFQLbEUT7m4akr89-73Dg__4giufbzbvLx6LYkqjJpX2vDCr_1C0L0dBubf9q6JxXZLR8X3BHrtZikkYVvQdCGywq1GS_n6N93T3MzZJ1uZ3vpY1YLgVEPqZwVAnHJ2fQYvXpkBjyWWOoeEwVEPBuYX4i/s380/4.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="379" data-original-width="380" height="319" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjr8h6LtnYxpj0wNr4DtSdCrWGazoTzpw8JFQLbEUT7m4akr89-73Dg__4giufbzbvLx6LYkqjJpX2vDCr_1C0L0dBubf9q6JxXZLR8X3BHrtZikkYVvQdCGywq1GS_n6N93T3MzZJ1uZ3vpY1YLgVEPqZwVAnHJ2fQYvXpkBjyWWOoeEwVEPBuYX4i/w320-h319/4.png" width="320" /></a></div><br /><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhtgNtiNLIQo23U_kq5FOvFL3ToSQ66_Hrdcy2M_29gMLG15tx7XLbrhHkoRcFdCXXjId08VMmaeTvar_SHuab9uwFbbTtRnIMzhvWrhMHZoPvSJV-7QdswmdMr4Sv_mg_uy3H42C9-CMUZYfJWv7X8yKtrWBxyU5uXwkENZ2NH7R-G3Ch6eLJpjXN7/s426/5.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="357" data-original-width="426" height="268" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhtgNtiNLIQo23U_kq5FOvFL3ToSQ66_Hrdcy2M_29gMLG15tx7XLbrhHkoRcFdCXXjId08VMmaeTvar_SHuab9uwFbbTtRnIMzhvWrhMHZoPvSJV-7QdswmdMr4Sv_mg_uy3H42C9-CMUZYfJWv7X8yKtrWBxyU5uXwkENZ2NH7R-G3Ch6eLJpjXN7/w320-h268/5.png" width="320" /></a></div><div class="separator" style="clear: both; text-align: center;">Graphical abstract and (top) palynological evidence of <i>Bicellum brasieri</i> (bottom) as shown in [13]. Epidermal layer (A and C), ellipsoid (D) and oblate (E) specimens Click to enlarge.</div><div class="separator" style="clear: both; text-align: center;"><br /></div><div class="separator" style="clear: both; text-align: left;">Since these pre-Cambrian explosion phenotypes are very simple, we can look to fossil evidence for much more complex embryo phenotypes in the late Cretaceous. Xing et.al [17] report on an <i>in-ovo</i> therapod dinosaur embryo, where the body is folded into an elongated egg. The authors are able to demonstrate how the fully formed head and legs are folded into different prehatching postures.</div><div class="separator" style="clear: both; text-align: center;"><br /></div><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg3HniGhQ9q-Hzt-mGBj4VnBT-SMpF5y-VObgyu0L9ZFYpF2cPDdjFT6h5wgTQwwu70vFwh6HUAGJ_1HccyeBeYwulPPNwRtWVLzM4iQOJ9wG0qdALdyZepuPfHwEBsMAO5VMTOVB-f2vHaUl1qrENj-V3vzz3eDBfWCfIf7KqGnhJlG_c-b323fCQx/s579/8.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="571" data-original-width="579" height="316" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg3HniGhQ9q-Hzt-mGBj4VnBT-SMpF5y-VObgyu0L9ZFYpF2cPDdjFT6h5wgTQwwu70vFwh6HUAGJ_1HccyeBeYwulPPNwRtWVLzM4iQOJ9wG0qdALdyZepuPfHwEBsMAO5VMTOVB-f2vHaUl1qrENj-V3vzz3eDBfWCfIf7KqGnhJlG_c-b323fCQx/w320-h316/8.png" width="320" /></a></div><br /><div class="separator" style="clear: both; text-align: center;">Graphical abstract showing developmental stages of Caveasphera [15]. Click to enlarge.</div><div class="separator" style="clear: both; text-align: center;"><br /></div><div class="separator" style="clear: both; text-align: left;">While the early phylogeny of nervous system origins is the very definition of a tangled tree [18], the first nervous systems coincide with the emergence of discrete body types in the Cambrian [19]. Brains emerged in part from the developmental toolkit responsible for patterning and segmentation [20]. This toolkit consists of genes and regulatory mechanisms that were co-opted for the development of excitable cells [21], synapses [22], and neuronal networks [2]. While the strongest evidence for early embryos only show evidence for bilaterian organization, radial symmetry is actually the basal condition for Metazoans [23]. Therefore, early embryos should yield at least two types of nervous system configurations that are observed in modern phenotypes: a centralized nervous system that converges in the head (the brains of bilaterians), and a distributed nervous system (the nerve nets of cnidarians). Centralized nervous systems originated from the mesoderm layer of triploblastic embryos, while distributed nervous systems are derived from the endoderm of diploblastic embryos. While there is a distinct literature on fossil radial embryos from China [24], there does not seem to be fossil evidence of germ layers formation and subsequent differentiation in any early embryos to date.</div><div class="separator" style="clear: both; text-align: center;"><br /></div><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhAP7fWAWz6p8yq5JzhCYog-y25jaXRhwVNky0Qqr2nJaroWReIEI-bKN9DN986MCAQYFjrKk91n1UdI68MLMJO7-AkLGO8cH3Fo2WVbgpAWbQGqXtVjOTr6RwfI_lyeOS9LofOFHuzCQD_YNpp47cw3nQ8ICNFshyForhx9ub4LoY86jZv9QEc-rB3/s716/9.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="372" data-original-width="716" height="208" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhAP7fWAWz6p8yq5JzhCYog-y25jaXRhwVNky0Qqr2nJaroWReIEI-bKN9DN986MCAQYFjrKk91n1UdI68MLMJO7-AkLGO8cH3Fo2WVbgpAWbQGqXtVjOTr6RwfI_lyeOS9LofOFHuzCQD_YNpp47cw3nQ8ICNFshyForhx9ub4LoY86jZv9QEc-rB3/w400-h208/9.png" width="400" /></a></div><div class="separator" style="clear: both; text-align: center;">Image of Baby Yingliang (therapod dinosaur late-stage embryo) [17]. Click to enlarge.</div><div class="separator" style="clear: both; text-align: center;"><br /></div><div class="separator" style="clear: both; text-align: left;">But what happened before the earliest embryos (1000-650 million years ago)? What ecological conditions might have driven this innovation? One trigger may have been the great oxygenation event, which occurred in two stages: the first at 2.4 billion years ago, and the second at 950 million years ago. It was the second event that increased oxygen content to a level more resembling the present, and in turn drove diversification of distinct fungi, plants, and animals. It is of note that LECA (the last Eukaryotic common ancestor) lies well-beforehand [25]. The earliest embryos (or at least multicellular packings) might have resulted from selection pressure for retaining a low-oxygenation environment. But while these findings may lead to significant speculation, it seems that embryos are unique to Eukaryotic evolution, having no Bacterial or Archaebacterial counterpart despite evolving under the same conditions. It is most likely the interaction of genomic factors, developmental contingencies, and environmental conditions that ultimately lead to the emergence of embryos [26].</div><div class="separator" style="clear: both; text-align: center;"><br /></div><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjvQKEPjgXwNFZ1_xV1Ogqu8S121o2pVd515LbfgDgMHl0cjqs2c0AQIkhzg6zC9aG68D3NS3NK2aqEW3eTYYi7N5NVHEoP-OCmTZ9AR6OssWYVoghhGEXUFxfzbLHCblYIlV1g-DcEgdrXvAFHtZRJhQVNptSSv02zEIOPARsBLBtZXePZTmoV06xx/s960/3.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="540" data-original-width="960" height="360" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjvQKEPjgXwNFZ1_xV1Ogqu8S121o2pVd515LbfgDgMHl0cjqs2c0AQIkhzg6zC9aG68D3NS3NK2aqEW3eTYYi7N5NVHEoP-OCmTZ9AR6OssWYVoghhGEXUFxfzbLHCblYIlV1g-DcEgdrXvAFHtZRJhQVNptSSv02zEIOPARsBLBtZXePZTmoV06xx/w640-h360/3.png" width="640" /></a></div><br /><div class="separator" style="clear: both; text-align: center;">Phylogeny with evolution transitions from LUCA to embryos in plants and animals. Included are the two oxygenation events of Earth's history. Transitions derived from Refs [14, 27-31]. Click to enlarge.</div><div class="separator" style="clear: both; text-align: center;"><br /></div><div class="separator" style="clear: both; text-align: center;"><b>References</b></div><div class="separator" style="clear: both; text-align: center;"><br /></div><div class="separator" style="clear: both; text-align: left;">[1] Hug, L.A. et.al (2016). <a href="https://www.nature.com/articles/nmicrobiol201648">A new view of the tree of life</a>. <i>Nature Microbiology</i>, 1, 16048. </div><div class="separator" style="clear: both; text-align: left;"><br /></div><div class="separator" style="clear: both; text-align: left;"><div class="separator" style="clear: both;">[2] Valentine, J.W., Jablonski, D., and Erwin, D.H. 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(5 more authors) (2017). <a href="https://www.nature.com/articles/nature23261">Evidence for early life in Earth’s oldest hydrothermal vent precipitates</a>. <i>Nature</i>, 543 (7643). pp. 60-64. <b>AND</b> Hassenkam, T., Andersson, M., Dalby, K., MacKensie, D.M.A., and Rosing, M.T. (2017). <a href="https://www.nature.com/articles/nature23261">Elements of Eoarchean life trapped in mineral inclusions</a>. <i>Nature</i>, 548, 78–81.</div><div class="separator" style="clear: both;"><div class="separator" style="clear: both;"><br /></div><div class="separator" style="clear: both;">[31] Tree of Life: Feng, D-F., Cho, G., and Doolittle, R.F. (1997). <a href="https://www.pnas.org/doi/10.1073/pnas.94.24.13028">Determining divergence times with a protein clock: Update and reevaluation</a>. <i>PNAS</i>, 94, 13028-13033.</div></div>Bradly Aliceahttp://www.blogger.com/profile/06482487682656113637noreply@blogger.com1tag:blogger.com,1999:blog-1792896637814721350.post-75287200809673073672022-12-27T13:22:00.003-06:002022-12-27T13:22:26.125-06:00The 500k Apex<p style="text-align: justify;"><span style="font-family: times; font-size: medium;">I am pleased to report that as of the beginning of December 2022, Synthetic Daisies blog has reached 500,000 reads. The blog started over the 2008 Holiday season (14 years ago) and took about a year to garner significant readership. Over the years, Synthetic Daisies has participated in the Carnival of Evolution, several SciComm (Science Communication) initiatives, and charted the research progress of a number of initiatives (including the <a href="https://devoworm.weebly.com/">DevoWorm group</a>).</span></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg2qacc6u3fZOb1U7rUlryrRhLSUqPeCQ8XlmXlHv2mJo8xAlDofD7igk0FjyvQZZM1t9ZfirWOjrPjKSUkacfPxAQ9Gv_ZwGE_VSlyUauVz-ouzX3zeNiyxqDr8W5FHy6x9I8fzKA81tlCoYa_M8_RSVUT61mFJsEnxRFtpSaJER-92RmuXFc8v184/s1054/chart.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="653" data-original-width="1054" height="248" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg2qacc6u3fZOb1U7rUlryrRhLSUqPeCQ8XlmXlHv2mJo8xAlDofD7igk0FjyvQZZM1t9ZfirWOjrPjKSUkacfPxAQ9Gv_ZwGE_VSlyUauVz-ouzX3zeNiyxqDr8W5FHy6x9I8fzKA81tlCoYa_M8_RSVUT61mFJsEnxRFtpSaJER-92RmuXFc8v184/w400-h248/chart.png" width="400" /></a></div><div style="text-align: center;"><span style="font-family: times; font-size: medium;">Number of posts by year. Click to enlarge.</span></div><p style="text-align: justify;"><span style="font-family: times; font-size: medium;">Although the number of time investment has declined in recent years, the posts have continued to accumulate reads. Synthetic Daisies has a <a href="https://github.com/synthetic-daisies">Github repository</a> and <a href="https://synthetic-daisies.github.io/">overlay site</a> where some of the more popular posts are profiled. The Github repo also features associated code and other items from these posts. </span></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhN_I_hNjD6srAK2RoioCqOKyhkUJzAkaFBxn9Axlj85tjg5sJOPFJ-35dEtPaOzZmt0Q0qvZibiH11mvZKKkuv0mHM4uPA1iZA9rHF7MpzgrDSpFI0v_Grqsh4SiWFjB4gr9NnxZPhnz_fHV24ca8nz1J5x1llWpZ9uMnk5zUt18SfkjTpHSBrboVC/s909/blog.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="298" data-original-width="909" height="210" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhN_I_hNjD6srAK2RoioCqOKyhkUJzAkaFBxn9Axlj85tjg5sJOPFJ-35dEtPaOzZmt0Q0qvZibiH11mvZKKkuv0mHM4uPA1iZA9rHF7MpzgrDSpFI0v_Grqsh4SiWFjB4gr9NnxZPhnz_fHV24ca8nz1J5x1llWpZ9uMnk5zUt18SfkjTpHSBrboVC/w640-h210/blog.png" width="640" /></a></div><p style="text-align: center;"><span style="font-family: times; font-size: medium;">Number of readers over the course of 14 years. Click to enlarge.</span></p><p style="text-align: left;"><span style="font-family: times; font-size: medium;">More to report in another 200,000 to 300,000 reads!</span></p>Bradly Aliceahttp://www.blogger.com/profile/06482487682656113637noreply@blogger.com0tag:blogger.com,1999:blog-1792896637814721350.post-40924983578298135972022-12-23T14:00:00.002-06:002022-12-24T00:47:33.470-06:00Learning on Graphs (LoG) conference recap<p style="text-align: center;"> </p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhBDFSrY1N8XSby52rvFfhB6i7rLtM6SobdfKoIGb5fJt2RY2Mw3ysdsbDX5Vz4lKIJ_UFlskZRsOPqTjCICpIyP4aE7_2PaJsk9TiqlxEzJCEfTsJxEzGAgWFLIbfKZee-via77dTJesFnxep1sD8NW20RiQzcRUi90LWihNFXH3KknJJDl_gmaZal/s400/logo_conf_below_512_512_hu0b3b5122a793f6cbe7d94790c745769e_24489_400x0_resize_lanczos_3.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="400" data-original-width="400" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhBDFSrY1N8XSby52rvFfhB6i7rLtM6SobdfKoIGb5fJt2RY2Mw3ysdsbDX5Vz4lKIJ_UFlskZRsOPqTjCICpIyP4aE7_2PaJsk9TiqlxEzJCEfTsJxEzGAgWFLIbfKZee-via77dTJesFnxep1sD8NW20RiQzcRUi90LWihNFXH3KknJJDl_gmaZal/w200-h200/logo_conf_below_512_512_hu0b3b5122a793f6cbe7d94790c745769e_24489_400x0_resize_lanczos_3.png" width="200" /></a></div><p></p><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-align: justify;"><span style="font-size: medium;"><br /></span></p><div style="text-align: left;"><div style="text-align: justify;"><span style="font-size: medium;"><span style="font-family: times; white-space: pre-wrap;">The </span><a href="https://logconference.org/" style="font-family: times; white-space: pre-wrap;">Learning on Graphs (LoG)</a><span style="font-family: times; white-space: pre-wrap;"> conference took place from December 9-12 and featured a broad diversity of research on </span><a href="https://en.wikipedia.org/wiki/Graph_neural_network" style="font-family: times; white-space: pre-wrap;">Graph Neural Networks (GNNs)</a><span style="font-family: times; white-space: pre-wrap;">. GNNs [1] encompass a relatively new area of machine learning research which have a number of interesting connections to applied math and network science. The daily sessions (keynote talks and oral presentations), in addition to the seven workshop sessions, are available from the conference </span><a href="https://www.youtube.com/@learningongraphs" style="font-family: times; white-space: pre-wrap;">YouTube channel</a><span style="font-family: times; white-space: pre-wrap;">.</span></span></div><span style="font-size: medium;"><div style="font-family: times; text-align: justify; white-space: pre-wrap;"><br /></div></span></div><div style="text-align: justify;"><span style="font-size: medium;"><span style="font-family: times;"><span style="background-color: transparent; color: black; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">GNNs are a way to take data that yield graphical relationships in the real world and analyze then using the power of neural networks. While GNNs are specialized for problems that can be represented as a graph (discrete, interconnected systems), any problem with a set of complex geometric relationships is appropriate for GNNs. </span></span><span style="font-family: times; white-space: pre-wrap;">While the output of GNNs are typically </span><a href="https://en.wikipedia.org/wiki/Embedding" style="font-family: times; white-space: pre-wrap;">embeddings</a><span style="font-family: times; white-space: pre-wrap;"> (graph topologies embedded in the feature space), some problems require different approaches such as functions or more formal representations. </span></span></div><div style="text-align: justify;"><span style="font-size: medium;"><br /></span></div><div style="text-align: justify;"><span style="font-family: times; font-size: medium;"><span style="background-color: transparent; color: black; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">It is the analysis of these graphical relationships which make it a useful analytical approach. </span><span style="background-color: transparent; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">In all their forms, GNNs yield useful representations of graph data partly because they take into consideration the intrinsic symmetries of graphs, such as <a href="https://en.wikipedia.org/wiki/Invariant_(physics)">invariance</a> and <a href="https://en.wikipedia.org/wiki/Equivariant_map">equivariance</a> of graph topology with respect to a relabeling of the nodes [2]. </span><span style="background-color: transparent; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Based on what was featured at LoG, GNNs had many potential applications in the biological arena, including precision medicine, drug discovery, and characterizing molecular systems (such as <a href="https://scholar.google.de/citations?user=npqoAWwAAAAJ&hl=en">Stefan Gunnemann's (Technical University of Munich)</a> talk in the <a href="https://www.youtube.com/watch?v=wp5S9GHyAgw">Friday session</a>).</span></span></div><div style="text-align: justify;"><span style="font-family: times;"><span style="background-color: transparent; color: black; font-size: medium; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br /></span></span></div><div style="text-align: center;"><span style="font-family: times; font-size: medium;"><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgkVIvb3bNN2VI31hX9rTo2GKwTr5DMZtM-Q5GLAmSLoiGwlN4z6Q_hOb3DwsIxeo5ncFOfafu1eABO4D0tGjlGAmexB2cR9oQhHj-CY9uVNqs_CdigYmh_WlH-iL-VVQ9muVsOuAOJigCruiIrmIbOGoli3GLcCoRXEj2QwqXCffqmUm2yAnU-WtnW/s4480/Screenshot%202022-12-23%20at%201.00.14%20PM.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="2520" data-original-width="4480" height="225" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgkVIvb3bNN2VI31hX9rTo2GKwTr5DMZtM-Q5GLAmSLoiGwlN4z6Q_hOb3DwsIxeo5ncFOfafu1eABO4D0tGjlGAmexB2cR9oQhHj-CY9uVNqs_CdigYmh_WlH-iL-VVQ9muVsOuAOJigCruiIrmIbOGoli3GLcCoRXEj2QwqXCffqmUm2yAnU-WtnW/w400-h225/Screenshot%202022-12-23%20at%201.00.14%20PM.png" width="400" /></a></div><div style="text-align: justify;"><br /></div></span></div><div style="text-align: justify;"><span style="font-size: medium;"><span style="font-family: times;"><span style="background-color: transparent; color: black; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">GNNs can be evaluated using the <a href="https://en.wikipedia.org/wiki/Graph_isomorphism_problem">isomorphism (or </a></span><span style="background-color: transparent; color: black; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><i><a href="https://en.wikipedia.org/wiki/Graph_isomorphism_problem">k</a></i></span><span style="background-color: transparent; color: black; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><a href="https://en.wikipedia.org/wiki/Graph_isomorphism_problem">-WL) test</a>, which evaluates whether two graphs are isomorphic. Given that a graph can be drawn from the source data, the source data graph should be isomorphic with the output graph. The <a href="https://towardsdatascience.com/expressive-power-of-graph-neural-networks-and-the-weisefeiler-lehman-test-b883db3c7c49">Weisfeiler-Lehman heuristic for graph isomorphism</a> can be summarized in the 1-D case as the <a href="https://en.wikipedia.org/wiki/Colour_refinement_algorithm">color refinement algorithm</a>. </span></span><span style="font-family: times; white-space: pre-wrap;">A related issue in GNN research is algorithmic expressiveness. Expressivity is the breadth of ideas that can be represented and communicated using a particular type of representation. One current challenge of GNNs as they are applied to various problem domains is their ability to be functionally robust. </span><span><span style="font-family: times; white-space: pre-wrap;">One solution to this is by using </span><span style="font-family: times; white-space: pre-wrap;">GNNs as a generative model. Generating alternate graph representations allows us to use <a href="https://en.wikipedia.org/wiki/Graphon">graphons</a> [3], functions that capture different GNN topologies of the same type. The collection of graphs associated with a graphon can then be evaluated.</span><span style="font-family: times; white-space: pre-wrap;"> </span><a href="https://scholar.google.com/citations?user=JBGlsDoAAAAJ&hl=en" style="font-family: times; white-space: pre-wrap;">Soledad Villar's (Johns Hopkins)</a><span style="font-family: times; white-space: pre-wrap;"> presentation during the <a href="https://www.youtube.com/watch?v=wp5S9GHyAgw">Sunday session</a> featured an in-depth discussions of expressiveness and graphons as they relate to GNN performance.</span></span></span></div><div style="text-align: justify;"><span style="font-size: medium;"><br /></span></div><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi2pupjPwNwMfkTc3ihXKCQ-5_Umnr-UzIrcmXjChdOTsb_8WCEUCo2ag-81JHYyST_5hTNdPoem6cQEV0xleOwc4yQS5nfqWcWs2YWROTHERjWr4QMC_Obe4i632Ru0gE0ThdQXWg2ZMwbQoXkx7LDDS_Y6agQ2n_G_nomI5sS83z5L_jgTqYP9zx6/s4480/Screenshot%202022-12-23%20at%2012.50.12%20PM.png" style="margin-left: 1em; margin-right: 1em;"><span style="font-size: medium;"><img border="0" data-original-height="2520" data-original-width="4480" height="225" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi2pupjPwNwMfkTc3ihXKCQ-5_Umnr-UzIrcmXjChdOTsb_8WCEUCo2ag-81JHYyST_5hTNdPoem6cQEV0xleOwc4yQS5nfqWcWs2YWROTHERjWr4QMC_Obe4i632Ru0gE0ThdQXWg2ZMwbQoXkx7LDDS_Y6agQ2n_G_nomI5sS83z5L_jgTqYP9zx6/w400-h225/Screenshot%202022-12-23%20at%2012.50.12%20PM.png" width="400" /></span></a></div><div style="text-align: justify;"><span style="font-size: medium;"><br /></span></div><div style="text-align: justify;"><span style="font-size: medium;"><br /></span></div><div style="text-align: justify;"><span style="font-size: medium;"><span style="font-family: times; white-space: pre-wrap;">GNNs can be combined with various analytical techniques traditionally used in <a href="https://en.wikipedia.org/wiki/Complex_network">complex network</a> analysis. One of these involves the analysis of graphical models using tools from network science. These include the use of <a href="https://en.wikipedia.org/wiki/Random_graph">random graphs</a> and <a href="https://en.wikipedia.org/wiki/Stochastic_block_model">stochastic block models</a> to uncover the presence of topological structure and community formation, respectively. </span><span style="font-family: times; white-space: pre-wrap;">GNNs have ties to </span><a href="https://en.wikipedia.org/wiki/Category_theory" style="font-family: times; white-space: pre-wrap;">category theory</a><span style="font-family: times;"> as well.</span><span style="font-family: times; white-space: pre-wrap;"> The </span><a href="http://cats.for.ai" style="font-family: times; white-space: pre-wrap;">cats.for.ai</a><span style="font-family: times; white-space: pre-wrap;"> workshop (October 2022) featured applications of category theory to GNNs. I</span><span style="font-family: times; white-space: pre-wrap;">n the Saturday session,</span><span style="font-family: times; white-space: pre-wrap;"> </span><a href="https://scholar.google.com/citations?user=a3q4YxEAAAAJ" style="font-family: times; white-space: pre-wrap;">Taco Cohen (Qualcomm AI)</a><span style="font-family: times; white-space: pre-wrap;"> discussed how the techniques of category theory, </span><a href="https://en.wikipedia.org/wiki/Monad_(functional_programming)" style="font-family: times; white-space: pre-wrap;">monads</a><span style="font-family: times; white-space: pre-wrap;"> in particular, can be applied to GNNs. GNNs can also form <a href="https://en.wikipedia.org/wiki/Directed_acyclic_graph">directed acyclic graphs (DAGs)</a>, which are amenable to causal models. </span></span></div><div style="text-align: left;"><span style="font-family: times; font-size: medium;"><div style="text-align: justify;"><span style="white-space: pre-wrap;"><br /></span></div><div style="text-align: center;"><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjuf89qismqqOLTVVdSTiiYUNJoDUdYumwie3EbXivS5LP2hiy0kfElObWrs5bUTx1saEF7p6plcMqS8myUw2eS22xcz-vC0X1ROOlA_b81JUo7YpjQd1rJ0SvcWgpiPT1mxVv0IBXen2NOTdBpEPT5s38AorkPpZkwhAcoNR02Sr83qqsFFvgvDYNv/s4480/Screenshot%202022-12-23%20at%2012.53.55%20PM.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="2520" data-original-width="4480" height="225" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjuf89qismqqOLTVVdSTiiYUNJoDUdYumwie3EbXivS5LP2hiy0kfElObWrs5bUTx1saEF7p6plcMqS8myUw2eS22xcz-vC0X1ROOlA_b81JUo7YpjQd1rJ0SvcWgpiPT1mxVv0IBXen2NOTdBpEPT5s38AorkPpZkwhAcoNR02Sr83qqsFFvgvDYNv/w400-h225/Screenshot%202022-12-23%20at%2012.53.55%20PM.png" width="400" /></a></div><div style="text-align: justify;"><br /></div><span><div style="text-align: justify; white-space: pre-wrap;"><br /></div></span></div></span></div><div style="text-align: left;"><span id="docs-internal-guid-570044e3-7fff-4b41-4a60-3c41744e96d8" style="font-size: medium;"><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-align: justify;"><span style="font-family: "Times New Roman"; font-variant-east-asian: normal; font-variant-numeric: normal; vertical-align: baseline; white-space: pre-wrap;"><span>GNNs are constructed using a series of inferential techniques. One technique discussed at LoG is <a href="https://en.wikipedia.org/wiki/Message_passing">message passing</a> neural networks (MPNNs). Discrete forward passes from node to node (along edges) allow for approximation of the true, original network topology to be reconstructed. MPNN is a standard technique that lends itself to a wide variety of problem domains. The MPNN approach [4] can be extended to directed <a href="https://en.wikipedia.org/wiki/Multigraph">multigraphs</a> and other types of graphs that capture complex systems, but can suffer shortcomings such as over-smoothing, over-squashing and under-reaching. While message passing has been the standard in the GNN field, continuous methods using approaches inspired by differential geometry and algebraic topology might serve as powerful alternatives [5]. </span></span><span style="color: black; font-variant-east-asian: normal; font-variant-numeric: normal; vertical-align: baseline; white-space: pre-wrap;"><span style="font-family: times;">Aside from approximations of real-world networks and graph-like structures, we can also think of GNN outputs in terms of time (capturing delays) and space (capturing translations). </span></span><span style="font-family: times; white-space: pre-wrap;">GNNs are also well-suited to mapping problems from algorithmic domains, in particular dynamic programming [6].</span></p></span></div><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-align: justify;"><span style="background-color: transparent; color: black; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span style="font-family: times; font-size: medium;"><br /></span></span></p><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-align: justify;"><span style="background-color: transparent; color: black; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span style="font-family: times; font-size: medium;">GNNs are particularly useful for task-specific architectures. The <a href="https://devoworm.weebly.com/">DevoWorm</a> group’s <a href="https://github.com/DevoLearn/DevoGraph">D-GNN work (DevoGraph)</a> is an example of this, being specialized for embryogenetic image processing or capturing biological growth and differentiation processes. But GNNs can also engage in transfer learning, which is the transfer of learned information from one context to another. Successful graph transfer learning is characterized by the reproduction of a graph of a similar but different size, or problems that require changes in network size over time.</span></span></p><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-align: justify;"><span style="font-size: medium;"><br /></span></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiL_CCN5O5PphG2WcRVAoomaOFFwRB7ntpfZHGJg4VNNwgy97FwSxhynWI7PSLBv-ZVypVyswoWV0okcZdlEgMjvz2edkqIX0BDnBWIslKtx6n3VeeSSXz_BnO2A_5ShVCeDPS1_tenj47Uc7ngwFXtAlCV7g__hzBg3v0fTdNQL6QP11Ll3LDIvDBM/s1400/1_CWUg-DZBQNONJXuxQdLrFQ.png" style="margin-left: 1em; margin-right: 1em;"><span style="font-size: medium;"><img border="0" data-original-height="597" data-original-width="1400" height="170" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiL_CCN5O5PphG2WcRVAoomaOFFwRB7ntpfZHGJg4VNNwgy97FwSxhynWI7PSLBv-ZVypVyswoWV0okcZdlEgMjvz2edkqIX0BDnBWIslKtx6n3VeeSSXz_BnO2A_5ShVCeDPS1_tenj47Uc7ngwFXtAlCV7g__hzBg3v0fTdNQL6QP11Ll3LDIvDBM/w400-h170/1_CWUg-DZBQNONJXuxQdLrFQ.png" width="400" /></span></a></div><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-align: justify;"><span style="font-size: medium;">From "<a href="https://towardsdatascience.com/do-we-need-deep-graph-neural-networks-be62d3ec5c59">Do we need deep graph neural networks?</a>" by Michael Bronstein, <i>Towards Data Science</i>, July 20, 2020.</span></p><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-align: justify;"><span style="background-color: transparent; color: black; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span style="font-family: times; font-size: medium;"><br /></span></span></p><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-align: justify;"><span style="background-color: transparent; color: black; font-style: normal; font-variant: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><b><span style="font-family: times; font-size: medium;">Workshops</span></b></span></p><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-align: justify;"><span style="font-family: times;"><span style="font-size: medium; white-space: pre-wrap;">Several of the workshops were particularly interesting with respect to some of the points mentioned above. There were also a number of outstanding <a href="https://logconference.org/schedule-orals/">oral presentations</a> and <a href="https://logconference.org/schedule-posters/">posters</a> not discussed here, but are worth checking out in the <a href="https://www.youtube.com/@learningongraphs/streams">daily session recordings</a> or on <a href="https://openreview.net/group?id=logconference.io/LOG/2022/Conference">OpenReview</a>.</span></span></p><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-align: justify;"><span style="background-color: transparent; color: black; font-style: normal; font-variant: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><b><span style="font-family: times; font-size: medium;"><br /></span></b></span></p><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-align: justify;"><span style="font-family: times; font-size: medium;"><span style="background-color: transparent; color: black; font-style: normal; font-variant: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><b>Neural Algorithmic Reasoning</b> (<a href="https://www.youtube.com/watch?v=SKQ96tDZhgw">video</a>).</span><span style="background-color: transparent; color: black; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> GNNs serve as excellent processors (neural networks in latent space) that can be aligned with more traditional algorithms [7]. This recasts many optimization problems as neural representation learning, particularly in cases where optimization algorithms do not represent the system being analyzed in a realistic manner.</span></span></p><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-align: justify;"><span style="font-family: times;"><span style="background-color: transparent; color: black; font-size: medium; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br /></span></span></p><p style="text-align: center;"><span style="font-size: medium;"><b style="font-weight: normal;"></b></span></p><div class="separator" style="clear: both; text-align: center;"><b style="font-weight: normal;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgAFXdR6wlDJ3fPftFEMaTHPFydKUBg-EmgrVQ19r1l-5sGvYebboq7NXJvYTk26n33k-ooXB9LBsuPX80XUGQuOyflPMw5q8d8tf0ovRtYQnraMsx_TYiCavLYONuxALqMZgR_U9fXarwjz4HO2VUCZ7nmL7fZRR9VYdgmt9pW3VJfZ1ePmFl2N87u/s4480/Screenshot%202022-12-23%20at%201.01.04%20PM.png" style="margin-left: 1em; margin-right: 1em;"><span style="font-size: medium;"><img border="0" data-original-height="2520" data-original-width="4480" height="225" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgAFXdR6wlDJ3fPftFEMaTHPFydKUBg-EmgrVQ19r1l-5sGvYebboq7NXJvYTk26n33k-ooXB9LBsuPX80XUGQuOyflPMw5q8d8tf0ovRtYQnraMsx_TYiCavLYONuxALqMZgR_U9fXarwjz4HO2VUCZ7nmL7fZRR9VYdgmt9pW3VJfZ1ePmFl2N87u/w400-h225/Screenshot%202022-12-23%20at%201.01.04%20PM.png" width="400" /></span></a></b></div><b style="font-weight: normal;"><span style="font-family: times; font-weight: 700; text-align: justify; white-space: pre-wrap;"><div style="text-align: left;"><span style="font-weight: normal; text-align: center;"><span style="font-size: medium; font-weight: 700; text-align: justify;"><br /></span></span></div></span></b><p></p><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-align: justify;"><span style="font-family: times; font-size: medium;"><span style="color: black; font-variant-east-asian: normal; font-variant-numeric: normal; vertical-align: baseline; white-space: pre-wrap;"><b>Expressive GNNs</b></span><span style="color: black; font-variant-east-asian: normal; font-variant-numeric: normal; vertical-align: baseline; white-space: pre-wrap;"> (<a href="https://www.youtube.com/watch?v=ASQYjbUBYzs">video</a>). This tutorial covers a range of techniques that can be used to increase the expressivity of GNNs. Borrowing from areas such as topological data analysis and group theory, there is great potential for a variety of highly effective strategies for improving GNN architectures for a host of problems.</span></span></p><div><span style="font-size: medium; text-align: center;"><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-align: justify;"><span style="font-family: times;"><span style="color: black; font-variant-east-asian: normal; font-variant-numeric: normal; vertical-align: baseline; white-space: pre-wrap;"><br /></span></span></p><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-align: justify;"><span style="font-family: times;"><span style="color: black; font-variant-east-asian: normal; font-variant-numeric: normal; vertical-align: baseline; white-space: pre-wrap;"><b>Graph Rewiring</b></span><span style="color: black; font-variant-east-asian: normal; font-variant-numeric: normal; vertical-align: baseline; white-space: pre-wrap;"> (<a href="https://www.youtube.com/watch?v=AumdG5bazhg">video</a>, <a href="https://ellisalicante.org/tutorials/GraphRewiring">web</a>). Graph rewiring is presented as a way to overcome the limitations of the MPNN approach. Rewiring is based on the reconstruction of graph edges from iterative adaptive sampling of the input data. There are a number of different techniques that allow us to evaluate edge relevance using techniques such as diffusion and spectral approaches.</span></span></p><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-align: justify;"><span style="font-family: times;"><span style="color: black; font-variant-east-asian: normal; font-variant-numeric: normal; vertical-align: baseline; white-space: pre-wrap;"><br /></span></span></p><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-align: justify;"><span style="font-family: times;"><span style="color: black; font-variant-east-asian: normal; font-variant-numeric: normal; vertical-align: baseline; white-space: pre-wrap;"><b>GNNs on TensorFlow</b></span><span style="color: black; font-variant-east-asian: normal; font-variant-numeric: normal; vertical-align: baseline; white-space: pre-wrap;"> (<a href="https://www.youtube.com/watch?v=JqWROPYeqjA">video</a>). This tutorial introduces nascent modelers to implementing their own GNN models in the open-source <a href="https://github.com/tensorflow/gnn">TF-GNN</a> framework. The tutorial uses heterogeneous input data to show how to implement the GNN and deal with missing label and edge information. </span></span></p><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-align: justify;"><span style="font-family: times;"><span style="color: black; font-variant-east-asian: normal; font-variant-numeric: normal; vertical-align: baseline; white-space: pre-wrap;"><br /></span></span></p></span></div><p style="text-align: center;"><b style="font-weight: normal;"><span style="font-family: times; font-size: medium; font-weight: 700; text-align: justify; white-space: pre-wrap;"></span></b></p><div style="text-align: left;"><b style="font-weight: normal;"><span style="font-weight: normal; text-align: center;"><span style="font-size: medium; font-weight: 700; text-align: justify;">References</span></span></b></div><p></p><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-align: justify;"><span style="font-size: medium;"><span style="font-family: times;"><span style="background-color: transparent; color: black; font-style: normal; font-variant: normal; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span>[1] </span></span><span class="s1" style="-webkit-text-stroke-color: rgb(0, 0, 0); font-kerning: none; text-align: left;">Sanchez-Lengeling, B., Reif, E., Pearce, A., and Wiltschko</span><span class="s2" style="-webkit-text-stroke-color: rgba(0, 0, 0, 0.8); font-kerning: none; text-align: left;">, A.B. (2021). </span></span><span style="font-family: times;"><span style="-webkit-text-stroke-color: rgb(0, 0, 0); text-align: left;"><a href="https://distill.pub/2021/gnn-intro/">A Gentle Introduction to Graph Neural Networks</a>. </span><span style="-webkit-text-stroke-color: rgba(0, 0, 0, 0.8); text-align: left;"><i>Distill</i>, doi:</span></span><span style="font-family: times;">10.23915/distill.00033.</span></span></p><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-align: justify;"><span style="background-color: transparent; color: black; font-style: normal; font-variant: normal; font-weight: 700; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span style="font-family: times; font-size: medium;"><br /></span></span></p><p dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-align: justify;"><span style="font-family: times; font-size: medium;"><span style="background-color: transparent; color: black; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">[2] Chen, Z., Villar, S., Chen, L., and Bruna, J. (2019). <a href="https://papers.nips.cc/paper/2019/hash/71ee911dd06428a96c143a0b135041a4-Abstract.html">On the equivalence between graph isomorphism testing and function approximation with GNNs</a>. </span><span style="background-color: transparent; color: black; font-style: italic; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Proceedings of Neural Information Processing Systems</span><span style="background-color: transparent; color: black; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">, 32</span><span style="background-color: transparent; color: black; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">.</span></span></p><p style="text-align: left;"><span style="font-family: times; font-size: medium;"><b style="font-weight: normal;"><span style="text-align: justify; white-space: pre-wrap;">[3] Ruiz, L., Chamon, L.F.O., and Ribeiro, A. (2020). </span><a href="https://arxiv.org/abs/2006.03548" style="text-align: justify; white-space: pre-wrap;">Graphon Neural Networks and the Transferability of Graph Neural Networks</a><span style="text-align: justify; white-space: pre-wrap;">. <i>arXiv</i>, 2006.03548.</span></b></span></p><p style="text-align: justify;"><span style="font-size: medium;">[4] Heydari, S. and Livi, L. (2022). <a href="https://arxiv.org/abs/2203.16995v2">Message Passing Neural Networks for Hypergraphs</a>. <i>arXiv</i>, 2203. 16995.</span></p><p style="text-align: justify;"><span style="font-size: medium;"><span>[5] </span><span><span class="s1" style="-webkit-text-stroke-color: rgb(0, 0, 0);">Bronstein, M. (2022). </span><span class="s2" style="-webkit-text-stroke-color: rgb(26, 26, 26); color: #1a1a1a; font-kerning: none;"><a href="https://thegradient.pub/graph-neural-networks-beyond-message-passing-and-weisfeiler-lehman/">Beyond Message Passing: a Physics-Inspired Paradigm for Graph Neural Networks</a>. <i>The Gradient</i>, May 7.</span></span></span></p><p style="text-align: justify;"><span style="font-size: medium;"><span style="font-family: times;">[6] </span><span style="font-family: times;">Dudzik, A. and Velickovic, P. (2022). </span><a href="https://arxiv.org/abs/2203.15544" style="font-family: times;">Graph Neural Networks are Dynamic Programmers</a><span style="font-family: times;">. </span><i style="font-family: times;">arXiv</i><span style="font-family: times;">, 2203.15544.</span></span></p><p style="text-align: justify;"><span style="font-size: medium;">[7] Velickovic, P. and Blundell, C. (2021). <a href="https://arxiv.org/abs/2105.02761">Neural Algorithmic Reasoning</a>. <i>arXiv</i>, 2105.02761.</span></p>Bradly Aliceahttp://www.blogger.com/profile/06482487682656113637noreply@blogger.com1tag:blogger.com,1999:blog-1792896637814721350.post-16942099021351302222022-10-24T16:34:00.000-05:002022-10-24T16:34:16.532-05:00OAWeek 2022: Managing Virtual and Hybrid Meetings<p></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjyV96m4D1AuaOBGepQsknN5n0lgR8nxWjf1Yd1o1u2W0Yo9LP4WOyK1dEUWLEGVtu83aL_gNeuoN3kRsightaNLfYyBurf9E7VArqS026Y8EOkzJnUO7lZsHJggn3LLrCr5zB7zmdRCVasnCpo6fzA-BTO8kZ-KNAZPSlVrxU2auPqluonlnc-wMqw/s944/oa_week_2022.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="251" data-original-width="944" height="106" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjyV96m4D1AuaOBGepQsknN5n0lgR8nxWjf1Yd1o1u2W0Yo9LP4WOyK1dEUWLEGVtu83aL_gNeuoN3kRsightaNLfYyBurf9E7VArqS026Y8EOkzJnUO7lZsHJggn3LLrCr5zB7zmdRCVasnCpo6fzA-BTO8kZ-KNAZPSlVrxU2auPqluonlnc-wMqw/w400-h106/oa_week_2022.png" width="400" /></a></div><div class="separator" style="clear: both; text-align: center;"><br /></div><div class="separator" style="clear: both; text-align: left;">Welcome to International Open Access Week, 2022 edition! Last year, we discussed the <a href="https://syntheticdaisies.blogspot.com/2021/10/opening-access-virtual-distributed-lab.html">vision of a distributed research organization</a>. This year, we will explore this theme a bit further. One aspect of distributed organizations is the need to work both synchronously and asynchronously. This brings the real-world experience closer to the collaborator without the travel, carbon emissions, or expense of being at a centralized institute. As our collaborators live in many time zones and have different lifestyles, it is important to capture their full attention in different ways. </div><p></p><p>One way this is done is through the live attendance and replay of group meetings. The <a href="https://orthogonal-research.weebly.com/">Orthogonal Research and Education Lab</a> (OREL) offers a number of regular topical meetings, in addition to a general meeting on Saturdays, that engages collaborators from all over the world using a number of different pedagogical and technological techniques. </p><p><br /></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi7s1vgnL535yOE6v93w63uOhLC2pKf2LsaWFlXQgXLIzKISnw70cBLoSQsL2-bk1m3uUOUXKEipIP1qxThDbLEHWuCct9XnL2jbXBupgrV8sHAlaQ8SXSozLpYOF7PjRK9BgcPeGURGvKpmeIsJjHaFNYnRmrYwPdLLyaH65eebRiFyXadsFNqQh-f/s1919/11%20(1).png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="981" data-original-width="1919" height="205" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi7s1vgnL535yOE6v93w63uOhLC2pKf2LsaWFlXQgXLIzKISnw70cBLoSQsL2-bk1m3uUOUXKEipIP1qxThDbLEHWuCct9XnL2jbXBupgrV8sHAlaQ8SXSozLpYOF7PjRK9BgcPeGURGvKpmeIsJjHaFNYnRmrYwPdLLyaH65eebRiFyXadsFNqQh-f/w400-h205/11%20(1).png" width="400" /></a></div><div style="text-align: center;">An example of a virtual distributed meeting with collaborators dropping in from different parts of the globe.</div><div style="text-align: center;"><br /></div><div style="text-align: left;">An open meeting has a number of moving parts that need to be thoughtfully considered to ensure success. The first of these is choosing a meeting platform. OREL has found success with <a href="https://jitsi.org/">Jitsi</a>, as it is lightweight and free to use (open source). While Jitsi can be used as a service, installing it on your own server opens up its many customizable features. Jitsi even works with Virtual Reality, with interactions between the 2-D meeting world and immersive 3-D being available in the <a href="https://wolvic.com/en/">Wolvic</a> browser and <a href="https://www.meta.com/quest/">Meta Quest </a>casting option.</div><div style="text-align: left;"><br /></div><div style="text-align: left;"><br /></div><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhcw79ZVG0pvu-4rPb1_6_ZFTWdr0LgcA5bNDY0p0kXv59xdzBb31VkPo3jKcVdFJQqQxZ9J68FiuL-EkUCU_KIrfFGTpV4c2SJqWQbDOE1Aa0IFIox-gkSosWj2IqOKUeEPlP4ufPyVexXr0XK2UnFe9kagPCn3cKeGa5fx3IBRH7YgU0oC4MiZcSM/s1284/test-1.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="720" data-original-width="1284" height="179" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhcw79ZVG0pvu-4rPb1_6_ZFTWdr0LgcA5bNDY0p0kXv59xdzBb31VkPo3jKcVdFJQqQxZ9J68FiuL-EkUCU_KIrfFGTpV4c2SJqWQbDOE1Aa0IFIox-gkSosWj2IqOKUeEPlP4ufPyVexXr0XK2UnFe9kagPCn3cKeGa5fx3IBRH7YgU0oC4MiZcSM/s320/test-1.png" width="320" /></a></div><br /><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhldLS_8_nTEKtkkeilu2hrxjq3XdTdNst5QNVOL7snv_FHw58GaTysmMJplGR9eUBWYnbYU63qEhYP3IbJ77r55VU-9iOKKOQl6Kd2-kXcuhciIRQmy2Bpy-quKSkVlJBlW4tkdOCY2RKXobdIxHLvfQQv69tiZ5W8ipH_CtuIrUYl3T6_l5g9wdNU/s1284/test-2.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="722" data-original-width="1284" height="180" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhldLS_8_nTEKtkkeilu2hrxjq3XdTdNst5QNVOL7snv_FHw58GaTysmMJplGR9eUBWYnbYU63qEhYP3IbJ77r55VU-9iOKKOQl6Kd2-kXcuhciIRQmy2Bpy-quKSkVlJBlW4tkdOCY2RKXobdIxHLvfQQv69tiZ5W8ipH_CtuIrUYl3T6_l5g9wdNU/s320/test-2.png" width="320" /></a></div><br /><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjEV0vRgCqi24Q5fIPbajqn3fQE3FVbAPwONJhaoN_spG7JJfwpNkggCFwh0eDSROR9bPTRww-ZsQT-HbVVyjVxgT8oSeXnBQVN_RlKc09_l1fYgO7DewTXBxRbHCXXLArtXNhxBsyGcBLsvE4a6vYp0lyZV7UuvQTjA6aldEci_wOw98AwzKxw7BoM/s1287/test-3.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="726" data-original-width="1287" height="181" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjEV0vRgCqi24Q5fIPbajqn3fQE3FVbAPwONJhaoN_spG7JJfwpNkggCFwh0eDSROR9bPTRww-ZsQT-HbVVyjVxgT8oSeXnBQVN_RlKc09_l1fYgO7DewTXBxRbHCXXLArtXNhxBsyGcBLsvE4a6vYp0lyZV7UuvQTjA6aldEci_wOw98AwzKxw7BoM/s320/test-3.png" width="320" /></a></div><br /><div style="text-align: center;">Sample scenes from screensharing within Meta Quest and the casting option.</div><div style="text-align: left;"><br /></div><div style="text-align: left;">Secondly, programming the meeting is a non-trivial detail that can make the most of your time. For our <a href="https://www.youtube.com/playlist?list=PL4RJ4xCetB63f4DkdrrysVZr5LlVzmfF8">Saturday Morning NeuroSim</a> meetings, we have settled on the following format: updates, light features, discussion, open collaboration, and finally, papers of the week. Agenda-setting should be flexible with respect to your attendee's availability. Not everyone can make an entire meeting, so allowing them to "drop into" participation is encouraged. </div><div style="text-align: left;"><br /></div><div style="text-align: left;">Notetaking and live feeds are also good for augmenting our meetings. The OREL Lab Manager (Jesse Parent) We use notetaking tools such as Obsidian and Notion with allied feeds (Slack and Discord) for coordinating the various fragments of ideas and themes that emerge during meeting time. Feed technology is also good for sharing papers, and the vision of a stream feed is key to realizing the multimedia aspect of real-time meeting immersion, even when attendees are asynchronous. </div><div style="text-align: left;"><br /></div><div style="text-align: left;"><br /></div><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhtRTlbMEtuEuK7Gz4chkdELIpO7zq_PqEnVq7Y517BDu7Xt7HyIO4vxo2wUmC8KVPEA81-SMD-PNMAwnPE6K_5l0cdpHMIG6bjP2wyutteJYLVQ10qzMr369hrCpwA7hculsbKqbUM5FAS7p5rhlLNRYqSddBhx1qTILvgpm4yxR1NmQrAVABla3BI/s1920/ex-1.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="1080" data-original-width="1920" height="180" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhtRTlbMEtuEuK7Gz4chkdELIpO7zq_PqEnVq7Y517BDu7Xt7HyIO4vxo2wUmC8KVPEA81-SMD-PNMAwnPE6K_5l0cdpHMIG6bjP2wyutteJYLVQ10qzMr369hrCpwA7hculsbKqbUM5FAS7p5rhlLNRYqSddBhx1qTILvgpm4yxR1NmQrAVABla3BI/s320/ex-1.png" width="320" /></a></div><br /><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhAIx8zRiwYaQqTDygdkWOV0T4NY6EsyZb4bXp0eojQsDj5GBrTNmNNBkC7ceRRsP1PfwjRUW2AFbdEqA2b1bzUIiRqBFFypACpc36vWPSOVZrRhqcz0n-0HGTuH9zQL7tvryWh4-rIlXJV2B2oM36uNYrxGPDhXRddtdTIW9IGw2SaN59EzfkO-NRe/s1920/ex-2.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="1080" data-original-width="1920" height="180" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhAIx8zRiwYaQqTDygdkWOV0T4NY6EsyZb4bXp0eojQsDj5GBrTNmNNBkC7ceRRsP1PfwjRUW2AFbdEqA2b1bzUIiRqBFFypACpc36vWPSOVZrRhqcz0n-0HGTuH9zQL7tvryWh4-rIlXJV2B2oM36uNYrxGPDhXRddtdTIW9IGw2SaN59EzfkO-NRe/s320/ex-2.png" width="320" /></a></div><div style="text-align: center;">Different types of notetaking and stream feeding within a meeting (from the <a href="https://forms.gle/Y7S14E95pjEvtS4w9">Cognition Futures Reading Group</a>).</div><p>As a tool for participatory engagement, this can be done in a number of different ways. Lead by <a href="https://www.danielarifriedman.com/#/">Daniel Ari Friedman</a> and <a href="https://www.bleuknight.com/">Bleu Knight</a>, the <a href="https://www.activeinference.org/">Active Inference Institute</a> has taken the route of invited livestreams and summary podcasts. These materials introduce collaborators to difficult academic concepts while making them more accessible. While YouTube has options for live streaming, it is not always the best option. I use <a href="https://obsproject.com/">OBS Studio</a> (free and open source) to compose a desktop recording and edit before making it public. </p><p>Recorded meetings are also good for coding demos, particularly when they do not go as planned. One can either prepare a recording in advance to include in the meeting recording or strip the demo down to a minimal approach using a <a href="https://colab.research.google.com/?authuser=1">CoLab notebook</a>. This reduces the friction of failed screenshares and execution errors, while also easing the burden of performing in front of a group.</p><p><br /></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhOpxupyGq5ze-9us4UqaBZCrv7z2pOa0oEhc1pdBwsEwqoirPkMV5DShYyZlAVqPKwuGBbx4MKQD8MTolCubtPAAzG9Uy0_uO3wXPrUpaiOXk6fikAAccoJOcb_oFXb8sVgxZF4LLXlrQoQTy1hVmYlT9_kCr5Km8NUkkXeBlBRHPaD-zRn6BY04yU/s4480/Screen%20Shot%202022-10-21%20at%202.12.51%20PM.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="2520" data-original-width="4480" height="222" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhOpxupyGq5ze-9us4UqaBZCrv7z2pOa0oEhc1pdBwsEwqoirPkMV5DShYyZlAVqPKwuGBbx4MKQD8MTolCubtPAAzG9Uy0_uO3wXPrUpaiOXk6fikAAccoJOcb_oFXb8sVgxZF4LLXlrQoQTy1hVmYlT9_kCr5Km8NUkkXeBlBRHPaD-zRn6BY04yU/w395-h222/Screen%20Shot%202022-10-21%20at%202.12.51%20PM.png" width="395" /></a></div><br /><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhKsiaCj52ymwD1XWrfbGdWo0GRYyG1N4dIemKsGNjiMfkuGeeg9mTHK5pYD_qv8RHE21Fve-xeP-Y5jRIgffA1ZkoirSytn4YlFD25Wgv_htAL7v9LYI0qTvwaKjpd7l0qCEKCYRzmjGYe5IiG6GMjLzgc_guzbLSvuSBySOe-QAkZf19p8-75jU5Q/s4480/Screen%20Shot%202022-10-21%20at%202.13.32%20PM.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="2520" data-original-width="4480" height="221" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhKsiaCj52ymwD1XWrfbGdWo0GRYyG1N4dIemKsGNjiMfkuGeeg9mTHK5pYD_qv8RHE21Fve-xeP-Y5jRIgffA1ZkoirSytn4YlFD25Wgv_htAL7v9LYI0qTvwaKjpd7l0qCEKCYRzmjGYe5IiG6GMjLzgc_guzbLSvuSBySOe-QAkZf19p8-75jU5Q/w395-h221/Screen%20Shot%202022-10-21%20at%202.13.32%20PM.png" width="395" /></a></div><p style="text-align: center;">Coding demos from a recent Saturday Morning NeuroSim meeting.</p><p>But completely virtual experiences are not the only option for bringing people together from around the world. OREL has been experimenting with hybrid meetings. This type of meeting brings the ethos of virtual meetings to more traditional in-person meetings. This enables more inclusive participation from distant geographical points. Last Spring, we experimented with our own virtual meeting experience at the <a href="https://nycwic.org/">New York Celebration of Women in Computing (NYCWiC)</a>, hosted live at Fort William Henry, NY. The hybrid session "<a href="https://youtu.be/tncQLZKGJ5s">Frontiers in Data Privacy and Tech Ethics</a>" featured a buffet of topics on AI and technology ethics. Soem of the participants were live, while others were virtual (recorded or located in different parts of the globe). For this type of meeting, experimenting with ways to optimize live/virtual synchronization and media capture quality are essential. We plan to experiment with this more in the near future. </p><p><br /></p><p></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgMUUsUwaQzS5VI2fUpH9swZIHikTmJl_s5pmoHE5RK_I1VIfHQBw_jJEh_7wRXx_U-GG1dE7KBLCO1isOXKUqef2hPj3VaLDIUdYou2leQWGTKdYfg_OEWT5wYqEWu6T6g9qVUksvGcXo3YoGkZrDmfBRbIZgNMZVU-rtdMan38vHow3il8cTkRZbT/s1912/data-privacy.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="962" data-original-width="1912" height="201" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgMUUsUwaQzS5VI2fUpH9swZIHikTmJl_s5pmoHE5RK_I1VIfHQBw_jJEh_7wRXx_U-GG1dE7KBLCO1isOXKUqef2hPj3VaLDIUdYou2leQWGTKdYfg_OEWT5wYqEWu6T6g9qVUksvGcXo3YoGkZrDmfBRbIZgNMZVU-rtdMan38vHow3il8cTkRZbT/w400-h201/data-privacy.png" width="400" /></a></div><br /><p></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg2AIIIFPFLn0f9v9bKIxI-DFn53x7s022fTHEdFkxWTURMkZuZocT625_p7vXd67EK8WQFkaQMP-91dhGevixaDCWPYTNPE2zImmcOS03Qa8Qaq3zQheMae_zT2h8gTaDdMW1qCYd1X5sYrT3ZZv271Z42VwqmWaB_AoYUpppjh1d2mEoBu9XE_9YY/s6240/IMG_7728.JPG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="6240" data-original-width="4160" height="400" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg2AIIIFPFLn0f9v9bKIxI-DFn53x7s022fTHEdFkxWTURMkZuZocT625_p7vXd67EK8WQFkaQMP-91dhGevixaDCWPYTNPE2zImmcOS03Qa8Qaq3zQheMae_zT2h8gTaDdMW1qCYd1X5sYrT3ZZv271Z42VwqmWaB_AoYUpppjh1d2mEoBu9XE_9YY/w266-h400/IMG_7728.JPG" width="266" /></a></div><div style="text-align: center;">Virtual (top) and in-person (bottom) components of the session.</div>Bradly Aliceahttp://www.blogger.com/profile/06482487682656113637noreply@blogger.com1tag:blogger.com,1999:blog-1792896637814721350.post-7368990391618795292022-08-09T21:24:00.001-05:002022-08-09T21:24:07.269-05:00New Paper on Developmental Braitenberg Vehicles now live!<p style="text-align: center;"> <a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh3EJkX7FX9mensDZ7b4KTQT7B6P052jWOveElLelZJQblzjBUMZPWS3CnvTNfqvhJklsYYMbXTFIZInguGFhqV4tzz1QPeHDnSFXQtvOiFY3CzmiOPa2lS3unkEP2c_YabuCXzMeyDOW7TTXxT6hSbv6TTMa6QhPtwVWntFAwvWkAqVDLfykN2JRmZ/s992/tweet.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="992" data-original-width="903" height="400" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh3EJkX7FX9mensDZ7b4KTQT7B6P052jWOveElLelZJQblzjBUMZPWS3CnvTNfqvhJklsYYMbXTFIZInguGFhqV4tzz1QPeHDnSFXQtvOiFY3CzmiOPa2lS3unkEP2c_YabuCXzMeyDOW7TTXxT6hSbv6TTMa6QhPtwVWntFAwvWkAqVDLfykN2JRmZ/w364-h400/tweet.png" width="364" /></a></p><p>The <a href="https://direct.mit.edu/artl/issue/28/3">special issue of <i>Artificial Life</i> on Embodied Intelligence</a> is now live! Inside you will find our paper "<a href="https://direct.mit.edu/artl/article-abstract/28/3/369/112444/Braitenberg-Vehicles-as-Developmental?redirectedFrom=fulltext">Braitenberg Vehicles as Developmental Neurosimulation</a>", which has lived on the <i>arXiv</i> since 2020. This paper lays out an approach to Developmental Neurosimulation, involving three adversarial approaches to the agent-based development of embodied brains and embodied cognition. Here is the abstract:</p><blockquote style="border: none; margin: 0 0 0 40px; padding: 0px;"><p style="text-align: justify;">Connecting brain and behavior is a longstanding issue in the areas of behavioral science, artificial intelligence, and neurobiology. As is standard among models of artificial and biological neural networks, an analogue of the fully mature brain is presented as a blank slate. However, this does not consider the realities of biological development and developmental learning. Our purpose is to model the development of an artificial organism that exhibits complex behaviors. We introduce three alternate approaches to demonstrate how developmental embodied agents can be implemented. The resulting developmental Braitenberg vehicles (dBVs) will generate behaviors ranging from stimulus responses to group behavior that resembles collective motion. We will situate this work in the domain of artificial brain networks along with broader themes such as embodied cognition, feedback, and emergence. Our perspective is exemplified by three software instantiations that demonstrate how a BV-genetic algorithm hybrid model, a multisensory Hebbian learning model, and multi-agent approaches can be used to approach BV development. We introduce use cases such as optimized spatial cognition (vehicle-genetic algorithm hybrid model), hinges connecting behavioral and neural models (multisensory Hebbian learning model), and cumulative classification (multi-agent approaches). In conclusion, we consider future applications of the developmental neurosimulation approach.</p></blockquote><p>There are many themes to follow up on in this paper. Just of few examples include:</p><blockquote style="border: none; margin: 0px 0px 0px 40px; padding: 0px; text-align: left;"><p>* brain/body scaling in an embodied agent.</p><p>* the role of multisensory integration in the development of cognition.</p><p>* ways to classify shapes and motifs in the emergence of multi-agent collectives. </p></blockquote><blockquote style="border: none; margin: 0 0 0 40px; padding: 0px;"><p style="text-align: left;">* spatial cognition and transfer learning in developmental embodied systems.</p></blockquote><p>Congratulations to Stefan Dvoretskii, Ziyi Gong, Ankit Gupta, Jesse Parent, and Bradly Alicea for their hard work.</p>Bradly Aliceahttp://www.blogger.com/profile/06482487682656113637noreply@blogger.com1tag:blogger.com,1999:blog-1792896637814721350.post-33146388729073193792022-06-15T00:47:00.005-05:002022-10-19T00:30:39.192-05:00Google Summer of Code 2022 in the OpenWorm Community (DevoWorm)<div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgjwFZTC2F-CChOitsBm60l_v1EfWll4tMznDyypeaq74WKTguxCkAWyutJ9hOmK9hCHmzrmP4Ll2hVQZvq_pN__d-7-4pZHweWEv34rjoieAGFtBR2VLuoEx19CPddW3IuIPgCmINADwyfA6UV-Mip9WLD7XYxSqvuUA_wXyIzFar4CIY07NChMb0C/s192/GSoC-icon-192.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="192" data-original-width="192" height="192" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgjwFZTC2F-CChOitsBm60l_v1EfWll4tMznDyypeaq74WKTguxCkAWyutJ9hOmK9hCHmzrmP4Ll2hVQZvq_pN__d-7-4pZHweWEv34rjoieAGFtBR2VLuoEx19CPddW3IuIPgCmINADwyfA6UV-Mip9WLD7XYxSqvuUA_wXyIzFar4CIY07NChMb0C/s1600/GSoC-icon-192.png" width="192" /></a></div><div class="separator" style="clear: both; text-align: center;"><br /></div><div class="separator" style="clear: both; text-align: left;"><br /></div><div class="separator" style="clear: both; text-align: left;"><span style="font-family: times;">W<span>elcome to Google Summer of Code 2022! I am pleased to announce that this year, we have two funded projects: D-GNNs and Digital Microspheres! These projects will both take place in conjunction with the DevoWorm part of the OpenWorm community. </span><span style="background-color: white; color: #24292f;"><a href="https://devoworm.weebly.com/">DevoWorm</a> is an interdisciplinary group engaged in both computational and biological data analysis. We have </span><a href="https://meet.jit.si/DevoWorm" style="background-color: white;">weekly meetings on Jit.si</a><span style="background-color: white; color: #24292f;">, and are a part of the </span><a href="https://openworm.org" style="background-color: white;">OpenWorm Foundation</a><span style="background-color: white; color: #24292f;">. </span></span></div><p><span style="font-family: times;">This year, we were able to fund two students per project. They will be working on complementary solutions to each problem, and we will see how far they get by the end of the Summer. </span></p><p><span style="font-family: times;"><b>D-GNNs (Developmental Graph Neural Networks)</b></span></p><p><span style="font-family: times;">The description for this project is as follows:</span></p><blockquote style="border: none; margin: 0px 0px 0px 40px; padding: 0px;"><p style="background-color: white; box-sizing: border-box; color: #24292f; margin-bottom: 16px; margin-top: 0px; text-align: left;"><span style="font-family: times;">Biological development features many different types of networks: neural connectomes, gene regulatory networks, interactome networks, and anatomical networks. Using cell tracking and high-resolution microscopy, we can reconstruct the origins of these networks in the early </span><span style="font-family: times;">embryo. Building on our group's past work in deep learning and pre-trained models, we look to apply graph neural networks (GNNs) to developmental biological analysis.</span></p></blockquote><blockquote style="border: none; margin: 0px 0px 0px 40px; padding: 0px;"><p style="background-color: white; box-sizing: border-box; color: #24292f; margin-bottom: 16px; margin-top: 0px; text-align: left;"><span style="font-family: times;">The contributor will create graph embeddings that resemble actual biological networks found throughout development. Potential activities include growing graph embeddings using biological rules, differentiation of nodes in the network, and GNNs that generate different types of movement output based on movement seen in microscopy movies. The goal is to create a library of GNNs that can simulate developmental processes by analyzing time-series microscopy data.</span></p></blockquote><p dir="auto" style="background-color: white; box-sizing: border-box; color: #24292f; margin-bottom: 16px; margin-top: 0px;"><span style="font-family: times;">When completed, D-GNNs will become part of the <a href="https://devoworm.github.io/DevoWormAi/">DevoWorm AI</a> library. </span><span style="font-family: times;">Ultimately, we will be integrating the GNN work with the DevoLearn (open-source pre-trained deep learning) software. </span></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhupq99DK8UHCusm7zXMmQjfmIImIo8Jv1Z8fBCJmI1G4zc5WNsp30fCy3WRE-bdOAmBkz6FTyiq-XItvWhncD3vTzkL7rd4FFhA323GYH0bkqVMPX20E92wTFyZikngbW5MMG-sVUABUVkc20YNath3TAU5TnGaRMgd_NXrINEvT9XMNv8ocak9mv1/s345/jiahang.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="318" data-original-width="345" height="184" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhupq99DK8UHCusm7zXMmQjfmIImIo8Jv1Z8fBCJmI1G4zc5WNsp30fCy3WRE-bdOAmBkz6FTyiq-XItvWhncD3vTzkL7rd4FFhA323GYH0bkqVMPX20E92wTFyZikngbW5MMG-sVUABUVkc20YNath3TAU5TnGaRMgd_NXrINEvT9XMNv8ocak9mv1/w200-h184/jiahang.png" width="200" /></a></div><div class="separator" style="clear: both; text-align: center;"><br /></div><div class="separator" style="clear: both; text-align: center;">Jiahang Li</div><div class="separator" style="clear: both; text-align: center;"><br /></div><blockquote style="border: none; margin: 0px 0px 0px 40px; padding: 0px;"><div class="separator" style="clear: both; text-align: left;"><div class="separator" style="clear: both; text-align: left;"><span style="font-family: times;">Jiahang Li is a first year MPhil candidate in Computing Department at <a href="https://www.polyu.edu.hk/">Hong Kong Polytechnic University</a>. His research interests cover graph representation learning and its applications. Jiahang's approach to the project is to provide a pipeline that converts microscopic video data of <i>C. elegans</i> and other organisms into graph structures, on which advanced network analysis techniques and graph neural networks will be employed to obtain high-level representation of embryogenesis and to solve applied problems.</span></div></div></blockquote><div class="separator" style="clear: both; text-align: center;"><br /></div><div class="separator" style="clear: both; text-align: center;"><br /></div><div class="separator" style="clear: both; text-align: center;"><br /></div><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEit5v0EWr3qZQmlQNSytPLl0BMT__F1lvg6pzCVQEIps2ImXaWwiuTMVIxKuCE-Db1ZcAv419rglHRmqhP_Sn0Hzf_RBrLTsZ6GqHg3nWlOjQYZMPfqETBRt-DbWkJMYdwjF0CUjGWKE2cUgEycWoFwALbLAwR16bRIqtp3BoZog1eWrOe-0VEsK5_U/s578/wataru.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="422" data-original-width="578" height="158" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEit5v0EWr3qZQmlQNSytPLl0BMT__F1lvg6pzCVQEIps2ImXaWwiuTMVIxKuCE-Db1ZcAv419rglHRmqhP_Sn0Hzf_RBrLTsZ6GqHg3nWlOjQYZMPfqETBRt-DbWkJMYdwjF0CUjGWKE2cUgEycWoFwALbLAwR16bRIqtp3BoZog1eWrOe-0VEsK5_U/w217-h158/wataru.png" width="217" /></a></div><div class="separator" style="clear: both; text-align: center;"><br /></div><div class="separator" style="clear: both; text-align: center;">Wataru Kawakami</div><div><br /></div><blockquote style="border: none; margin: 0px 0px 0px 40px; padding: 0px;"><div style="text-align: left;"><span style="font-family: times;">Wataru is a student at <a href="https://www.kyoto-u.ac.jp/en">Kyoto University</a> with interests in Machine Learning (in particular Graph Neural Networks) and Neuroimaging.</span></div></blockquote><span style="font-family: times;"><br /></span><p><b><span style="font-family: times;">Digital Microspheres</span></b></p><p><span style="font-family: times;">The description for this problem is as follows: </span></p><blockquote style="border: none; margin: 0px 0px 0px 40px; padding: 0px;"><p style="background-color: white; box-sizing: border-box; color: #24292f; margin-bottom: 16px; margin-top: 0px; text-align: left;"><span style="font-family: times;">This project will build upon the specialized microscopy techniques to develop a shell composed of projected microscopy images, arranged to represent the full external surface of a sphere. This will allow us to create an atlas of the embryo’s outer surface, which in some species (e.g. Axolotl) enables us to have a novel perspective on neural development.</span></p></blockquote><blockquote style="border: none; margin: 0px 0px 0px 40px; padding: 0px;"><p style="background-color: white; box-sizing: border-box; color: #24292f; margin-bottom: 16px; margin-top: 0px; text-align: left;"><span style="font-family: times;">The contributor will build a computational tool that allows us to visualize 4D data derived from the surface of an Axolotl embryo. The spatial model and animation (4th dimension) of microscopy image data can be created in a 3-D modeling software of your choice.</span></p></blockquote><p dir="auto" style="background-color: white; box-sizing: border-box; color: #24292f; margin-bottom: 16px; margin-top: 0px;"><span style="font-family: times;">This project is based on previous research by DevoWorm contributors Richard Gordon and Susan Crawford-Young. The flipping and ball microscopy research involve the design and fabrication of specialized microscopes to image embryos in a 4-D context (3 dimensions of space plus time).</span></p><p dir="auto" style="background-color: white; box-sizing: border-box; color: #24292f; margin-bottom: 16px; margin-top: 0px;"><span style="font-family: times;"><span><b>Spherical Embryo Maps:</b> </span><span>Gordon, R. (2009). </span><a href="https://link.springer.com/article/10.1162/BIOT_a_00010">Google Embryo for Building Quantitative Understanding of an Embryo As It Builds Itself</a><span>. II. Progress Toward an Embryo Surface Microscope. </span><i>Biological Theory</i><span>, 4, 396–412.</span></span></p><p dir="auto" style="background-color: white; box-sizing: border-box; color: #24292f; margin-bottom: 16px; margin-top: 0px;"><span style="font-family: times;"><b>Flipping Microscopy:</b> Crawford-Young, S., Dittapongpitch, S., Gordon, R., and Harrington, K. (2018). <a href="https://www.sciencedirect.com/science/article/abs/pii/S0303264718302995">Acquisition and reconstruction of 4D surfaces of axolotl embryos with the flipping stage robotic microscope</a>. <i>Biosystems</i>, 173, 214-220.</span></p><p><span style="font-family: times;"><b>Ball Microscopy: </b>Crawford-Young, S.J. and Young Williment, J.L. (2021). <a href="https://www.sciencedirect.com/science/article/abs/pii/S0303264721001453">A ball microscope for viewing the entire surface of amphibian embryos</a>. <i>Biosystems</i>, 208, 104498.</span></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjuix_4PEn2YFMnCcpL-ueqgR_84lJ0EtUy5ndS1QWf6UaJJMqDlbEQDmcNemc3ExFGgiFaE2vqjQAzl8iDnSS2_6yjuLKnO3Ztx70NF20QwaJ7fVjJ5QJ-PqgY-2Oet6mlQZ4W3_TxklomdHNSu_5mzhq5i66E4W0AJ_srEowLRuEB4pVpUXOeqwj7/s366/karan.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="329" data-original-width="366" height="180" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjuix_4PEn2YFMnCcpL-ueqgR_84lJ0EtUy5ndS1QWf6UaJJMqDlbEQDmcNemc3ExFGgiFaE2vqjQAzl8iDnSS2_6yjuLKnO3Ztx70NF20QwaJ7fVjJ5QJ-PqgY-2Oet6mlQZ4W3_TxklomdHNSu_5mzhq5i66E4W0AJ_srEowLRuEB4pVpUXOeqwj7/w200-h180/karan.png" width="200" /></a></div><p style="text-align: center;"><span style="font-family: times;">Karan Lohaan</span></p><p style="text-align: left;"><span style="font-family: times;">Karan is a student<span> at <a data-cke-saved-href="https://www.amrita.edu/" href="https://www.amrita.edu/" style="background-color: white; font-weight: 600; opacity: 0.75; transition: opacity 300ms ease-in-out 0s;" target="_blank">Amrita Vishwa Vidyapeetham University</a>, and is a member of the AMFoss program there. He is interested in Machine Learning and Image Processing. </span></span></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhU5TbIvkJA1jgkXEljBQhnmVRT0zB3U6Wb1UANNXzhG2Ug_jy2BgNg00RY4BIQ6M-SgsAxjl0ZvrePey7D0MXMINsWpuMNsXcxiwVyl8yONKqJFr3NRAXAo30kaRk1ViuoCekMsLgNyku2rKU8Av0LyyMvjbOQFySySewfdP29ek1M3ol5knCqVTyy/s261/harikrishna.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="256" data-original-width="261" height="196" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhU5TbIvkJA1jgkXEljBQhnmVRT0zB3U6Wb1UANNXzhG2Ug_jy2BgNg00RY4BIQ6M-SgsAxjl0ZvrePey7D0MXMINsWpuMNsXcxiwVyl8yONKqJFr3NRAXAo30kaRk1ViuoCekMsLgNyku2rKU8Av0LyyMvjbOQFySySewfdP29ek1M3ol5knCqVTyy/w200-h196/harikrishna.png" width="200" /></a></div><p style="text-align: center;">Harikrishna Pillai</p><blockquote style="border: none; margin: 0px 0px 0px 40px; padding: 0px;"><p style="text-align: left;"><span style="font-family: times;">I am Harikrishna pursuing my B.Tech in Computer Science and Artificial Intelligence from </span><a data-cke-saved-href="https://www.amrita.edu/" href="https://www.amrita.edu/" style="background-color: white; font-family: times; font-weight: 600; opacity: 0.75; transition: opacity 300ms ease-in-out 0s;" target="_blank">Amrita Vishwa Vidyapeetham University</a><span style="font-family: times;">. I completed my schooling in Mumbai. I started with python as my first language and eventually developed interest for AI. Due to my interest in Android apps, I have done Android development in Kotlin. Also, I have been interested in open source for some time now and therefore, I wanted to start my open source journey with GSoC.</span></p></blockquote><p><span style="font-family: times;">We also have two GSoC mentors for these projects: Bradly Alicea is a mentor for D-GNNs and Digital Microspheres, and Jesse Parent is a mentor for D-GNNs. Richard Gordon and Susan Crawford-Young are serving as collaborators for the Digital Microspheres project.</span></p><p><span style="font-family: times;">If you would like to check on their progress, please check out our weekly meetings available on our <a href="https://www.youtube.com/channel/UChGTq41_rJwmZ1I4j7SezWQ">YouTube channel</a>.</span></p>Bradly Aliceahttp://www.blogger.com/profile/06482487682656113637noreply@blogger.com1tag:blogger.com,1999:blog-1792896637814721350.post-34660390232498422332022-03-31T23:13:00.002-05:002022-06-09T11:42:12.301-05:00Updates on Open Source Community Tools<div style="background-color: white; box-sizing: border-box; color: var(--il-blue); margin: 0px 0px 1.25rem; padding: 0px; text-align: center;"><b><span style="font-family: times;">All hail the Guidance (and Attribution) Tree!</span></b></div><p style="text-align: justify;"><span style="font-family: times;"><span face=""Source Sans Variable", "Source Sans", sans-serif" style="background-color: white; color: #252525;">The guidance tree is a concept that grew out of my days on the OpenWorm Community Committee. I have implemented a guidance tree for the Rokwire Community, and is available in Beta version for other communities to implement (HTML, Markdown) under a CC-BY license. Check out this </span><a href="https://www.youtube.com/watch?v=FGQ8VNcb7Nc" style="background-color: white; box-sizing: inherit; transition: color 0.3s ease 0s;">19-minute tour</a><span face=""Source Sans Variable", "Source Sans", sans-serif" style="background-color: white; color: #252525;"> of a guidance tree based on the Rokwire Community.</span></span></p><p style="text-align: center;"></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj3fMYmAOX06PrVS7o5FUHON1DSslHkcD_Cbx7DxEsUpc3VjNXcQe80bDXXUnzuZJh6o-iAuuVMFgUI69JneD1HjonqlfLr5zkzJ-iysXxeydQ5VHWYKUKiFokfQ6CG-u1ZYhIMBqK1csG7YI4oJDQ6pj-Rc5ldEKHR2uasp8UPqZPgUygX4bQUO04E/s318/cc-by.png" style="margin-left: 1em; margin-right: 1em;"><span style="font-family: times;"><img border="0" data-original-height="158" data-original-width="318" height="71" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj3fMYmAOX06PrVS7o5FUHON1DSslHkcD_Cbx7DxEsUpc3VjNXcQe80bDXXUnzuZJh6o-iAuuVMFgUI69JneD1HjonqlfLr5zkzJ-iysXxeydQ5VHWYKUKiFokfQ6CG-u1ZYhIMBqK1csG7YI4oJDQ6pj-Rc5ldEKHR2uasp8UPqZPgUygX4bQUO04E/w143-h71/cc-by.png" width="143" /></span></a></div><div class="separator" style="clear: both; text-align: center;"><span style="font-family: times;"><br /></span></div><div class="separator" style="clear: both; text-align: justify;"><span face=""Source Sans Variable", "Source Sans", sans-serif" style="background-color: white; color: #252525; font-family: times; text-align: left;">A guidance tree allows new community members to find a starting point in your community easily, while optimally leveraging their skills. This is something I am calling Community Wayfinding. Community managers who want to adopt the guidance tree have to analyze their own set of community resources (Github repositories, web resources, and documentation) to see where members might fit in. Adopting a guidance tree of your own also requires a definition of community roles, which will be unique to different communities. In the Beta version, a user encounters a set of binary choices that bifurcate towards a specific contribution path. Future versions might map this possibility space to a VR (virtual) world where the options are presented as 3-D objects or as activity rooms.</span></div><div style="text-align: justify;"><span style="font-family: times;"><br /></span></div><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjGL5igwlaGJkzcSgSwAXLypZ_yC34uh6cH2EMYcH8JHA3RBiLOC-TruJeih_NpYa3h49vBHJBI2_jJUSHJrIDooWHGDlyEviwAYZNXu2rCe5l9EXNDfC_IxYTVlcYFlJGUNGHvcAIpg82g8JO9C_HC5EJO9E7djRhvNx7pzJHPQsqwOURCg7mVa8h1/s960/guidance-tree-map.png" style="margin-left: 1em; margin-right: 1em;"><span style="font-family: times;"><img border="0" data-original-height="540" data-original-width="960" height="180" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjGL5igwlaGJkzcSgSwAXLypZ_yC34uh6cH2EMYcH8JHA3RBiLOC-TruJeih_NpYa3h49vBHJBI2_jJUSHJrIDooWHGDlyEviwAYZNXu2rCe5l9EXNDfC_IxYTVlcYFlJGUNGHvcAIpg82g8JO9C_HC5EJO9E7djRhvNx7pzJHPQsqwOURCg7mVa8h1/s320/guidance-tree-map.png" width="320" /></span></a></div><p style="text-align: justify;"><span style="font-family: times;"><span face=""Source Sans Variable", "Source Sans", sans-serif" style="background-color: white; color: #252525;">Would you be interested in a system for tracing attribution or authorship on an open-source (or open science) project? When the formal release version of guidance tree is released, it will be accompanied by the </span><a href="https://figshare.com/articles/journal_contribution/The_Authorship_Tree/4731913" style="background-color: white; box-sizing: inherit; transition: color 0.3s ease 0s;">Authorship Tree</a><span face=""Source Sans Variable", "Source Sans", sans-serif" style="background-color: white; color: #252525;">, an idea I worked on circa 2017 in the </span><a href="https://orthogonal-research.weebly.com/" style="background-color: white; box-sizing: inherit; transition: color 0.3s ease 0s;">Orthogonal Research and Education Lab</a><span face=""Source Sans Variable", "Source Sans", sans-serif" style="background-color: white; color: #252525;">. The Authorship (or attribution tree) solves the problem of authorship order by showing the relative contributions of each individual in the form of a tree structure. This not only allows for primary contributions to be visualized, but also for deeper contributions (informal conversations, data sources, stakeholders) to be recognized. This is particularly good for publicly recognizing different types of contributors and whose who have been active at various levels of contribution.</span></span></p><span style="background-color: white;"><div class="separator" style="clear: both; color: #252525; font-family: "Source Sans Variable", "Source Sans", sans-serif; font-size: 18px; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgX7nvWvV8iF7cyqf7-PNH110K9nobtVrX46a9uyHG2dw9Vq2JtzNGe7gZ1pTjWk1ZCClzeGM2qcQymR5WWsfbmRaVmT9e0gJ37HEQFwvx9pz9dxfBboyupqvoEkr_pIaXDdCxZM8eXnYBluPmFhQrTFkn7LlrPugZgR8jEywWidGBSs1SIYl_TlGNg/s1440/authorshiptree.pptx.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="1440" data-original-width="1440" height="320" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgX7nvWvV8iF7cyqf7-PNH110K9nobtVrX46a9uyHG2dw9Vq2JtzNGe7gZ1pTjWk1ZCClzeGM2qcQymR5WWsfbmRaVmT9e0gJ37HEQFwvx9pz9dxfBboyupqvoEkr_pIaXDdCxZM8eXnYBluPmFhQrTFkn7LlrPugZgR8jEywWidGBSs1SIYl_TlGNg/s320/authorshiptree.pptx.png" width="320" /></a></div><div style="box-sizing: border-box; color: var(--il-blue); font-family: "Source Sans Variable", "Source Sans", sans-serif; margin: 0px 0px 1.25rem; padding: 0px; text-align: center;"><b><span style="font-size: large;"><br /></span></b></div><div style="box-sizing: border-box; color: var(--il-blue); margin: 0px 0px 1.25rem; padding: 0px; text-align: center;"><b><span style="font-family: times;">Recombining your Technical Stack</span></b></div><div style="box-sizing: border-box; color: var(--il-blue); margin: 0px 0px 1.25rem; padding: 0px; text-align: justify;"><span style="font-family: times;"><span>During the month of March 2021, we considered how we might strive for a </span><a href="https://publish.illinois.edu/bradly-alicea/2021/03/05/defining-a-full-stack-community/" style="box-sizing: inherit; transition: color 0.3s ease 0s;">Full Stack community</a><span>. The basic idea was that depending on the task one wants to carry out, there exist a series of possible technologies to achieve your goals. The challenge is to pick the best set of tools, for all aspects of your open source project. These tools should be compatible with one another, easy to learn/use, and provide accessibility to future contributors. </span></span></div><div style="box-sizing: border-box; margin: 0px 0px 1.25rem; padding: 0px; text-align: center;"><div class="separator" style="clear: both; color: var(--il-blue); text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhgSBp8kPGxg0hMEVZZNRqZ-VBy0o6pP5_in4XgMOUlqzri2Fmkm6ps8Vu4HxtFTUpot_9Z4uukD_RlaHSqX2KUn9BTjIywUlmN3S09ZjRTOaZP8hQ3D-_joR3paBjtCAUF-BYisCVBedF3D0aTwQt0BVrC5QxkSM7liNrEeb-BS1kdxGp_3DRcMqWg/s1200/blog-featured-churn-analysis.jpeg" style="margin-left: 1em; margin-right: 1em;"><span style="font-family: times;"><img border="0" data-original-height="600" data-original-width="1200" height="160" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhgSBp8kPGxg0hMEVZZNRqZ-VBy0o6pP5_in4XgMOUlqzri2Fmkm6ps8Vu4HxtFTUpot_9Z4uukD_RlaHSqX2KUn9BTjIywUlmN3S09ZjRTOaZP8hQ3D-_joR3paBjtCAUF-BYisCVBedF3D0aTwQt0BVrC5QxkSM7liNrEeb-BS1kdxGp_3DRcMqWg/s320/blog-featured-churn-analysis.jpeg" width="320" /></span></a></div><div style="text-align: justify;"><span style="font-family: times;"><br /></span></div><div style="text-align: justify;"><span face=""Source Sans Variable", "Source Sans", sans-serif" style="color: #252525; font-family: times;">But tools are constantly changing. Sometimes you outgrow your current set of tools. Some platforms are okay for small numbers of users, but become unmanageable as you community scales up. This is the nature of the constant tradeoffs one makes in managing a dynamic community. In other cases, tools simply cease to exist, forcing you to migrate to another solution. And sometimes a tool becomes unaffordable as your user needs change. So the question becomes: how do you go about changing out your stack? </span></div><div style="text-align: justify;"><span face=""Source Sans Variable", "Source Sans", sans-serif" style="color: #252525; font-family: times;"><br /></span></div><div style="text-align: center;"><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjmnhA-SaN275HBBuRhXGEmruxVg5n0Z1FnwHvEXWEkh3d174nFkDYQcHh-qU_iDyrdihZzM3cZNzzx4cOVN7mVp1Xj771cJGboWsVDZYBGTrGPIgPLrVGPGHzclNXHPDOdcAKfPP44uqLpI_YOjhOGfjJxaw_pRVAFtqxrHethPBWc6cLWrNluixtk/s900/DfM3XOHWAAE3ImI.jpeg" style="margin-left: 1em; margin-right: 1em;"><span style="font-family: times;"><img border="0" data-original-height="506" data-original-width="900" height="180" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjmnhA-SaN275HBBuRhXGEmruxVg5n0Z1FnwHvEXWEkh3d174nFkDYQcHh-qU_iDyrdihZzM3cZNzzx4cOVN7mVp1Xj771cJGboWsVDZYBGTrGPIgPLrVGPGHzclNXHPDOdcAKfPP44uqLpI_YOjhOGfjJxaw_pRVAFtqxrHethPBWc6cLWrNluixtk/s320/DfM3XOHWAAE3ImI.jpeg" width="320" /></span></a></div><div class="separator" style="clear: both; text-align: center;"><span style="font-family: times;"><br /></span></div><div class="separator" style="clear: both; text-align: justify;"><span style="font-family: times;"><span face=""Source Sans Variable", "Source Sans", sans-serif" style="color: #252525;">My personal preference is to stick to open source tools whenever possible. There are two reasons for this: it eliminates the cost constraint, and it allows for open source solutions to emerge from the user community. Your open source community might also be able to develop customized tools for such platforms, thus helping you keep your technology stack consistent. The </span><a href="https://jitsi.org/" style="box-sizing: inherit; transition: color 0.3s ease 0s;">Jitsi platform</a><span face=""Source Sans Variable", "Source Sans", sans-serif" style="color: #252525;"> is a good example of this. Jitsi instances can be started through a web browser or mobile app, and Jitsi servers can be </span><a href="https://community.jitsi.org/" style="box-sizing: inherit; transition: color 0.3s ease 0s;">customized by specific organizations</a><span face=""Source Sans Variable", "Source Sans", sans-serif" style="color: #252525;">. </span></span></div><div style="text-align: justify;"><span style="font-family: times;"><br /></span></div><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi247Qn-GLgyDgAU1XRpTo0t0o1_8d6rNLgRzupruY4IC51YSsWqK0nfx61kfQK-KLOwlp-AVnBByvsTeF0JKbfV7yWESdFGbiABrpbR_yAuxAOdRmR3ZUeTJ0BcFBbQ3apkeTKMZEHlcgO_c4Lg1fwILlFF7KA_kMUYrxy7Bj8X7elf_yOM_gGifaU/s278/download.jpeg" style="margin-left: 1em; margin-right: 1em;"><span style="font-family: times;"><img border="0" data-original-height="181" data-original-width="278" height="181" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi247Qn-GLgyDgAU1XRpTo0t0o1_8d6rNLgRzupruY4IC51YSsWqK0nfx61kfQK-KLOwlp-AVnBByvsTeF0JKbfV7yWESdFGbiABrpbR_yAuxAOdRmR3ZUeTJ0BcFBbQ3apkeTKMZEHlcgO_c4Lg1fwILlFF7KA_kMUYrxy7Bj8X7elf_yOM_gGifaU/s1600/download.jpeg" width="278" /></span></a></div><span style="font-family: times;"><br /></span></div></div></span><p></p><p style="background-color: white; box-sizing: border-box; color: #252525; margin: 0px 0px 1.5625rem; padding: 0px; text-align: initial;"><span style="font-family: times;">When you do need to change out elements in your stack, the first step is to make sure that the solution works well with your other tools. For example, if you change your video conferencing tool, be sure to make sure your <a href="https://jamboard.google.com/" style="background-color: transparent; box-sizing: inherit; transition: color 0.3s ease 0s;">whiteboard</a> (Jamboard) and <a href="https://www.igniterealtime.org/" style="background-color: transparent; box-sizing: inherit; transition: color 0.3s ease 0s;">file sharing</a> (Ignite RealTime) tools also work well with this shift. Doing a series of contingency tests based on common use cases may help. Adopting <a href="https://obsproject.com/" style="background-color: transparent; box-sizing: inherit; transition: color 0.3s ease 0s;">OBS</a> for screen recordings and streaming is an example of this. Once you know your tool runs stably and provides the desired output, then you will have fewer glitches down the road. </span></p><div style="box-sizing: border-box; margin: 0px 0px 1.25rem; padding: 0px; text-align: center;"><p style="background-color: white; box-sizing: border-box; color: #252525; margin: 0px 0px 1.5625rem; padding: 0px; text-align: initial;"><span style="font-family: times;">Secondly, make sure that you community leaders (people most likely to run a community meeting) can use the new tool. You might offer a primer or training session to get people up to speed on the new tool, in addition to how it connects with other tools in the stack. This primer should then be available in the form of video and written documentation to the community, as your meeting and discussion leaders may change over time. Tools that <a href="https://go.zenhub.com/long-ppc/?utm_term=zenhub&utm_campaign=Brand&utm_source=adwords&utm_medium=ppc&hsa_acc=8479887336&hsa_cam=14577630669&hsa_grp=127140912379&hsa_ad=544547662297&hsa_src=g&hsa_tgt=kwd-101658533602&hsa_kw=zenhub&hsa_mt=e&hsa_net=adwords&hsa_ver=3&gclid=Cj0KCQjw29CRBhCUARIsAOboZbLPCZJAhCOgE5RB2MtcwQe1tl42Lr1CEB7cuQ8Fn__5qX4n_Xk3RZMaAv1rEALw_wcB" style="background-color: transparent; box-sizing: inherit; transition: color 0.3s ease 0s;">visualize Github tasks and milestones</a> (ZenHub) is one example of a tool with multiple dependencies.</span></p><p style="background-color: white; box-sizing: border-box; color: #252525; margin: 0px 0px 1.5625rem; padding: 0px; text-align: initial;"><span style="font-family: times;">A third step is to do an audit of how the tool is actually being used, to ensure that there is a match between desired functionality and the functionality that is available to everyday users. Perhaps your community is really interested in sharing files during their video meetings. This may require the addition of a new tool, or an addition to an existing tool. Only a post-implementation audit (or a quarterly solicitation of use cases) will reveal an actionable path.</span></p></div>Bradly Aliceahttp://www.blogger.com/profile/06482487682656113637noreply@blogger.com1tag:blogger.com,1999:blog-1792896637814721350.post-61794372578508618442022-02-15T00:01:00.003-06:002022-03-17T12:59:48.079-05:00Gyrification of the Tree of Mammals<div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/a/AVvXsEhahZLuQhjzPxGjzHHA2xrnjmWlG_zTDm4UZn9rMVgV1jf7DgfWnhB08ptvl54F7uSS4ddZ63XYx_Cgomnu4fd4XDxmwpTVGF8S3bC9YHVp6e-iClolqj1dYjx6d2_tIuhR4oQDmj56z486dwYXIMk6GzeyX49yP6lVg_OOLP0xQfupZ9Y96RPswLCw=s1024" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="614" data-original-width="1024" height="192" src="https://blogger.googleusercontent.com/img/a/AVvXsEhahZLuQhjzPxGjzHHA2xrnjmWlG_zTDm4UZn9rMVgV1jf7DgfWnhB08ptvl54F7uSS4ddZ63XYx_Cgomnu4fd4XDxmwpTVGF8S3bC9YHVp6e-iClolqj1dYjx6d2_tIuhR4oQDmj56z486dwYXIMk6GzeyX49yP6lVg_OOLP0xQfupZ9Y96RPswLCw=s320" width="320" /></a></div><p style="text-align: justify;">For this year's Darwin Day post, I will be reviewing the evolutionary origins and developmental emergence of gyrification of the Mammalian brain. <a href="https://en.wikipedia.org/wiki/Gyrification">Gyrification</a> occurs when the neocortex, or six layered cortex on the dorsal surface of Mammalian brains, exhibits wrinkles and folds rather than a smooth surface (<a href="https://en.wikipedia.org/wiki/Lissencephaly">lissencephaly</a>). Gyrification is measured using the gyrification index (or GI). GI can range from 5.6 in Pilot whales (<i>Globicephala</i>) to 3.8 in Elephants (<i>Loxodonta</i>) and 2.6 in Humans (<i>Homo</i>) [1]. A more extensive phylogenetic analysis (Figure 1) shows the evolutionary trajectory for this in Hominids, and a highly gyrified brain is associated with other traits that emerge as early as the divergence of Primates. </p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/a/AVvXsEgkvPo5Ueh6Jktd065wEknPJKW482GSjwEqSkT0lQBOlGY69jZFntrD567lwdDYg5e4yJ7LOkp4L0GjqvRp-OQ8pGNGPMlzWGID3UIncGuOmMpYQ9fFfvWEZXAmBmDj39ib2Tp0vinXXVbQTZda27f9cKC_vcLrldMp8TVjTMUyuFvx50GQ01kLBQkT=s747" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="519" data-original-width="747" height="444" src="https://blogger.googleusercontent.com/img/a/AVvXsEgkvPo5Ueh6Jktd065wEknPJKW482GSjwEqSkT0lQBOlGY69jZFntrD567lwdDYg5e4yJ7LOkp4L0GjqvRp-OQ8pGNGPMlzWGID3UIncGuOmMpYQ9fFfvWEZXAmBmDj39ib2Tp0vinXXVbQTZda27f9cKC_vcLrldMp8TVjTMUyuFvx50GQ01kLBQkT=w640-h444" width="640" /></a></div><br /><div class="separator" style="clear: both; text-align: center;">Figure 1. A phylogeny of primate brain evolution (with Mammalian outgroups), with a focus on the origin of traits found in the human brain. <b>COURTESY</b> [2].</div><p style="text-align: justify;">The evolutionary origins of gyrification may either be mono- or polyphyletic, as different genes have been identified as potential associated factors. Gyrification might also be a product of convergent evolution, as this trait may simply be a by-product of larger neocortical sheets. Steidter [3] points out that gyrification may simply be due to physical constraints related to fitting a vastly enlarged cortical sheet into a skull scaled to an organism's body size. </p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/a/AVvXsEjdXO-lcmmv9i2ZwHT0rVM-ca6sCSPrYsSefV06RP7t_hALiEqzNydlNF9Gml_c714kR_N3N4pt0-7YhcKj-pa7hZJKAuBeeyYMH5byGY-hK8N9DOK8tMz9sp1i62524DTgQ6EYYB0zyVVx_4mul2cg0r5nggmrq8hPQQc9YGYil8DcCwpHi88LolG9=s1280" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="1280" data-original-width="1187" height="320" src="https://blogger.googleusercontent.com/img/a/AVvXsEjdXO-lcmmv9i2ZwHT0rVM-ca6sCSPrYsSefV06RP7t_hALiEqzNydlNF9Gml_c714kR_N3N4pt0-7YhcKj-pa7hZJKAuBeeyYMH5byGY-hK8N9DOK8tMz9sp1i62524DTgQ6EYYB0zyVVx_4mul2cg0r5nggmrq8hPQQc9YGYil8DcCwpHi88LolG9=s320" width="297" /></a></div><p style="text-align: center;">Figure 2. Allometric scaling across select Mammalian brain, showing an increase in gyrification for larger brains. <b>COURTESY</b> [4].</p><p style="text-align: justify;">In Figure 2, we see that in general larger brains also have a larger GI value. The curvilinear relationship shown in the figure is known as an allometric scaling. Allometry [5] is a convenient way to quantitatively assess relative growth across different species, and the resulting regression parameters are suggestive of underlying mechanisms that control and predict growth across evolution.</p><p style="text-align: justify;">In this case, the allometric relationship is brain size versus tangential expansion. Tangential matter is expansion of gray matter relative to the constraints of white matter, or a grey-to-white matter proportion [4]. As the amount of gray matter increases, brain size also tends to increase, and so does the GI value. However, the proportion of gray to white matter saturates, while brain sizes continue to expand along with increasing GI values. </p><p><br /></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/a/AVvXsEhrBkPYblBbRw-Em2Fl4rNHHxBp2cU3tzGKBym_u9CU5B-wLmmjIGju5G6bjGiAqoLv4Aq6qZ6r_XRHAxUUCD1hWoRKRd1Gbs0N9tF3jRPSqJGHWM6YzKrhTR2AXcnIGCjSNBrBfgNt6dcamx2bH0FjSGoqqVBi_miNPbYZd6sGroX-cp58DUCrfrvf=s669" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="265" data-original-width="669" height="254" src="https://blogger.googleusercontent.com/img/a/AVvXsEhrBkPYblBbRw-Em2Fl4rNHHxBp2cU3tzGKBym_u9CU5B-wLmmjIGju5G6bjGiAqoLv4Aq6qZ6r_XRHAxUUCD1hWoRKRd1Gbs0N9tF3jRPSqJGHWM6YzKrhTR2AXcnIGCjSNBrBfgNt6dcamx2bH0FjSGoqqVBi_miNPbYZd6sGroX-cp58DUCrfrvf=w640-h254" width="640" /></a></div><br /><p style="text-align: center;"><br /></p><p style="text-align: center;">Figure 3. Simulating gyrification as a by-product of physical processes. 3-D printed models based on MRI data for brains from different stages of development. <b>COURTESY</b> [6].</p><p style="text-align: justify;">Genetic analyses implicate the role of specific genes in controlling brain volume, which then sets the stage for gyrification [7]. Developmental mutations in the human genetic loci collectively known as MCPH 1-18 [8] lead to a condition called microcephaly, where the mature microcephalic brain remains small and lacks gyrification. In a study of 34 species [9], the largest source of explained variance between species can be explained by random Brownian motion. Furthermore, the data within the order Primates shows that fold wavelength is stable (~12mm) despite a 20-fold difference in volume [9]. </p><p style="text-align: justify;">As an alternative hypothesis to evolutionary origins, gyrification can result from various physical processes in developmental morphogenesis (Figure 3). The gyrification process consists of gyral (ridge-like) and sulcal (groove-like) convolutions. In the earliest stages of development, no gyrification is expressed in the phenotype. However, as the neocortex grows faster relative to the rest of the brain, a mechanical instability results that leads to buckling [6]. Buckling thus creates gyrification, although the consistency of their localization and timing in development suggests underlying cellular and molecular mechanisms. Demonstration of biophysical mechanisms does not preclude a phylogenetic explanation, however. As we will see later on, surface physics relies upon the presence of certain cell types and growth conditions.</p><p style="text-align: justify;"><br /></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/a/AVvXsEh58_sqGqtUAQXcdUb9KG8vS7XZeeKW88HY5bY7IWFfmoia0w5yYJV7QQsVZuSNf31xjOtejTZ3ZG7u2ngqLELjJfEPx0Wnjm8JOWULQOXKkDyZKngZasaRUtgYhg9mmGHSE4fbMmP1jvucDNpqwW3gyhJfs-QCGabHXBHwgInm48DHGjLUvBs5fjnI=s670" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="551" data-original-width="670" height="329" src="https://blogger.googleusercontent.com/img/a/AVvXsEh58_sqGqtUAQXcdUb9KG8vS7XZeeKW88HY5bY7IWFfmoia0w5yYJV7QQsVZuSNf31xjOtejTZ3ZG7u2ngqLELjJfEPx0Wnjm8JOWULQOXKkDyZKngZasaRUtgYhg9mmGHSE4fbMmP1jvucDNpqwW3gyhJfs-QCGabHXBHwgInm48DHGjLUvBs5fjnI=w400-h329" width="400" /></a></div><p style="text-align: center;">Figure 4. An overview of the evolution of development (Evo-Devo) of gyrification. Gyrification and lissencephaly occur through mechanisms that affect changes in brain size and GI relative to the last common ancestor (in this figure, transitional form). <b>COURTESY</b> [10].</p><p style="text-align: justify;">There are also several cellular and molecular factors that contribute to neocortical growth, and thus towards gyrification. In Figure 4, we see four archetypes that result from increases and decreases of brain size coupled with increases and decreases of GI. For example, increases in basal radial ganglion (bRG) precursor cells and transit-amplifying progenitor cells (TAPs) contribute to increases of both brain size and GI [10]. Decreases in brain size and GI are controlled by changes in cell cycle timing and associated heterochronic changes. Heterochrony has to do with the timing of the rate and termination of growth in development and is but one factor that suggests lissencephaly is actually the derived condition. Thus, smooth brains would be an evolutionary reversal from the ancestral gyrified state that occurred multiple times across the tree of Mammals. </p><p style="text-align: left;">Once again, an evolutionary conundrum. Happy evolutioning!</p><p><b>NOTES:</b></p><p><span style="font-family: times;">[1] Johnson, S. <a href="https://carta.anthropogeny.org/about/carta">Number and Complexity of Cortical Gyrii</a>. Center for Academic </span><span style="font-family: times;">Research and Training in Anthropogeny. La Jolla, CA. Accessed: February 13, </span><span style="font-family: times;">2022. </span></p><p><span style="font-family: times;">[2] Franchini, L.F. (2021). <a href="https://www.frontiersin.org/articles/10.3389/fcell.2021.591017/full">Genetic Mechanisms Underlying Cortical Evolution in Mammals</a>. <i>Frontiers in Cell and Developmental Biology</i>, 9, 591017.</span></p><p>[3] Striedter, G. (2005). Principles of brain evolution. Sinauer, Sunderland, MA.</p><p><span style="font-family: times;">[4] Tallinen, T., Chung, J.Y. , Biggins, J.S., and Mahadevan, L. (2014). <a href="https://www.pnas.org/content/111/35/12667">Gyrification from constrained cortical expansion</a>. <i>PNAS</i>, 111(35), 12667-12672.</span></p><p><span style="font-family: times;">[5] Shingleton, A. (2010) <a href="https://www.nature.com/scitable/knowledge/library/allometry-the-study-of-biological-scaling-13228439/">Allometry: The Study of Biological Scaling</a>. <i>Nature Education Knowledge</i>, 3(10), 2.</span></p><p><span style="font-family: times;">[6] Tallinen, T., Chung, J.Y., Rousseau, F., Girard, N., Lefevre, J., and Mahadevan, L. (2016). <a href="https://www.nature.com/articles/nphys3632">On the growth and form of cortical convolutions.</a> <i>Nature Physics</i>, 12, 588–593.</span></p><div style="font-family: times;"><span style="font-variant-east-asian: normal; font-variant-numeric: normal; vertical-align: baseline; white-space: pre-wrap;"><span style="white-space: normal;">[7] </span><span style="font-variant-east-asian: normal; font-variant-numeric: normal; text-align: justify; vertical-align: baseline;">Zilles, K., Palomero-Gallagher, N., and Amunts, K. (2013). <a href="https://www.cell.com/trends/neurosciences/fulltext/S0166-2236(13)00018-0?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0166223613000180%3Fshowall%3Dtrue">Development of cortical folding during evolution and ontogeny</a>. </span><span style="font-style: italic; font-variant-east-asian: normal; font-variant-numeric: normal; text-align: justify; vertical-align: baseline;">Trends in Neurosciences</span><span style="font-variant-east-asian: normal; font-variant-numeric: normal; text-align: justify; vertical-align: baseline;">, 36(5), 275-284. </span></span></div><p><span style="font-family: times;"></span></p><div style="font-family: times;"><span style="font-variant-east-asian: normal; font-variant-numeric: normal; vertical-align: baseline; white-space: pre-wrap;"><span style="font-variant-east-asian: normal; font-variant-numeric: normal; text-align: justify; vertical-align: baseline;">[8] Jayaraman, D., Bae, B-I., and Walsh, C.A. (2018). <a href="https://www.annualreviews.org/doi/10.1146/annurev-genom-083117-021441">The Genetics of Primary Microcephaly</a>. <i>Annual Review of Genomics and Human Genetics</i>, 19, 177-200. </span></span></div><p><span style="font-family: times; font-variant-east-asian: normal; font-variant-numeric: normal; text-align: justify; vertical-align: baseline; white-space: pre-wrap;">[9] Heuer, K., Gulban, O.F., Bazin, P-L., Osoianu, A., Valabregue, R., Santin, M., Herbin, M., and Toro, R. (2019). <a href="https://www.sciencedirect.com/science/article/abs/pii/S0010945219301704?via%3Dihub">Evolution of neocortical folding: A phylogenetic comparative analysis of MRI from 34 primate species</a>. </span><span style="font-family: times; font-style: italic; font-variant-east-asian: normal; font-variant-numeric: normal; text-align: justify; vertical-align: baseline; white-space: pre-wrap;">Cortex</span><span style="font-family: times; font-variant-east-asian: normal; font-variant-numeric: normal; text-align: justify; vertical-align: baseline; white-space: pre-wrap;">, 118, 275-291.</span></p><span id="docs-internal-guid-d99db6cf-7fff-9bc1-0ee2-3693846193c5"><span style="font-family: times;"><div><span style="font-variant-east-asian: normal; font-variant-numeric: normal; vertical-align: baseline; white-space: pre-wrap;"><span style="font-variant-east-asian: normal; font-variant-numeric: normal; text-align: justify; vertical-align: baseline;"><p style="font-family: Times; text-align: left; white-space: normal;"><span style="font-family: times;">[10] Kelava, I., Lewitus, E., and Huttner, W.B. (2013). <a href="https://www.frontiersin.org/articles/10.3389/fnana.2013.00016/full">The secondary loss of gyrencephaly as an example of evolutionary phenotypical reversal</a>. <i>Frontiers in Neuroanatomy</i>, 7, 16.</span></p><div><span style="font-family: times;"><br /></span></div><span id="docs-internal-guid-d99db6cf-7fff-9bc1-0ee2-3693846193c5" style="font-family: Times; text-align: left; white-space: normal;"><span style="font-family: times;"></span></span></span></span></div></span></span>Bradly Aliceahttp://www.blogger.com/profile/06482487682656113637noreply@blogger.com1tag:blogger.com,1999:blog-1792896637814721350.post-31887182396467186812021-12-03T01:28:00.002-06:002021-12-03T01:28:33.417-06:00MAIN and Neuromatch Conference Presentations<div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh2njPi8N_YGLNa7Jyi5yeaMpTPFtJhGaIucaFwaejdPU5rFIfI8i_3GaR1Va3FXaZWm6Lv5MtDtF8Mtnaxyv5ZTkgBx6vahKjwL4MCOCXqUVb_SMpypE39Iahy7nN1xnZW9vAyeho7F48/s597/1.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="314" data-original-width="597" height="214" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh2njPi8N_YGLNa7Jyi5yeaMpTPFtJhGaIucaFwaejdPU5rFIfI8i_3GaR1Va3FXaZWm6Lv5MtDtF8Mtnaxyv5ZTkgBx6vahKjwL4MCOCXqUVb_SMpypE39Iahy7nN1xnZW9vAyeho7F48/w408-h214/1.png" width="408" /></a></div><div class="separator" style="clear: both; text-align: center;"><br /></div><div class="separator" style="clear: both; text-align: left;">The <a href="https://orthogonal-research.weebly.com/">Orthogonal Research and Education Lab</a> is on the virtual move! We have been featured at two conferences this week. The first conference is <a href="https://www.main2021.org/">MAIN (Montreal Artificial Intelligence-Neuroscience)</a> conference, a hybrid conference that focused on cutting-edge research in Neuro-AI. Our submission (<a href="https://www.youtube.com/watch?v=4O2B-DY-aKk">Developmental Embodied NeuroSimulation</a>) is a group effort and summarizes our work in this area over the past few years. The graphical abstract can be found below.</div><p style="text-align: center;"></p><div class="separator" style="clear: both; text-align: center;"><br /></div><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiYDkP9xbl5zDFtxkQfrM-h-AV1gHvtZZZh0L2mDXkXXGsfju1vj02DxytF8RRNjcdSLh9KCFFyoZe0hlUSemp-PkhPLlvseysa5kVtZw-7Hr8IUawl8tT2woa-EE_Mkhmh32momuYNnAI/s1920/Developmental-Embodied-NeuroSim.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="1920" data-original-width="1920" height="468" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiYDkP9xbl5zDFtxkQfrM-h-AV1gHvtZZZh0L2mDXkXXGsfju1vj02DxytF8RRNjcdSLh9KCFFyoZe0hlUSemp-PkhPLlvseysa5kVtZw-7Hr8IUawl8tT2woa-EE_Mkhmh32momuYNnAI/w468-h468/Developmental-Embodied-NeuroSim.png" width="468" /></a></div><div class="separator" style="clear: both; text-align: center;">Graphical Abstract for <a href="https://www.youtube.com/watch?v=4O2B-DY-aKk">Developmental Embodied NeuroSimulation</a>.</div><br /><div style="text-align: left;">We also had a presence at <a href="https://conference.neuromatch.io/">Neuromatch 4</a>, with four flash talk presentations on four different topics. Neuromatch 4 was a great time, with two days of keynote talks, short talks, flash talks, and debate panels. </div><p></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhhIYborxPe3GW2BR8Q3sW4qOyYMytF84sRZJhF7rgv3aYzz0L9PAVf_qDUyWqQa16u5hWT5Zc-hEU0Jyapojm6KlDy1Tn-4jAKr2Re-979nuUVF6Bhc8st6-DJ9Jbc2cu3qzy0sVzUvXg/s716/nm4.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="716" data-original-width="596" height="462" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhhIYborxPe3GW2BR8Q3sW4qOyYMytF84sRZJhF7rgv3aYzz0L9PAVf_qDUyWqQa16u5hWT5Zc-hEU0Jyapojm6KlDy1Tn-4jAKr2Re-979nuUVF6Bhc8st6-DJ9Jbc2cu3qzy0sVzUvXg/w384-h462/nm4.png" width="384" /></a></div><div class="separator" style="clear: both; text-align: center;"><br /></div><div class="separator" style="clear: both; text-align: left;">Each flash talk was 7.5 minutes long, which requires an efficiency of words and ideas not typical of a longer format. The first talk is "<a href="https://twitter.com/Orthogonal_Lab/status/1466084548458991623">The Universal Theory of Switching</a>", which focuses on transitory "switching" phenomena. Switching behavior is ubiquitous across biological, physical, and algorithmic systems, and is controlled by sudden, first-order phase transition-like behavior we characterize as zeroth-order cybernetic regulation. </div><div class="separator" style="clear: both; text-align: left;"><br /></div><div class="separator" style="clear: both; text-align: left;">Another talk is on "<a href="https://t.co/l3hChNAlwV">Allostatic Kinds</a>". Allostatic Kinds are a way to regulate the boundaries of meaning and regulation of internal emotional and conscious states. This talk is presented by Jesse Parent, and features a mix of complex systems regulation, philosophy of mind, and consciousness studies. This talk was in conjunction with <a href="https://ceealar.org/">CEEALAR (Center for Enabling EA Learning and Research)</a>, an academic hostel located in Blackpool, UK.</div><div class="separator" style="clear: both; text-align: left;"><br /></div><div class="separator" style="clear: both; text-align: left;">Daniela Cialfi has built upon the lab's work on <a href="https://t.co/r4KMXWeXgq">Meta-brain Models</a> to develop "<a href="https://t.co/AWolb17Nef">Economic Meta-brains</a>", which are bio-economic agents that behave according to the free energy principle. Meta-brains are layered computational models that enable different levels of representation in the same agent. These model layers can be configured in geometrically specific ways, which in turn affects their function. The free energy principle enriches the meta-brains approach by adding a mathematically rigorous energetic component to a meta-brain agent. </div><div class="separator" style="clear: both; text-align: left;"><br /></div><div class="separator" style="clear: both; text-align: left;">Finally, our presentation on "<a href="https://t.co/PxZfrlQqft">Gibsonian Information</a>" comes with a <a href="https://t.co/BHD6kon3kT">preprint</a>. Gibsonian Information is the information content of direct perceptual processing (<i>sensu</i> J.J. Gibson). We draw parallels between Shannon and Gibsonian Information, in addition to the role of such information in the dynamic interactions between agents and their environments. See our graphical abstract below, which simplifies the mathematics in the preprint. The talk also features a number of naturalistic settings in which Gibsonian Information can be demonstrated.</div><div class="separator" style="clear: both; text-align: center;"><br /></div><div class="separator" style="clear: both; text-align: center;"><br /></div><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgp7gZ-u58Cexl4P3q0v4pEpvbZDH-NxTzXmploYHd3pyexseLX7KUt7AMV9amSbQalpl-5b3UElxcdIq-wJQ4jMEEc8SyjtivTBGI2Q6G09RKMcqt5oEa9hvkjtcm8vJUOMmJlpUOP1jI/s960/Graphical+Abstract+for+Gibsonian+Information.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="960" data-original-width="960" height="406" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgp7gZ-u58Cexl4P3q0v4pEpvbZDH-NxTzXmploYHd3pyexseLX7KUt7AMV9amSbQalpl-5b3UElxcdIq-wJQ4jMEEc8SyjtivTBGI2Q6G09RKMcqt5oEa9hvkjtcm8vJUOMmJlpUOP1jI/w406-h406/Graphical+Abstract+for+Gibsonian+Information.png" width="406" /></a></div><br /><div class="separator" style="clear: both; text-align: center;">Graphical abstract for the Gibsonian Information paper/presentation (direct perception as information content).</div><br /><p style="text-align: center;"><br /></p>Bradly Aliceahttp://www.blogger.com/profile/06482487682656113637noreply@blogger.com1tag:blogger.com,1999:blog-1792896637814721350.post-45219809159838116502021-11-03T00:01:00.075-05:002021-11-03T00:01:00.172-05:00Ten years of "Virtual Reality in Neuroscience Research and Therapy"<p><span style="font-size: medium;">Ten years ago today (November 3), me and co-authors <a href="https://sciences.ucf.edu/psychology/person/corey-bohil/">Corey Bohil</a> and <a href="https://people.njit.edu/faculty/biocca">Frank Biocca</a> published the paper "<a href="http://www.nature.com/nrn/journal/vaop/ncurrent/full/nrn3122.html">Virtual Reality in Neuroscience Research and Therapy</a>" in <a href="https://www.nature.com/nrn/">Nature Reviews Neuroscience</a>. Happy Birthday, paper!</span><br /><span style="background-color: white; font-family: "Open Sans"; font-size: 14px;"><br /></span></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjJ5eO3GdJpFwpzgjIJf32XQIcUX34Bh_FtrbL39AhwsGsDFhmna1539sE6OuC3iQcBvf2OsBSggstmPh_8qwBbMzMoz2e8ySdrI3vNRZY_cP-8acfcF0p8Mk2yGkWTktrP0p-DAKHAfAc/s834/new-NRN-paper.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="588" data-original-width="834" height="360" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjJ5eO3GdJpFwpzgjIJf32XQIcUX34Bh_FtrbL39AhwsGsDFhmna1539sE6OuC3iQcBvf2OsBSggstmPh_8qwBbMzMoz2e8ySdrI3vNRZY_cP-8acfcF0p8Mk2yGkWTktrP0p-DAKHAfAc/w509-h360/new-NRN-paper.png" width="509" /></a></div><div class="separator" style="clear: both; text-align: center;"><span style="font-family: times; font-size: medium;">Click to enlarge.</span></div><p></p><p><span style="font-size: medium;">This article <a href="https://syntheticdaisies.blogspot.com/2011/12/virtual-reality-news.html">made the issue cover</a> of the containing issue. <span style="background-color: white; font-family: "Open Sans";">A closeup of the cover art (below) is entitled "<a href="http://www.nature.com/nrn/journal/v12/n12/covers/index.html">Virtual Reality Reaches New Heights</a>" by Kirsten Lee. Great image of a digital mountain range.</span></span></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiIMj2VzF1epeapFr6jGRsOdv1fbun0Svk6iM8Fmyoidg6vzhZNmzpUeWbfItlOGMosq0_bxsD69fqjkL7hC1Rjq7nQyMOjBgRa8j2KQVyY7ATC4Fj9_0ViLgQwgKVRwAxGLH_DYOa9RA8/s362/large_cover201112.jpg" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="294" data-original-width="362" height="260" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiIMj2VzF1epeapFr6jGRsOdv1fbun0Svk6iM8Fmyoidg6vzhZNmzpUeWbfItlOGMosq0_bxsD69fqjkL7hC1Rjq7nQyMOjBgRa8j2KQVyY7ATC4Fj9_0ViLgQwgKVRwAxGLH_DYOa9RA8/s320/large_cover201112.jpg" width="320" /></a></div><div class="separator" style="clear: both; text-align: center;"><span style="font-size: medium;">Click to enlarge.</span></div><div><span style="font-size: medium;"><br /></span></div><div><span style="font-size: medium;">After 10 years, this <a href="https://scholar.google.com/citations?view_op=view_citation&hl=en&user=UaAdJi0AAAAJ&citation_for_view=UaAdJi0AAAAJ:u5HHmVD_uO8C">publication has been cited</a> about 730 times. Even after 10 years, the citation rate per year is still increasing. Not only does the paper cover examples of human engagement with VR, but examples from model organisms as well. This paper is different than many other reviews of VR in that it does not focus on the latest technology, but more fundamental research questions and applications. </span></div><div><br /></div><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgY7hzutCoRZcllCey_ldq5hDsg46AzKdkXDBq8cmX9MAdtTT5cnurGByfIZFNKc_96cpFTg2rAMxSbx0fe8tnWQA44aWZuiH8nF0nxtqMpefUq3AaRg7oCz1DSbfpFoQFp05PeZmaXttM/s654/google-scholar.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="630" data-original-width="654" height="308" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgY7hzutCoRZcllCey_ldq5hDsg46AzKdkXDBq8cmX9MAdtTT5cnurGByfIZFNKc_96cpFTg2rAMxSbx0fe8tnWQA44aWZuiH8nF0nxtqMpefUq3AaRg7oCz1DSbfpFoQFp05PeZmaXttM/s320/google-scholar.png" width="320" /></a></div><div class="separator" style="clear: both; text-align: center;"><span style="font-family: times; font-size: medium;"><b>COURTESY:</b> <a href="https://scholar.google.com/">Google Scholar</a>. Click to enlarge.</span></div><br /><div style="text-align: left;"><span style="font-family: times; font-size: medium;">About four years later, I single-authored a paper at <a href="https://f1000research.com/">F1000 Research</a> called "<a href="https://f1000research.com/articles/3-202/v2">Animal-oriented virtual environments: illusion, dilation, and discovery</a>", a paper that delved into speculation about neural mechanisms in model organisms during VR exposure. This was before the current VR hype came of age, so it was tough to find reviewers for this one. Nevertheless, there is much more to explore in this area.</span></div>Bradly Aliceahttp://www.blogger.com/profile/06482487682656113637noreply@blogger.com1tag:blogger.com,1999:blog-1792896637814721350.post-66955264422253041262021-10-25T01:01:00.000-05:002021-10-25T01:01:00.167-05:00Opening Access, Virtual, Distributed Lab Edition<div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi9P6VGIhORmxktJ9uIqd8Bl3R-p8GGo3W-H2kj9zUl3UCwGAGj2LSdDthXuYFwbnVlvSrdwu4e0pdPN9qE3COzpYJRyfO6K7RL1Os7H9tr7yUv835ctxLeotL_HfvsZ12MVaugI7TrIbU/s1200/OAW+2021_kvadrat.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="630" data-original-width="1200" height="246" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi9P6VGIhORmxktJ9uIqd8Bl3R-p8GGo3W-H2kj9zUl3UCwGAGj2LSdDthXuYFwbnVlvSrdwu4e0pdPN9qE3COzpYJRyfO6K7RL1Os7H9tr7yUv835ctxLeotL_HfvsZ12MVaugI7TrIbU/w469-h246/OAW+2021_kvadrat.jpg" width="469" /></a></div><br /><p style="text-align: justify;"><span style="text-align: left;">Welcome to </span><a href="http://www.openaccessweek.org/" style="text-align: left;">Open Access Week 2021</a><span style="text-align: left;">! This year's theme is building structural equity. In the </span><a href="https://orthogonal-research.weebly.com/" style="text-align: left;">Orthogonal Research and Education Lab</a><span style="text-align: left;"> and the </span><a href="https://devoworm.weebly.com/" style="text-align: left;">DevoWorm group</a><span style="text-align: left;">, this has been an ongoing priority: from the recruitment of scholars to the production and engagement with research. This week we will highlight some of the ways we open up the research process, and how this is the only way the principles of open access (Figure 1) can be fully realized.</span></p><p><br /></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEihGIu7NtQwrKFiBwU58r0CPOJyqLtg5pWBSyEJDYbP1NP0H-BLoEouaua_N4ptD4GoBTofbv-zpVSrrEyYE-KIno53tHXVM4kJKLndkV1_brwpEhrXxNzN2eKnsSEen9NCp9e-SXsiqnY/s1085/OA_acc_to_phd_comics.jpg" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="497" data-original-width="1085" height="257" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEihGIu7NtQwrKFiBwU58r0CPOJyqLtg5pWBSyEJDYbP1NP0H-BLoEouaua_N4ptD4GoBTofbv-zpVSrrEyYE-KIno53tHXVM4kJKLndkV1_brwpEhrXxNzN2eKnsSEen9NCp9e-SXsiqnY/w560-h257/OA_acc_to_phd_comics.jpg" width="560" /></a></div><p style="text-align: center;">Figure 1. From the short film "<a href="http://phdcomics.com/comics.php?f=1533">What is Open Access</a>" (PhD Comics, 2012).</p><p style="text-align: justify;">One thing that enables Open Access is an open collaboration structure. Both Orthogonal Lab and DevoWorm are based on a virtual, distributed framework. People can join in and collaborate as long as they have an internet connection and the initiative to work on a related problem. The communication structure is likewise flexible: you can join in our weekly meetings, participate in our Slack channels or Github teams, or join in on a collaborative doc. We also sponsor or participate in various open educational initiatives. Two of these are <a href="https://summerofcode.withgoogle.com/">Google Summer of Code</a> and <a href="https://academy.neuromatch.io/">Neuromatch Academy</a>.</p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiwv97ehPBCkJxQ2eX7oEq7PYzaatKGs3-_EjEgSeFrhXn6viRnRgWsCgFYcsJxqICD9f3v2lJyqlNe0hTDLkmweKTwZ0XKew_osNGWwxF8BC-pEE0Y1EcfXmd3T0w0y5g02N1y_fIQkqw/s441/222.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="403" data-original-width="441" height="325" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiwv97ehPBCkJxQ2eX7oEq7PYzaatKGs3-_EjEgSeFrhXn6viRnRgWsCgFYcsJxqICD9f3v2lJyqlNe0hTDLkmweKTwZ0XKew_osNGWwxF8BC-pEE0Y1EcfXmd3T0w0y5g02N1y_fIQkqw/w357-h325/222.png" width="357" /></a></div><div class="separator" style="clear: both; text-align: center;">Figure 2. The global reach (physical and virtual) of the Orthogonal Lab.</div><p style="text-align: justify;">This brings together participants from multiple continents and research specialties, while also enabling students, professional academics, and lifelong learners to collaborate in ways large and small. We participate in the academic community through virtual and hybrid conferences, peer-reviewed publication venues, book chapters, and preprints. Self-publication platforms (blogging platforms) and social media are also good for advancing fledgling ideas and chronicling progress. Along with an emphasis on open code and data, these venues are utilized to maximize access and reusability.</p><p style="text-align: justify;">More recently, we have been focusing on the role of professional development in enabling the virtual, distributed research process. As many of our contributors aspire to further their research careers through participation, we have become more active in cultivating an individual's research agenda. Between active recruitment of participants and enabling them to take ownership of a research topic, we can contribute to greater equity and diversity in the research enterprise.</p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiRHwXfWyx3HnEkhynl4gJfmlSKgslqFYD2fnv34ZU1nZ6nAj5RKdjZFENw1HJog5sSW2skdFztqrdqvyo8SA-ZxHTW1Q9b2NokbHiMn-baCVqJsm4jicwvEZMp4q5EVEfkfM9CCzLJkVY/s350/73323973.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="350" data-original-width="350" height="139" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiRHwXfWyx3HnEkhynl4gJfmlSKgslqFYD2fnv34ZU1nZ6nAj5RKdjZFENw1HJog5sSW2skdFztqrdqvyo8SA-ZxHTW1Q9b2NokbHiMn-baCVqJsm4jicwvEZMp4q5EVEfkfM9CCzLJkVY/w139-h139/73323973.png" width="139" /></a> <a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjRMLgo_zXJTA32ycrSeZVoqnJhOkCAUscCs184iDMgGHc1lJGinIz0TbuOS1of6GNe65YUjgY_I5Wj5Hx8XoGU8baQ88CnoZ5LKfCF3Jphyphenhyphenu0JjDf8BAYkApIAQa3-6DoEUgrQ5ZNyaVQ/s1057/dw-logo-2020.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="599" data-original-width="1057" height="92" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjRMLgo_zXJTA32ycrSeZVoqnJhOkCAUscCs184iDMgGHc1lJGinIz0TbuOS1of6GNe65YUjgY_I5Wj5Hx8XoGU8baQ88CnoZ5LKfCF3Jphyphenhyphenu0JjDf8BAYkApIAQa3-6DoEUgrQ5ZNyaVQ/w162-h92/dw-logo-2020.png" width="162" /></a></div><br /><p style="text-align: justify;">Finally, our Open Access agenda includes an interdisciplinary focus, as both Orthogonal Lab and DevoWorm engage individuals from a variety of different backgrounds. There is an intentionality towards enabling interdisciplinary skillsets, as well as a focus on providing individuals space to pursue these connections between traditional disciplines. For more information on how these components work to form a virtual, distributed lab, see our preprint "<a href="https://osf.io/preprints/metaarxiv/4k3z6/">Building a Distributed Virtual Laboratory Adjacent to Academia</a>". </p><p style="text-align: justify;">While there are still many administrative and functional barriers to pursuing this as a full-fledged research organization on par with a large corporation or University, this is a unique and emergent way of opening access. If you would like to participate, please <a href="mailto:Orthogonal.Lab@outlook.com">contact us</a>. Additionally, be sure to check out the <a href="https://syntheticdaisies.blogspot.com/search?q=OAWeek">#OAWeek</a> hashtag for this blog (Synthetic Daisies), as we have content going back to 2016 on a variety of topics. </p><p style="text-align: center;"></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjR7LLHm1gGjTB6YW5SStKQQ2dCuXNzsnYXe25DwcKi0ORU7Llakk8BW57WI6UTdhvTnbvYTDw31Oik9FQ6NnkCYz0z_NZiosGKwJOVsaVnGdJb9kn4SJ8bra4EXmjr_mJ8Y8oOm5o7gIo/s1280/OA_cake_1_%25285091180896%2529.jpg" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="960" data-original-width="1280" height="193" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjR7LLHm1gGjTB6YW5SStKQQ2dCuXNzsnYXe25DwcKi0ORU7Llakk8BW57WI6UTdhvTnbvYTDw31Oik9FQ6NnkCYz0z_NZiosGKwJOVsaVnGdJb9kn4SJ8bra4EXmjr_mJ8Y8oOm5o7gIo/w257-h193/OA_cake_1_%25285091180896%2529.jpg" width="257" /></a></div><br /><p></p>Bradly Aliceahttp://www.blogger.com/profile/06482487682656113637noreply@blogger.com1tag:blogger.com,1999:blog-1792896637814721350.post-86292688948172229642021-09-29T18:01:00.018-05:002021-09-29T18:01:00.269-05:00OpenWorm Annual Meeting 2021 (DevoWorm update)<p><span style="font-family: times;">This week we had our <a href="https://syntheticdaisies.blogspot.com/2020/09/openworm-annual-meeting-devoworm-slides.html">OpenWorm Annual Meeting</a> for 2021, which featured administrative business as well as updates from our research groups and educational initiatives. Much activity going on inside of the <a href="https://openworm.org/">OpenWorm Foundation</a> -- join the <a href="https://launchpass.com/openworm">OpenWorm Slack</a> or follow <a href="http://www.twitter.com/openworm">OpenWorm on Twitter</a> for more information. <span style="background-color: white;">Below are the slides I presented on progress and the latest activities in the <a href="http://devoworm.weebly.com">DevoWorm</a> group. If anything looks interesting to you, and you would like to contribute, please <a href="mailto:balicea@openworm.org">let me know</a>. Click on any slide to enlarge.</span></span></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiSCWwa91ltjcTngbVzua9BF4ZGnxhy9YOrQgPa6Qs7JsfkUMuDVRK0d1hXd6lYd0DMF3ApeIDEIMc82BZ-f9Zlrse1p5B3SlpQl158C5kaD_Y-AyGXyaainOPoYF5jcUHESsb1RNMpQfY/s720/Presentation+to+OW+General+Meeting.001.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="405" data-original-width="720" height="225" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiSCWwa91ltjcTngbVzua9BF4ZGnxhy9YOrQgPa6Qs7JsfkUMuDVRK0d1hXd6lYd0DMF3ApeIDEIMc82BZ-f9Zlrse1p5B3SlpQl158C5kaD_Y-AyGXyaainOPoYF5jcUHESsb1RNMpQfY/w400-h225/Presentation+to+OW+General+Meeting.001.png" width="400" /></a></div><br /><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh3qxDzjMesw70ye_ijPhjwoUi8MESK8p0gk5P4GnFTi35euiHW-baD20RMcyvqMkzL7_ixgG6QWon2L7cIaQBP16ZzmlmlEWCuYWMkQ1MkZAdhgn_49fQ2FH1SbEsfROFP0miD5DR_9us/s720/Presentation+to+OW+General+Meeting.002.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="405" data-original-width="720" height="225" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh3qxDzjMesw70ye_ijPhjwoUi8MESK8p0gk5P4GnFTi35euiHW-baD20RMcyvqMkzL7_ixgG6QWon2L7cIaQBP16ZzmlmlEWCuYWMkQ1MkZAdhgn_49fQ2FH1SbEsfROFP0miD5DR_9us/w400-h225/Presentation+to+OW+General+Meeting.002.png" width="400" /></a></div><br /><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgfamUhwNRi8nAM8OE8CgyTgXzbB3vE5vs3A9-VQWA4-lrGXl51wFb9FB1Aae7F-x4etr7wIKuAiO56PAjJn8PI8wzzaWnpXWGrbz8B0MGXho0QRXupABV53D9dPUBcrEsq03ZdnkuQO8k/s720/Presentation+to+OW+General+Meeting.003.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="405" data-original-width="720" height="225" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgfamUhwNRi8nAM8OE8CgyTgXzbB3vE5vs3A9-VQWA4-lrGXl51wFb9FB1Aae7F-x4etr7wIKuAiO56PAjJn8PI8wzzaWnpXWGrbz8B0MGXho0QRXupABV53D9dPUBcrEsq03ZdnkuQO8k/w400-h225/Presentation+to+OW+General+Meeting.003.png" width="400" /></a></div><br /><div class="separator" style="clear: both; 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margin-right: 1em;"><img border="0" data-original-height="405" data-original-width="720" height="225" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh0Kq8c34Imvi0LTl1oU1VSf9qWfyKOAXcZx2T2iS8CSqiNvCTspMBFM_P9KIPGChMlFR9fxcJpGNmYeL-SmLko_fhOKjjtEJCWf3lY3EPQNCz3Fux-9f9_8QCSgTH1RI4UlsrNzb1oIpE/w400-h225/Presentation+to+OW+General+Meeting.005.png" width="400" /></a></div><br /><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhj8GLeoX-LCmNjP3DR-2gcujfy5Dyi5T9kYDhG5QNSLt07326PyCaedJKeCB3b2fzK9BT7D6b8fA9mXHgduH6YDm3NGDGOcrJDqFhpj_D_4z6Mg4fdha5OWy56_7aYfn1pQfz4-8CfiSs/s720/Presentation+to+OW+General+Meeting.006.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="405" data-original-width="720" height="225" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhj8GLeoX-LCmNjP3DR-2gcujfy5Dyi5T9kYDhG5QNSLt07326PyCaedJKeCB3b2fzK9BT7D6b8fA9mXHgduH6YDm3NGDGOcrJDqFhpj_D_4z6Mg4fdha5OWy56_7aYfn1pQfz4-8CfiSs/w400-h225/Presentation+to+OW+General+Meeting.006.png" width="400" /></a></div><br /><div class="separator" style="clear: both; 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text-align: center;"><br /></div><div class="separator" style="clear: both; text-align: left;">The last slide is in recognition of <a href="https://docs.openworm.org/fullhistory.html">OpenWorm's 10th anniversary</a>, or at least the first release of OpenWorm 10 years ago this month. Looking forward to what the next 10 years will bring! </div><div class="separator" style="clear: both; text-align: left;"><br /></div><div class="separator" style="clear: both; text-align: left;">But in terms of what the next month will bring (for DevoWorm), we are hosting our second annual <a href="https://syntheticdaisies.blogspot.com/2020/10/hacktoberfest-now-live.html">Hacktoberfest</a>! Check out README files in our pinned repositories on <a href="http://www.github.com/devolearn">DevoLearn</a> and <a href="http://www.github.com/devoworm/digital-bacillaria">devoworm/digital-bacillaria</a> to get started!</div><div class="separator" style="clear: both; text-align: left;"><br /></div><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgx1JMrGDOHIA7XXNSi4WIqT4o7e4p5ke6PlDVzhc8hOKrAxp_xrt-xLUZ5KY7nU8Lz6MXNlT7Pe-WzWxs_X8Xa8fJLfEcAUhHTvFRmPW1mkmiwKxJt55xgnF1DfQd-Nypivr42J5FsGCk/s2263/hf_logo.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="557" data-original-width="2263" height="79" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgx1JMrGDOHIA7XXNSi4WIqT4o7e4p5ke6PlDVzhc8hOKrAxp_xrt-xLUZ5KY7nU8Lz6MXNlT7Pe-WzWxs_X8Xa8fJLfEcAUhHTvFRmPW1mkmiwKxJt55xgnF1DfQd-Nypivr42J5FsGCk/s320/hf_logo.png" width="320" /></a></div>Bradly Aliceahttp://www.blogger.com/profile/06482487682656113637noreply@blogger.com0tag:blogger.com,1999:blog-1792896637814721350.post-43002397359989184242021-08-24T00:22:00.001-05:002021-08-24T00:22:10.153-05:00OREL Medium: Trajectories in Cognitive Science Session @ CogSci 2021<p style="text-align: center;"> </p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhkxeHCY30NRpVtaKIRKHS4sjITIhGyj2fmLfioGT1_TCJgbIDIi5Pvbq6w8jcRR89Q_DED89Fg-SI7HGXk-4vbtlUZ6zGNrtRh8AVKOCWhILqqBR15EXdWSFSPUhGSD7Ketv0zzejr4wg/s1400/1_fK-hInjxRLNHrjSsRLpjZg.jpeg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="787" data-original-width="1400" height="227" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhkxeHCY30NRpVtaKIRKHS4sjITIhGyj2fmLfioGT1_TCJgbIDIi5Pvbq6w8jcRR89Q_DED89Fg-SI7HGXk-4vbtlUZ6zGNrtRh8AVKOCWhILqqBR15EXdWSFSPUhGSD7Ketv0zzejr4wg/w404-h227/1_fK-hInjxRLNHrjSsRLpjZg.jpeg" width="404" /></a></div><div class="separator" style="clear: both; text-align: center;"><br /></div><div class="separator" style="clear: both; text-align: left;"><span style="font-family: arial;">This content was originally posted to the <a href="https://medium.com/orel-group/">Orthogonal Research and Education Lab blog</a> on July 30.</span></div><p></p><p class="go gp cq gq b gr gs gt gu gv gw gx gy gz ha hb hc hd he hf hg hh hi hj hk hl ci dn" data-selectable-paragraph="" id="8f72" style="background-color: white; box-sizing: inherit; color: #292929; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;"><span style="font-family: arial;">Congratulations to Jesse Parent, Avery Lim, Bradly Alicea, and Anusha Sharma for heading up the “Trajectories in Cognitive Science” discussion group, held during the <a class="ei hm" href="https://cognitivesciencesociety.org/cogsci-2021/" rel="noopener" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;">CogSci 2021</a> conference. The event happened in six parts (which we will recap) and is now on YouTube. We are also archiving the slides and reference list on the <a class="ei hm" href="https://osf.io/jv96n/" rel="noopener" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;">Open Science Framework</a> (in progress).</span></p><div class="separator" style="clear: both;"><p class="go gp cq gq b gr gs gt gu gv gw gx gy gz ha hb hc hd he hf hg hh hi hj hk hl ci dn" data-selectable-paragraph="" id="0058" style="background-color: white; box-sizing: inherit; color: #292929; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;"><span style="font-family: arial;">Part I: <a class="ei hm" href="https://youtu.be/U0QFbN1wntM?t=447" rel="noopener" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;">Frontier Map and Cognitive Futures</a>. Presenter: Jesse Parent.</span></p><p class="go gp cq gq b gr gs gt gu gv gw gx gy gz ha hb hc hd he hf hg hh hi hj hk hl ci dn" data-selectable-paragraph="" id="0058" style="background-color: white; box-sizing: inherit; color: #292929; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; text-align: center; word-break: break-word;"></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi1V_SshGeeX2SIGqoZSXg959iZR6mng7Q4dMtSIEY7j3AwPIBR527d1SNpTIZzzViy6u1JLwLMBDGriKzGa_KlNqen6_mhPy6PbjElF81CZRb2nqqKAwUq4s1v2aCnh-0l78qvcAMi_Eo/s1279/1_KTECZgM8AoxXdF58sBPnYQ.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="717" data-original-width="1279" height="237" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi1V_SshGeeX2SIGqoZSXg959iZR6mng7Q4dMtSIEY7j3AwPIBR527d1SNpTIZzzViy6u1JLwLMBDGriKzGa_KlNqen6_mhPy6PbjElF81CZRb2nqqKAwUq4s1v2aCnh-0l78qvcAMi_Eo/w424-h237/1_KTECZgM8AoxXdF58sBPnYQ.png" width="424" /></a></div><p></p><p class="go gp cq gq b gr gs gt gu gv gw gx gy gz ha hb hc hd he hf hg hh hi hj hk hl ci dn" data-selectable-paragraph="" id="ee28" style="background-color: white; box-sizing: inherit; color: #292929; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;"><span style="font-family: arial;">The first part of the session involved an overview of Frontier Maps and the role of maps and visualizations in understanding how ideas form fields of study. Frontier Maps also enable casual learners to get an intellectual grasp on a certain area of study by learning its history and current trends.</span></p><p class="go gp cq gq b gr gs gt gu gv gw gx gy gz ha hb hc hd he hf hg hh hi hj hk hl ci dn" data-selectable-paragraph="" id="47ac" style="background-color: white; box-sizing: inherit; color: #292929; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;"><span style="font-family: arial;">Part II: <a class="ei hm" href="https://youtu.be/U0QFbN1wntM?t=1009" rel="noopener" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;">Adjacent Fu<span>tures</span></a><span>. Presenter: Bradly Alicea.</span></span></p><p class="go gp cq gq b gr gs gt gu gv gw gx gy gz ha hb hc hd he hf hg hh hi hj hk hl ci dn" data-selectable-paragraph="" id="47ac" style="background-color: white; box-sizing: inherit; color: #292929; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; text-align: center; word-break: break-word;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEihlsTNhAQlWsNu1fWT0k6aNY0C0oqpxvsNBGdq0gXfiLXPFJvDN-BesEVO-4snpzbPhwfYMQCHTZRtuRydxia_Dd1qMt1ETMcxMtTEsq0fKA40h85omy_eUoqNeGyLCGoL7Ib4OHw5a08/s1272/1_EKwtoU-B-WBrAcQXLPwYFw.png" imageanchor="1" style="font-family: arial; letter-spacing: -0.048px; margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="721" data-original-width="1272" height="239" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEihlsTNhAQlWsNu1fWT0k6aNY0C0oqpxvsNBGdq0gXfiLXPFJvDN-BesEVO-4snpzbPhwfYMQCHTZRtuRydxia_Dd1qMt1ETMcxMtTEsq0fKA40h85omy_eUoqNeGyLCGoL7Ib4OHw5a08/w423-h239/1_EKwtoU-B-WBrAcQXLPwYFw.png" width="423" /></a></p><p class="go gp cq gq b gr gs gt gu gv gw gx gy gz ha hb hc hd he hf hg hh hi hj hk hl ci dn" data-selectable-paragraph="" id="47ac" style="background-color: white; box-sizing: inherit; color: #292929; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;"><span style="font-family: arial; letter-spacing: -0.003em;">The second talk was given by Bradly Alicea, and involved introducing the idea of Adjacent Futures, which is based on the notion of the </span><a class="ei hm" href="https://www.edge.org/conversation/stuart_a_kauffman-the-adjacent-possible" rel="noopener" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit; font-family: arial; letter-spacing: -0.003em;">adjacent possible</a><span style="font-family: arial; letter-spacing: -0.003em;">. Our focus was on both the possibilities that define scientific discovery and interdisciplinary exploration and the factors (sometimes quite practical) that block combinatorial discovery that often define the boundaries of a given field.</span></p><p class="go gp cq gq b gr gs gt gu gv gw gx gy gz ha hb hc hd he hf hg hh hi hj hk hl ci dn" data-selectable-paragraph="" id="47ac" style="background-color: white; box-sizing: inherit; color: #292929; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;"><span style="font-family: arial; letter-spacing: -0.003em;">Part III:</span><span style="font-family: arial; letter-spacing: -0.003em;"> </span><a class="ei hm" href="https://youtu.be/U0QFbN1wntM?t=1825" rel="noopener" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit; font-family: arial; letter-spacing: -0.003em;">The Place of Development in the History of CogSci</a><span style="font-family: arial; letter-spacing: -0.003em;">. Presenters: Jesse Parent and Anusha Sharma.</span></p><p class="go gp cq gq b gr gs gt gu gv gw gx gy gz ha hb hc hd he hf hg hh hi hj hk hl ci dn" data-selectable-paragraph="" id="47ac" style="background-color: white; box-sizing: inherit; color: #292929; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; text-align: center; word-break: break-word;"></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjvZjwZJVCuw98rQ23sZPP0f0PeiFvYsxrqpq7ovQWIKW-7C49jhzpxrlEY4pCaEe2nK5vLOOoHiGpuH1MyV5gQVZ-9hG09c6nn7w-jGsb1zwidzUQeI5VXsuX_0uRD0zHbMTxGTYk4Sqc/s1280/1_o1db6ksxI0R8aVROhPN9lA.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="719" data-original-width="1280" height="237" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjvZjwZJVCuw98rQ23sZPP0f0PeiFvYsxrqpq7ovQWIKW-7C49jhzpxrlEY4pCaEe2nK5vLOOoHiGpuH1MyV5gQVZ-9hG09c6nn7w-jGsb1zwidzUQeI5VXsuX_0uRD0zHbMTxGTYk4Sqc/w421-h237/1_o1db6ksxI0R8aVROhPN9lA.png" width="421" /></a></div><p></p><p class="go gp cq gq b gr gs gt gu gv gw gx gy gz ha hb hc hd he hf hg hh hi hj hk hl ci dn" data-selectable-paragraph="" id="2e49" style="background-color: white; box-sizing: inherit; color: #292929; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;"><span style="font-family: arial;">This session (brought to us by Jesse Parent and Anusha Sharma) covered the rich history of developmental approaches in Cognitive Science, and how development has served as an alternative to the concept of “static adult minds”. The presentation was an in-depth presentation of the review article “<a class="ei hm" href="https://www.frontiersin.org/articles/10.3389/fpsyg.2019.00895/full" rel="noopener" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;">The Place of Development in the History of Psychology and Cognitive Science</a>” by <a class="ei hm" href="https://www.researchgate.net/profile/Gabriella-Airenti" rel="noopener" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;">Gabriella Airenti</a> (<em class="ie" style="box-sizing: inherit;">Frontiers in Psychology</em>, 10, 895). In the session, we explored the foundational concepts of Piaget as well as longstanding debates such as nature vs. nurture and representationalism vs. brain function.</span></p><div class="separator" style="clear: both;"><p class="go gp cq gq b gr gs gt gu gv gw gx gy gz ha hb hc hd he hf hg hh hi hj hk hl ci dn" data-selectable-paragraph="" id="7c3a" style="background-color: white; box-sizing: inherit; color: #292929; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;"><span style="font-family: arial;">Part IV: <a class="ei hm" href="https://youtu.be/U0QFbN1wntM?t=3598" rel="noopener" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;">Neurodiversity and Cognitive Science</a>. Presenter: Jesse Parent.</span></p><p class="go gp cq gq b gr gs gt gu gv gw gx gy gz ha hb hc hd he hf hg hh hi hj hk hl ci dn" data-selectable-paragraph="" id="7c3a" style="background-color: white; box-sizing: inherit; color: #292929; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; text-align: center; word-break: break-word;"></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgJUffHGi3-OWBLz7Hvr4u5QnWzeyM_xe_mEjvCHsaWIjYIHaas_dSk_G69w1UU66fqNhl8bY6OoE2nyta1Ulzg4DZRnT9oJxkG1_V9hJ9ZMe85YdqHLYWAT1stmK6GhRcP_mgLf5xMt_4/s1280/1_ju3XsCn5dmSLXK0irVSTaA.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="720" data-original-width="1280" height="262" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgJUffHGi3-OWBLz7Hvr4u5QnWzeyM_xe_mEjvCHsaWIjYIHaas_dSk_G69w1UU66fqNhl8bY6OoE2nyta1Ulzg4DZRnT9oJxkG1_V9hJ9ZMe85YdqHLYWAT1stmK6GhRcP_mgLf5xMt_4/w466-h262/1_ju3XsCn5dmSLXK0irVSTaA.png" width="466" /></a></div><p></p><p class="go gp cq gq b gr gs gt gu gv gw gx gy gz ha hb hc hd he hf hg hh hi hj hk hl ci dn" data-selectable-paragraph="" id="c958" style="background-color: white; box-sizing: inherit; color: #292929; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;"><span style="letter-spacing: -0.063px;"><span style="font-family: arial;">The fourth presentation was also by Jesse Parent, and covered the role of Neurodiversity in Cognitive Science. This was a short review of a book called “Neurodiversity Studies: a new critical paradigm”. Neurodiversity covers a number of alternative frameworks for understanding human cognition, including but not limited to queer, feminist, and critical race perspectives. Such perspectives contribute not only to the diversity of views in the field, but also lead to novel intellectual trajectories.</span></span></p><p class="go gp cq gq b gr gs gt gu gv gw gx gy gz ha hb hc hd he hf hg hh hi hj hk hl ci dn" data-selectable-paragraph="" id="c958" style="background-color: white; box-sizing: inherit; color: #292929; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;"><span style="font-family: arial;">Part V: <a class="ei hm" href="https://youtu.be/U0QFbN1wntM?t=3921" rel="noopener" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;">Trajectories of Interest in Developmental Psychobiology</a>. Presenter: Avery Lim.</span></p><p class="go gp cq gq b gr gs gt gu gv gw gx gy gz ha hb hc hd he hf hg hh hi hj hk hl ci dn" data-selectable-paragraph="" id="a5ab" style="background-color: white; box-sizing: inherit; color: #292929; font-family: charter, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 21px; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; text-align: center; word-break: break-word;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiUOrWGy5jST0HyqqnL1aKM1wASXuliEsGCweOerLVxHNZ8CGz6YdydpRtbfRdJ5ZDiOyXDI6xwdydFkDTdCjc6VYVbnhe0rydalpvQKlDErnYEQVQW2fpDrSKbcU5WQXZ4KCdZ5Ym27Qg/s1282/1_envp7d6h618NSV_UtW-63A.png" imageanchor="1" style="font-family: "Times New Roman"; font-size: medium; letter-spacing: -0.048px; margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="720" data-original-width="1282" height="259" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiUOrWGy5jST0HyqqnL1aKM1wASXuliEsGCweOerLVxHNZ8CGz6YdydpRtbfRdJ5ZDiOyXDI6xwdydFkDTdCjc6VYVbnhe0rydalpvQKlDErnYEQVQW2fpDrSKbcU5WQXZ4KCdZ5Ym27Qg/w461-h259/1_envp7d6h618NSV_UtW-63A.png" width="461" /></a></p><p class="go gp cq gq b gr gs gt gu gv gw gx gy gz ha hb hc hd he hf hg hh hi hj hk hl ci dn" data-selectable-paragraph="" id="a5ab" style="background-color: white; box-sizing: inherit; color: #292929; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;"><span style="font-family: arial;">Avery Lim presented on a number of possible trajectories for developmental psychobiology considered broadly. This possibility space (discussed in Part II) includes building off of the study of phenomenology such as developmental critical periods or computational models of psychophysiology. A number of open questions were also posed that motivated our discussions in Part VI.</span></p><p class="go gp cq gq b gr gs gt gu gv gw gx gy gz ha hb hc hd he hf hg hh hi hj hk hl ci dn" data-selectable-paragraph="" id="589b" style="background-color: white; box-sizing: inherit; color: #292929; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;"><span style="font-family: arial;">Part VI: <a class="ei hm" href="https://youtu.be/U0QFbN1wntM?t=4352" rel="noopener" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;">Open Discussion</a>!</span></p><p class="go gp cq gq b gr gs gt gu gv gw gx gy gz ha hb hc hd he hf hg hh hi hj hk hl ci dn" data-selectable-paragraph="" id="589b" style="background-color: white; box-sizing: inherit; color: #292929; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; text-align: center; word-break: break-word;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhwKlEcLTLJgOGrv3GeyZauoyi-S0Q-qeRIozv2UjQSWHHhDnrcPXGraCw5mEK3Ipg6dj8IlmaJbTmlGmC07CIYkdFpqsrIcLQ6BE4GwhGttwjQnoRtUc7P_-D7ePHKZT9vvljcQIwf3uc/s1278/1_Q7fqnOysjntbl4OOECvGPg.png" imageanchor="1" style="letter-spacing: -0.048px; margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="718" data-original-width="1278" height="274" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhwKlEcLTLJgOGrv3GeyZauoyi-S0Q-qeRIozv2UjQSWHHhDnrcPXGraCw5mEK3Ipg6dj8IlmaJbTmlGmC07CIYkdFpqsrIcLQ6BE4GwhGttwjQnoRtUc7P_-D7ePHKZT9vvljcQIwf3uc/w486-h274/1_Q7fqnOysjntbl4OOECvGPg.png" width="486" /></a></p><p class="go gp cq gq b gr gs gt gu gv gw gx gy gz ha hb hc hd he hf hg hh hi hj hk hl ci dn" data-selectable-paragraph="" id="589b" style="background-color: white; box-sizing: inherit; color: #292929; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;"><span style="font-family: arial;"><span style="letter-spacing: -0.063px;">If you are interested in discussing these topics further, you might be interested in joining the </span><a class="ei hm" href="https://launchpass.com/orthogonal-research" rel="noopener" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit; letter-spacing: -0.063px;">Orthogonal Lab Slack</a><span style="letter-spacing: -0.063px;"> or the </span><a class="ei hm" href="https://discord.gg/DT6CR6kQ" rel="noopener" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit; letter-spacing: -0.063px;">Computational Critical Periods Discord</a><span style="letter-spacing: -0.063px;">. You can also catch </span><a class="ei hm" href="https://www.youtube.com/playlist?list=PL4RJ4xCetB63f4DkdrrysVZr5LlVzmfF8" rel="noopener" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit; letter-spacing: -0.063px;">Saturday Morning NeuroSim weekly on YouTube</a><span style="letter-spacing: -0.063px;">, or </span><a class="ei hm" href="mailto:bradly.alicea@outlook.com" rel="noopener" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit; letter-spacing: -0.063px;">get in contact</a><span style="letter-spacing: -0.063px;"> to get on our mailing list and join in person.</span></span></p></div></div>Bradly Aliceahttp://www.blogger.com/profile/06482487682656113637noreply@blogger.com1tag:blogger.com,1999:blog-1792896637814721350.post-92083379461304214432021-06-04T01:22:00.000-05:002021-06-04T01:22:00.423-05:00Dispatches from the Emergent Interaction Workshop<p> <span style="font-size: medium;">This content has been cross-posted at the Orthogonal Lab Medium.</span></p><p><br /></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj38ul8ubsdtU_srC6oEnPeaSdkxWu0xVshcEORfw3aAg_x5Uj-r0EGSTjMlHN4IBhHSTfr7ZTb5mG2CcGmuDd6gFVdQ2H28iQqDqi0n-pj-qHcPDUuLYIMNrOmRRVwTcAfnJ11MBtj4fI/s1239/1_nNIdWPwjHLnzAnxrLwKP9w.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="1239" data-original-width="1188" height="474" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj38ul8ubsdtU_srC6oEnPeaSdkxWu0xVshcEORfw3aAg_x5Uj-r0EGSTjMlHN4IBhHSTfr7ZTb5mG2CcGmuDd6gFVdQ2H28iQqDqi0n-pj-qHcPDUuLYIMNrOmRRVwTcAfnJ11MBtj4fI/w455-h474/1_nNIdWPwjHLnzAnxrLwKP9w.png" width="455" /></a></div><br /><p></p><p><span style="font-size: medium;"><span style="background-color: white; color: #292929; font-family: charter, Georgia, Cambria, "Times New Roman", Times, serif; letter-spacing: -0.063px;">Last month, the Orthogonal Lab was represented at the </span><a class="cj ik" href="https://emergentinteraction.github.io/" rel="noopener nofollow" style="-webkit-tap-highlight-color: transparent; background-color: white; box-sizing: inherit; font-family: charter, Georgia, Cambria, "Times New Roman", Times, serif; letter-spacing: -0.063px;">Emergent Interaction</a><span style="background-color: white; color: #292929; font-family: charter, Georgia, Cambria, "Times New Roman", Times, serif; letter-spacing: -0.063px;"> Workshop (part of SIGCHI 2021). We contributed a paper titled “</span><a class="cj ik" href="https://emergentinteraction.github.io/assets/allostasis_machines.pdf" rel="noopener nofollow" style="-webkit-tap-highlight-color: transparent; background-color: white; box-sizing: inherit; font-family: charter, Georgia, Cambria, "Times New Roman", Times, serif; letter-spacing: -0.063px;">Allostasis Machines: a model for understanding internal states and technological environments</a><span style="background-color: white; color: #292929; font-family: charter, Georgia, Cambria, "Times New Roman", Times, serif; letter-spacing: -0.063px;">”, with a </span><a class="cj ik" href="https://www.youtube.com/watch?v=KgSVcAv5LZc&t=47s" rel="noopener nofollow" style="-webkit-tap-highlight-color: transparent; background-color: white; box-sizing: inherit; font-family: charter, Georgia, Cambria, "Times New Roman", Times, serif; letter-spacing: -0.063px;">companion presentation now on YouTube</a><span style="background-color: white; color: #292929; font-family: charter, Georgia, Cambria, "Times New Roman", Times, serif; letter-spacing: -0.063px;">. Thanks go to Bradly Alicea, Daniela Cialfi, Anson Lim, and Jesse Parent for their contribution. We are planning an expanded version of this work with Rishabh Chakraborty that will demonstrate Allostasis Machines as a Reinforcement Learning implementation.</span></span></p><p><span style="font-size: medium;"><span style="background-color: white; color: #292929; font-family: charter, Georgia, Cambria, "Times New Roman", Times, serif; letter-spacing: -0.063px;">The subtitle of this workshop was “Complexity, Dynamics, and Enaction in HCI”. Therefore, the focus was on advancing measurement and theory, in addition to better characterize complexity in the field of Human-Computer Interaction. The four-hour long session was </span><a class="cj ik" href="https://youtu.be/O1XB3f_bHg4?t=5157" rel="noopener nofollow" style="-webkit-tap-highlight-color: transparent; background-color: white; box-sizing: inherit; font-family: charter, Georgia, Cambria, "Times New Roman", Times, serif; letter-spacing: -0.063px;">summarized in our weekly meeting on May 22</a><span style="background-color: white; color: #292929; font-family: charter, Georgia, Cambria, "Times New Roman", Times, serif; letter-spacing: -0.063px;">. I have also provided supplemental readings in four workshop-related categories at the bottom of this post.</span></span></p><p style="text-align: center;"></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgFy77hcMTapou8E7PfK-hP2zYIYwklaPYLURK5eeR-eY6DECUULomc82ew-Ty_rVcrFwPIV9dhrXuGUSE9nUA0vOalxTylhJ1fAc-yfyqSSTe1QEx5pM2thd7ZE9LDdmoCdVi3o4uTXmg/s1920/1_E3IqUQIo9RUM-7Y9O7irgg.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="1080" data-original-width="1920" height="312" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgFy77hcMTapou8E7PfK-hP2zYIYwklaPYLURK5eeR-eY6DECUULomc82ew-Ty_rVcrFwPIV9dhrXuGUSE9nUA0vOalxTylhJ1fAc-yfyqSSTe1QEx5pM2thd7ZE9LDdmoCdVi3o4uTXmg/w556-h312/1_E3IqUQIo9RUM-7Y9O7irgg.png" width="556" /></a></div><span style="background-color: white; color: #292929; font-family: charter, Georgia, Cambria, "Times New Roman", Times, serif; letter-spacing: -0.063px; text-align: start;"><span style="font-size: medium;">Overview of the Emergent Interaction Miro board.</span></span><p></p><p style="text-align: center;"></p><div style="text-align: start;"><span style="font-size: medium;"><span style="background-color: white; color: #292929; font-family: charter, Georgia, Cambria, "Times New Roman", Times, serif; letter-spacing: -0.063px;">There were six other papers made available before the session. Two of the most interesting to the Orthogonal Lab group are “</span><a class="cj ik" href="https://emergentinteraction.github.io/assets/fields_of_affordances.docx" rel="noopener nofollow" style="-webkit-tap-highlight-color: transparent; background-color: white; box-sizing: inherit; font-family: charter, Georgia, Cambria, "Times New Roman", Times, serif; letter-spacing: -0.063px;">Fields of Affordances and Human Computer Interaction</a><span style="background-color: white; color: #292929; font-family: charter, Georgia, Cambria, "Times New Roman", Times, serif; letter-spacing: -0.063px;">” by Jelle Bruineberg and “</span><a class="cj ik" href="https://emergentinteraction.github.io/assets/social_acceptability.pdf" rel="noopener nofollow" style="-webkit-tap-highlight-color: transparent; background-color: white; box-sizing: inherit; font-family: charter, Georgia, Cambria, "Times New Roman", Times, serif; letter-spacing: -0.063px;">Simulating Social Acceptability With Agent-based Modeling</a><span style="background-color: white; color: #292929; font-family: charter, Georgia, Cambria, "Times New Roman", Times, serif; letter-spacing: -0.063px;">” by Alarith Uhde and Marc Hassenzahl.</span></span></div><div style="text-align: start;"><span style="background-color: white; color: #292929; font-family: charter, Georgia, Cambria, "Times New Roman", Times, serif; letter-spacing: -0.063px;"><span style="font-size: medium;"><br /></span></span></div><div style="text-align: start;"><span style="font-size: medium;"><span style="background-color: white; color: #292929; font-family: charter, Georgia, Cambria, "Times New Roman", Times, serif; letter-spacing: -0.063px;">The Emergent Interaction utilized Zoom, Slack, and a Miro board to enable discussion during the session. Check out the overview paper titled “</span><a class="cj ik" href="https://emergentinteraction.github.io/assets/complexity_chi.pdf" rel="noopener nofollow" style="-webkit-tap-highlight-color: transparent; background-color: white; box-sizing: inherit; font-family: charter, Georgia, Cambria, "Times New Roman", Times, serif; letter-spacing: -0.063px;">Emergent Interaction: Complexity, Dynamics, and Enaction in HCI</a><span style="background-color: white; color: #292929; font-family: charter, Georgia, Cambria, "Times New Roman", Times, serif; letter-spacing: -0.063px;">” for more information.</span></span></div><div style="text-align: start;"><span style="background-color: white; color: #292929; font-family: charter, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 21px; letter-spacing: -0.063px;"><br /></span></div><div style="text-align: center;"><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgIcDsRY-cEaiDwbOkF24SUwWgRglHSoNAuKeTUJ5d4wyFEn0OUMa32CyrM35jhuv_n5jnBlZS1WOto_VoV6SeeFSMukpN8g_Px1GP-SfU9nbC949ZROqrfMTOYSdod4Lq7KGmaET6GxOc/s967/1_5R7KidAxXl-gF_Z8ONIkVg.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="708" data-original-width="967" height="335" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgIcDsRY-cEaiDwbOkF24SUwWgRglHSoNAuKeTUJ5d4wyFEn0OUMa32CyrM35jhuv_n5jnBlZS1WOto_VoV6SeeFSMukpN8g_Px1GP-SfU9nbC949ZROqrfMTOYSdod4Lq7KGmaET6GxOc/w458-h335/1_5R7KidAxXl-gF_Z8ONIkVg.png" width="458" /></a></div><span style="background-color: white; color: #292929; font-family: charter, Georgia, Cambria, "Times New Roman", Times, serif; letter-spacing: -0.063px; text-align: start;"><span style="font-size: medium;">Testing, 1, 2, Emergent T-shirt….</span></span></div><div style="text-align: center;"><div style="text-align: start;"><span style="color: #292929; font-family: charter, Georgia, Cambria, Times New Roman, Times, serif; font-size: medium;"><span style="letter-spacing: -0.063px;"><br /></span></span></div><div style="text-align: start;"><span style="font-size: medium;"><span style="background-color: white; color: #292929; font-family: charter, Georgia, Cambria, "Times New Roman", Times, serif; letter-spacing: -0.063px;">There were a number of interesting and innovative topics discussed in the workshop. Dynamical approaches came up several times, along with topics such as multifractality, attractor analysis, and co-evolutionary experimental design. For more information regarding the first two topics, check out Alan Dix’s blog on </span><a class="cj ik" href="https://alandix.com/statistics/" rel="noopener nofollow" style="-webkit-tap-highlight-color: transparent; background-color: white; box-sizing: inherit; font-family: charter, Georgia, Cambria, "Times New Roman", Times, serif; letter-spacing: -0.063px;">Making Sense of Quantitative Data</a><span style="background-color: white; color: #292929; font-family: charter, Georgia, Cambria, "Times New Roman", Times, serif; letter-spacing: -0.063px;">, and Dan Bennett’s preprint “</span><a class="cj ik" href="https://psyarxiv.com/tq53k/" rel="noopener nofollow" style="-webkit-tap-highlight-color: transparent; background-color: white; box-sizing: inherit; font-family: charter, Georgia, Cambria, "Times New Roman", Times, serif; letter-spacing: -0.063px;">Multifractal Mice: Measuring Task Engagement and Readiness-to-hand via Hand Movement</a><span style="background-color: white; color: #292929; font-family: charter, Georgia, Cambria, "Times New Roman", Times, serif; letter-spacing: -0.063px;">”.</span></span></div><div style="text-align: start;"><span style="background-color: white; color: #292929; font-family: charter, Georgia, Cambria, "Times New Roman", Times, serif; letter-spacing: -0.063px;"><span style="font-size: medium;"><br /></span></span></div><div style="text-align: start;"><span style="font-size: medium;"><a class="cj ik" href="https://scholar.google.com/citations?user=uKd8pmUAAAAJ&hl=en" rel="noopener nofollow" style="-webkit-tap-highlight-color: transparent; background-color: white; box-sizing: inherit; font-family: charter, Georgia, Cambria, "Times New Roman", Times, serif; letter-spacing: -0.063px;">Tom Froese</a><span style="background-color: white; color: #292929; font-family: charter, Georgia, Cambria, "Times New Roman", Times, serif; letter-spacing: -0.063px;"> presented on his Enactive Artificial Intelligence and HCI work. His Google Scholar profile features some really interesting work that cuts across the worlds of Artificial Life, Cybernetics, and Cognitive Science, but his workshop topic was how modern Machine Learning approaches are insufficiently embodied. I have posted references to two of his key works (workshop-wise) in the Further Readings section of this post.</span></span></div><div style="text-align: start;"><span style="background-color: white; color: #292929; font-family: charter, Georgia, Cambria, "Times New Roman", Times, serif; letter-spacing: -0.063px;"><span style="font-size: medium;"><br /></span></span></div><div style="text-align: start;"><span style="font-size: medium;"><span style="background-color: white; color: #292929; font-family: charter, Georgia, Cambria, "Times New Roman", Times, serif; letter-spacing: -0.063px;">Later, </span><a class="cj ik" href="https://www.cardiff.ac.uk/people/view/634369-eslambolchilar-parisa" rel="noopener nofollow" style="-webkit-tap-highlight-color: transparent; background-color: white; box-sizing: inherit; font-family: charter, Georgia, Cambria, "Times New Roman", Times, serif; letter-spacing: -0.063px;">Parisa Eslambolchilar</a><span style="background-color: white; color: #292929; font-family: charter, Georgia, Cambria, "Times New Roman", Times, serif; letter-spacing: -0.063px;"> presented on first-order closed-loop feedback taking the form of sensor-based human interaction loops. She reviewed some of the things she developed in her Doctoral dissertation, then lead us into her more recent work. Learn more by reading “</span><a class="cj ik" href="http://ftp.dcs.glasgow.ac.uk/~rod/publications/EslMur09.pdf" rel="noopener nofollow" style="-webkit-tap-highlight-color: transparent; background-color: white; box-sizing: inherit; font-family: charter, Georgia, Cambria, "Times New Roman", Times, serif; letter-spacing: -0.063px;">A Model-Based Approach to Analysis and Calibration of Sensor-based Human Interaction Loops</a><span style="background-color: white; color: #292929; font-family: charter, Georgia, Cambria, "Times New Roman", Times, serif; letter-spacing: -0.063px;">”.</span></span></div><div style="text-align: start;"><span style="background-color: white; color: #292929; font-family: charter, Georgia, Cambria, "Times New Roman", Times, serif; letter-spacing: -0.063px;"><span style="font-size: medium;"><br /></span></span></div><div style="text-align: start;"><span style="font-size: medium;"><span style="background-color: white; color: #292929; font-family: charter, Georgia, Cambria, "Times New Roman", Times, serif; letter-spacing: -0.063px;">Then, </span><a class="cj ik" href="https://people.eng.unimelb.edu.au/vkostakos/" rel="noopener nofollow" style="-webkit-tap-highlight-color: transparent; background-color: white; box-sizing: inherit; font-family: charter, Georgia, Cambria, "Times New Roman", Times, serif; letter-spacing: -0.063px;">Vassilis Kostakos</a><span style="background-color: white; color: #292929; font-family: charter, Georgia, Cambria, "Times New Roman", Times, serif; letter-spacing: -0.063px;"> discussed his work on modeling interactions between technology users (or users and interfaces) as a complex system. He utilized the “</span><a class="cj ik" href="http://causalpatterns.org/resources/ecosystems/pdfs/s6_res_lynxhare.pdf" rel="noopener nofollow" style="-webkit-tap-highlight-color: transparent; background-color: white; box-sizing: inherit; font-family: charter, Georgia, Cambria, "Times New Roman", Times, serif; letter-spacing: -0.063px;">lynx-hare</a><span style="background-color: white; color: #292929; font-family: charter, Georgia, Cambria, "Times New Roman", Times, serif; letter-spacing: -0.063px;">” predator-prey analogy, inspired by </span><a class="cj ik" href="https://en.wikipedia.org/wiki/Lotka%E2%80%93Volterra_equations" rel="noopener nofollow" style="-webkit-tap-highlight-color: transparent; background-color: white; box-sizing: inherit; font-family: charter, Georgia, Cambria, "Times New Roman", Times, serif; letter-spacing: -0.063px;">Lotka-Volterra</a><span style="background-color: white; color: #292929; font-family: charter, Georgia, Cambria, "Times New Roman", Times, serif; letter-spacing: -0.063px;"> co-evolutionary dynamics. Read more in this paper published last year in </span><em class="iz" style="background-color: white; box-sizing: inherit; color: #292929; font-family: charter, Georgia, Cambria, "Times New Roman", Times, serif; letter-spacing: -0.063px;">Human-Computer Interaction</em><span style="background-color: white; color: #292929; font-family: charter, Georgia, Cambria, "Times New Roman", Times, serif; letter-spacing: -0.063px;">: “</span><a class="cj ik" href="https://people.eng.unimelb.edu.au/vkostakos/files/papers/hci20.pdf" rel="noopener nofollow" style="-webkit-tap-highlight-color: transparent; background-color: white; box-sizing: inherit; font-family: charter, Georgia, Cambria, "Times New Roman", Times, serif; letter-spacing: -0.063px;">Modeling interaction as a complex system</a><span style="background-color: white; color: #292929; font-family: charter, Georgia, Cambria, "Times New Roman", Times, serif; letter-spacing: -0.063px;">”.</span></span></div><div style="text-align: start;"><span style="background-color: white; color: #292929; font-family: charter, Georgia, Cambria, "Times New Roman", Times, serif; letter-spacing: -0.063px;"><span style="font-size: medium;"><br /></span></span></div><div style="text-align: start;"><span style="font-size: medium;"><span style="background-color: white; color: #292929; font-family: charter, Georgia, Cambria, "Times New Roman", Times, serif; letter-spacing: -0.063px;">Emergent Interaction is now on Twitter! </span><a class="cj ik" href="https://twitter.com/emergentHCI" rel="noopener nofollow" style="-webkit-tap-highlight-color: transparent; background-color: white; box-sizing: inherit; font-family: charter, Georgia, Cambria, "Times New Roman", Times, serif; letter-spacing: -0.063px;">Give them a follow</a><span style="background-color: white; color: #292929; font-family: charter, Georgia, Cambria, "Times New Roman", Times, serif; letter-spacing: -0.063px;"> to join the discussion.</span></span></div><div style="text-align: start;"><span style="background-color: white; color: #292929; font-family: charter, Georgia, Cambria, "Times New Roman", Times, serif; font-size: 21px; letter-spacing: -0.063px;"><br /></span></div><div style="text-align: center;"><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh1TDqwP2BnAKh7ijuYG6j9tOc18Y0twW_IvUsP5Mxn6TdcmG31J2op1PbpLB-J2I7yllscDd_FK6IquYBwvLw1myd7iLbJwV7AYh5RoN-e1EVtZtfs-9v_Zd1tV_2YphljMZcSPLI0hR8/s1697/1_XwVWhh3ot5F7T0r0tojPzA.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="965" data-original-width="1697" height="326" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh1TDqwP2BnAKh7ijuYG6j9tOc18Y0twW_IvUsP5Mxn6TdcmG31J2op1PbpLB-J2I7yllscDd_FK6IquYBwvLw1myd7iLbJwV7AYh5RoN-e1EVtZtfs-9v_Zd1tV_2YphljMZcSPLI0hR8/w574-h326/1_XwVWhh3ot5F7T0r0tojPzA.png" width="574" /></a></div></div></div><p></p><p class="hm hn ez ho b hp hq hr hs ht hu hv hw hx hy hz ia ib ic id ie if ig ih ii ij er cx" data-selectable-paragraph="" id="13a7" style="background-color: white; box-sizing: inherit; color: #292929; font-family: charter, Georgia, Cambria, "Times New Roman", Times, serif; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;"><span style="font-size: medium;"><span class="ho jc" style="box-sizing: inherit; font-weight: 700;">Further Reading: </span>Measurement techniques.</span></p><p class="hm hn ez ho b hp hq hr hs ht hu hv hw hx hy hz ia ib ic id ie if ig ih ii ij er cx" data-selectable-paragraph="" id="13a7" style="background-color: white; box-sizing: inherit; color: #292929; font-family: charter, Georgia, Cambria, "Times New Roman", Times, serif; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;"><span style="font-size: medium;"><span style="letter-spacing: -0.003em;">Rebout, N., Lone, J-C., De Marco, A., Cozzolino, R., Lemasson, A., and Thierry, B. (2021).</span><span style="letter-spacing: -0.003em;"> </span><a class="cj ik" href="https://doi.org/10.1098/rsos.200895" rel="noopener nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit; letter-spacing: -0.003em;">Measuring complexity in organisms and organizations</a><span style="letter-spacing: -0.003em;">.</span><span style="letter-spacing: -0.003em;"> </span><em class="iz" style="box-sizing: inherit; letter-spacing: -0.003em;">Royal Society Open Science</em><span style="letter-spacing: -0.003em;">, 8, 200895.</span></span></p><div style="text-align: center;"><div><div style="text-align: left;"><p class="hm hn ez ho b hp hq hr hs ht hu hv hw hx hy hz ia ib ic id ie if ig ih ii ij er cx" data-selectable-paragraph="" id="f221" style="background-color: white; box-sizing: inherit; color: #292929; font-family: charter, Georgia, Cambria, "Times New Roman", Times, serif; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;"><span style="font-size: medium;">Zhou, Q., Chua, C-C., Knibbe, J., Goncalves, J., and Velloso, E. (2021). <a class="cj ik" href="https://dl.acm.org/doi/10.1145/3411764.3445804" rel="noopener nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;">Dance and Choreography in HCI: A Two-Decade Retrospective</a>. <em class="iz" style="box-sizing: inherit;">Proceedings of CHI</em>, 262, 1–14. <a class="cj ik" href="https://www.youtube.com/watch?v=p030qXf3Wlg" rel="noopener nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;">Video</a></span></p><p class="hm hn ez ho b hp hq hr hs ht hu hv hw hx hy hz ia ib ic id ie if ig ih ii ij er cx" data-selectable-paragraph="" id="cc0b" style="background-color: white; box-sizing: inherit; color: #292929; font-family: charter, Georgia, Cambria, "Times New Roman", Times, serif; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;"><span style="font-size: medium;"><span class="ho jc" style="box-sizing: inherit; font-weight: 700;">Further Reading:</span> Enactive Approaches to Artificial Systems.</span></p><p class="hm hn ez ho b hp hq hr hs ht hu hv hw hx hy hz ia ib ic id ie if ig ih ii ij er cx" data-selectable-paragraph="" id="ee27" style="background-color: white; box-sizing: inherit; color: #292929; font-family: charter, Georgia, Cambria, "Times New Roman", Times, serif; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;"><span style="font-size: medium;">Froese, T. and Ziemke, T. (2009). <a class="cj ik" href="https://www.sciencedirect.com/science/article/pii/S0004370208002105" rel="noopener nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;">Enactive artificial intelligence: Investigating the systemic organization of life and mind</a>. <em class="iz" style="box-sizing: inherit;">Artificial Intelligence</em>, 173, 466–500.</span></p><p class="hm hn ez ho b hp hq hr hs ht hu hv hw hx hy hz ia ib ic id ie if ig ih ii ij er cx" data-selectable-paragraph="" id="66d7" style="background-color: white; box-sizing: inherit; color: #292929; font-family: charter, Georgia, Cambria, "Times New Roman", Times, serif; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;"><span style="font-size: medium;">Froese, T., McGann, M., Bigge, W., Spiers, A., and Seth, A.K. (2012). <a class="cj ik" href="https://ieeexplore.ieee.org/document/6060819" rel="noopener nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;">The Enactive Torch: A New Tool for the Science of Perception</a>. <em class="iz" style="box-sizing: inherit;">IEEE Transactions on Haptics</em>, 5(4), 365–375.</span></p><p class="hm hn ez ho b hp hq hr hs ht hu hv hw hx hy hz ia ib ic id ie if ig ih ii ij er cx" data-selectable-paragraph="" id="569e" style="background-color: white; box-sizing: inherit; color: #292929; font-family: charter, Georgia, Cambria, "Times New Roman", Times, serif; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;"><span style="font-size: medium;"><span class="ho jc" style="box-sizing: inherit; font-weight: 700;">Further Reading: </span>Agent-based Modeling approaches.</span></p><p class="hm hn ez ho b hp hq hr hs ht hu hv hw hx hy hz ia ib ic id ie if ig ih ii ij er cx" data-selectable-paragraph="" id="07e1" style="background-color: white; box-sizing: inherit; color: #292929; font-family: charter, Georgia, Cambria, "Times New Roman", Times, serif; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;"><span style="font-size: medium;">Bonabeau, E. (2002). <a class="cj ik" href="https://www.pnas.org/content/99/suppl_3/7280" rel="noopener nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;">Agent-based modeling: Methods and techniques for<br style="box-sizing: inherit;" />simulating human systems</a>. <em class="iz" style="box-sizing: inherit;">PNAS</em>, 99(3), 7280–7287.</span></p><p class="hm hn ez ho b hp hq hr hs ht hu hv hw hx hy hz ia ib ic id ie if ig ih ii ij er cx" data-selectable-paragraph="" id="83d1" style="background-color: white; box-sizing: inherit; color: #292929; font-family: charter, Georgia, Cambria, "Times New Roman", Times, serif; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;"><span style="font-size: medium;">Grimm, V., Revilla, E., Berger, U., Jeltsch, F., Mooij, W.M., Railsback, S.F., Thulke, H-H., Weiner, J., Wiegand, T., and DeAngelis, D.L. (2005).<br style="box-sizing: inherit;" /><a class="cj ik" href="https://pubmed.ncbi.nlm.nih.gov/16284171/" rel="noopener nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;">Pattern-Oriented Modeling of Agent-Based Complex Systems: Lessons from Ecology</a>. <em class="iz" style="box-sizing: inherit;">Science</em>, 310, 987.</span></p><p class="hm hn ez ho b hp hq hr hs ht hu hv hw hx hy hz ia ib ic id ie if ig ih ii ij er cx" data-selectable-paragraph="" id="def8" style="background-color: white; box-sizing: inherit; color: #292929; font-family: charter, Georgia, Cambria, "Times New Roman", Times, serif; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;"><span style="font-size: medium;"><span class="ho jc" style="box-sizing: inherit; font-weight: 700;">Further Reading:</span> Criticalities and Characterizing Systems.</span></p><p class="hm hn ez ho b hp hq hr hs ht hu hv hw hx hy hz ia ib ic id ie if ig ih ii ij er cx" data-selectable-paragraph="" id="1341" style="background-color: white; box-sizing: inherit; color: #292929; font-family: charter, Georgia, Cambria, "Times New Roman", Times, serif; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;"><span style="font-size: medium;">Dotov, D.G., Nie, L., and Chemero, A. (2010). <a class="cj ik" href="https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0009433" rel="noopener nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;">A Demonstration of the Transition from Ready-to-Hand to Unready-to-Hand</a>. <em class="iz" style="box-sizing: inherit;">PLoS One</em>, 5(3), e9433.</span></p><p class="hm hn ez ho b hp hq hr hs ht hu hv hw hx hy hz ia ib ic id ie if ig ih ii ij er cx" data-selectable-paragraph="" id="db33" style="background-color: white; box-sizing: inherit; color: #292929; font-family: charter, Georgia, Cambria, "Times New Roman", Times, serif; letter-spacing: -0.003em; line-height: 32px; margin: 2em 0px -0.46em; word-break: break-word;"><span style="font-size: medium;">Kelso, J.A.S. (2021). <a class="cj ik" href="https://www.mdpi.com/1099-4300/23/5/537" rel="noopener nofollow" style="-webkit-tap-highlight-color: transparent; box-sizing: inherit;">Unifying Large-and Small-Scale Theories of Coordination</a>. <em class="iz" style="box-sizing: inherit;">Entropy</em>, 23(5), 537.</span></p></div></div></div>Bradly Aliceahttp://www.blogger.com/profile/06482487682656113637noreply@blogger.com1tag:blogger.com,1999:blog-1792896637814721350.post-78179092661410538072021-05-02T14:37:00.007-05:002021-08-19T15:41:36.767-05:00DevoLearn (Open-source) Maintenance and Evangelism<p> 2021 has been a busy year for the <a href="https://github.com/DevoLearn/">DevoLearn</a> initiative. Not only has <a href="https://mayukhdeb.github.io/">Mayukh Deb</a> been busy maintaining and generating new versions of the <a href="https://pypi.org/project/devolearn/">DevoLearn pre-trained model</a>, but I (<a href="https://bradly-alicea.weebly.com/">Bradly Alicea)</a> has been engaging in <a href="https://en.wikipedia.org/wiki/Technology_evangelist">technology evangelism</a> to advance awareness and involvement in the initiative. The DevoLearn pre-trained model software (<a href="https://thenode.biologists.com/pre-trained-machine-learning-models-for-developmental-biology/uncategorized/">for <i>C. elegans</i> embryogenesis</a>) is now at version 0.3.0, and has garnered <a href="https://libraries.io/github/DevoLearn/devolearn/contributors">12 contributors making 165 commits</a> (largely since January 2021). Our involvement in <a href="https://summerofcode.withgoogle.com/">Google Summer of Code</a> has bolstered many of these contributions. While our popularity is currently limited, we are trying to spread the word.</p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiU5WnDXrKTxhP_ESNMXCj1WnAJUg9GeYoFS_CGF5nCZoRHVG6EfaPY8ZzLLJ6hVYaOEBX6T7uXzsN-7QAAvGC6TXVAKgqUvNkmgYc_-hzSRyieWJ2q5qjxFpvR8IR48pHbPAQjrNmH6vE/s660/EwlS5HRXMAI1WoD.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="596" data-original-width="660" height="361" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiU5WnDXrKTxhP_ESNMXCj1WnAJUg9GeYoFS_CGF5nCZoRHVG6EfaPY8ZzLLJ6hVYaOEBX6T7uXzsN-7QAAvGC6TXVAKgqUvNkmgYc_-hzSRyieWJ2q5qjxFpvR8IR48pHbPAQjrNmH6vE/w400-h361/EwlS5HRXMAI1WoD.png" width="400" /></a></div><p>To that end, we have presented two versions of a promotional talk on using DevoLearn for facilitating Computational Developmental Biology research and education. The first presentation (<a href="https://github.com/devoworm/Proposals-Public-Lectures/blob/master/Open%20Education%20Conference/Abstract-Slides.md">DevoLearn: Engaging learners with Computational Developmental Biology</a>) is a flash talk given to the <a href="https://www.cos.io/education-reseach-2021-virtual-unconference">OSF Education Un-conference on Open Scholarship Practices in Education Research</a>, held in February. The second presentation was a longer (15-minute) presentation to the <a href="https://neuroinformatics.incf.org/">INCF Assembly</a> (<a href="https://www.youtube.com/watch?v=-Kg3rgjFCnc&t=2s">DevoLearn: a platform for open Developmental Data Science, Machine Learning, and Education</a>), held in April.</p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgIWqdsdqoRZpy-8JZgR3LjW7UdHraC0F98LTMPJKbyk-RL-MC59CtIyCHt_4ItYY4PorwYhdRZ7nkUskH4Z-aUtcvd5ZACl9unFDorhpqO6P5Oq5vHVNupGwa3ZI5ZNcNKIRhdY-qk9h0/s960/Slide1.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="540" data-original-width="960" height="225" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgIWqdsdqoRZpy-8JZgR3LjW7UdHraC0F98LTMPJKbyk-RL-MC59CtIyCHt_4ItYY4PorwYhdRZ7nkUskH4Z-aUtcvd5ZACl9unFDorhpqO6P5Oq5vHVNupGwa3ZI5ZNcNKIRhdY-qk9h0/w400-h225/Slide1.png" width="400" /></a></div><div class="separator" style="clear: both; text-align: center;"><span style="text-align: left;"><br /></span></div><div class="separator" style="clear: both; text-align: left;">As for developing the broader platform, <a href="https://ujjwalll.github.io/">Ujjwal Singh</a> and I will be working this Summer to develop algorithms for colony morphogenesis and behavior in the Diatom genus <i>Bacillaria</i>. This will be added to the platform in a manner similar to the DevoLearn pre-trained model. In addition to the software development activities, Mayukh, myself, and <a href="https://github.com/krishnakatyal">Krishna Katyal</a> have been the main contributors to the <a href="https://github.com/devoworm/Proposals-Public-Lectures/blob/master/Onboarding%20Guide/onboarding-guide.md">DevoWorm Onboarding Guide</a>. Looking forward to an exciting future!</div><div class="separator" style="clear: both; text-align: left;"><br /></div><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhqhT5ZzhdLNzITiO95KI5MeZINz5ksU36aHXDZOhk1UKZmLruJ7FdtU7M1yIZHTVZHgNaj6iLHVC522YWIzqkMmZyavh9rI7WlcLS30ezlBmU7cG02pss_gN_BnbXxd90Dp8Ri9MQXFWw/s1920/EwA85rwXAAIaw1h.jpeg" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="1080" data-original-width="1920" height="225" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhqhT5ZzhdLNzITiO95KI5MeZINz5ksU36aHXDZOhk1UKZmLruJ7FdtU7M1yIZHTVZHgNaj6iLHVC522YWIzqkMmZyavh9rI7WlcLS30ezlBmU7cG02pss_gN_BnbXxd90Dp8Ri9MQXFWw/w400-h225/EwA85rwXAAIaw1h.jpeg" width="400" /></a></div><div class="separator" style="clear: both; text-align: center;"><br /></div><div class="separator" style="clear: both; text-align: left;"><b>Update, 8/19:</b></div><div class="separator" style="clear: both; text-align: left;"><br /></div><div class="separator" style="clear: both; text-align: left;">All of this work has paid off! From the #devolearn Slack channel (<a href="https://openworm.slack.com/">OpenWorm Slack team</a>).</div><div class="separator" style="clear: both; text-align: left;"><br /></div><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhnRpHWwLHnIkDw0Wsq2qd-7H7lkOJt_CGUB-HmEQTEw86ZU2Hs-UreENIIWUjnfeUxtwLKxLdg8qD85lZt-7MZLou25rh_rYCMbnx5YemOMbGfosDBTCTXeOHd3emxVAXb0eOxcHE91Yg/s1299/devolearn-milestone.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="753" data-original-width="1299" height="246" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhnRpHWwLHnIkDw0Wsq2qd-7H7lkOJt_CGUB-HmEQTEw86ZU2Hs-UreENIIWUjnfeUxtwLKxLdg8qD85lZt-7MZLou25rh_rYCMbnx5YemOMbGfosDBTCTXeOHd3emxVAXb0eOxcHE91Yg/w425-h246/devolearn-milestone.png" width="425" /></a></div><br /><div class="separator" style="clear: both; text-align: center;"><br /></div>Bradly Aliceahttp://www.blogger.com/profile/06482487682656113637noreply@blogger.com1tag:blogger.com,1999:blog-1792896637814721350.post-47241221896556764682021-03-30T10:51:00.006-05:002021-03-30T23:56:54.757-05:00The World of Physical Intelligence<p style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiBAt_W38KY2wS89qg75BmL9OeFbMlu5W3fGJB1070CZPHrFxp3m9YIsBYB6vGOB3-cBprPL7QRu3UU7FB0Ka5CxOR1UNOocsRaPEpDz-WK3pvclg_9iuyiB2hDA_79OhzEvOVl4qK0tPA/s1000/ei-logo-horizontal.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="430" data-original-width="1000" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiBAt_W38KY2wS89qg75BmL9OeFbMlu5W3fGJB1070CZPHrFxp3m9YIsBYB6vGOB3-cBprPL7QRu3UU7FB0Ka5CxOR1UNOocsRaPEpDz-WK3pvclg_9iuyiB2hDA_79OhzEvOVl4qK0tPA/s320/ei-logo-horizontal.png" width="320" /></a></p><div class="separator" style="clear: both; text-align: justify;"><span style="text-align: left;">As part of the Embodied Intelligence workshop this past week, I saw a presentation by </span><a href="https://www.is.mpg.de/person/sitti" style="text-align: left;">Metin Sitti </a><span style="text-align: left;">of the </span><a href="https://www.is.mpg.de/" style="text-align: left;">Max Planck Institute for Intelligent Systems</a><span style="text-align: left;"> on the <a href="https://t.co/mSZDsFx9CB?amp=1">emerging paradigm of Physical Intelligence</a>. What is Physical Intelligence? It is the intelligent behavior exhibited by motion and takes into account a morphology (embodiment) and action at multiple scales of spatial organization. The talk was wonderful and walked through a number of empirical studies involving both living and non-living systems. I will leave it up to the reader to appreciate all of the points raised in this talk.</span></div><p></p><p style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg3UmCWKIx5uZr9dhdmp4RnMi5hWG90N7O_A8AaAbRSscFjjO7NQq7QWqGo0TBMba0kD7RkIeDR46memtMwuzEydsYwZbl9iArjXTW411-VsgDNnaOs4zshqY4DTWhAtS_9wV3llZMqHD0/s591/OREL-physical-intelligence.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="537" data-original-width="591" height="364" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg3UmCWKIx5uZr9dhdmp4RnMi5hWG90N7O_A8AaAbRSscFjjO7NQq7QWqGo0TBMba0kD7RkIeDR46memtMwuzEydsYwZbl9iArjXTW411-VsgDNnaOs4zshqY4DTWhAtS_9wV3llZMqHD0/w400-h364/OREL-physical-intelligence.png" width="400" /></a></p><p style="text-align: center;"><a href="https://twitter.com/Orthogonal_Lab/status/1375916086357590016">Physical Intelligence</a> as an emerging idea.</p><p style="text-align: justify;">While Physical Intelligence is not a common paradigm, the general idea is actually not new. Other people have proposed very similar frameworks over the past 15 years or so, including <a href="https://t.co/3fpQyuw956?amp=1">yours truly</a>. Physical Intelligence involves some form of motor or movement behavior, which is generated by an embodied agent, that in turn interacts with the physical environment that can be defined by features such as inertial and gravitational forces, <a href="http://syntheticdaisies.blogspot.com/2012/11/merging-electronics-and-biology-future.html">surface textures</a>, and even light energy. </p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj9yOvqgm8WtqHRqElhKEp8R1GbLIuTwDR9gIluK03pOm0XQVHoJYeY8gX9OLRzPL0Woxp9ag9ogiCNaWmJszty8l7_Vw59WUnxucTSPk-ssEj7JJAXrSxg0vs227CTaheR6tSZINu_oQw/s560/d0tb01585g-f1.gif" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="560" data-original-width="560" height="320" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj9yOvqgm8WtqHRqElhKEp8R1GbLIuTwDR9gIluK03pOm0XQVHoJYeY8gX9OLRzPL0Woxp9ag9ogiCNaWmJszty8l7_Vw59WUnxucTSPk-ssEj7JJAXrSxg0vs227CTaheR6tSZINu_oQw/s320/d0tb01585g-f1.gif" /></a></div><p style="text-align: center;">Physical stimuli for soft robots or other autonomous agents from Figure 1 in <a href="https://pubs.rsc.org/en/content/articlelanding/2020/tb/d0tb01585g#!divAbstract">Shen et.al</a>, <i>Journal of Materials Chemistry B</i>, 8, 8972-8991 (2020).</p><p style="text-align: justify;">At its most human-centric, physical intelligence can be just another word for embodied intelligence, which is where the body shapes and determines what is experienced by the nervous system. In cases where the behaving agent has no nervous system, the body geometry shapes the agent's behavioral output. This is true both in cases of adaptive (intentional) behavior and reactive behavior. In some cases, physical intelligence is identical to Neuromechanics. In other cases, it resembles a range of fields, from Biophysics to Embodied Robotics. The important contribution of the Physical Intelligence paradigm is the principles that guide this diverse topical terrain. Both <a href="https://t.co/3fpQyuw956?amp=1">my talk</a> and <a href="https://t.co/mSZDsFx9CB?amp=1">Metin's talk</a> provide some of these potential principles, and <a href="https://t.co/WTauSmnFI8?amp=1">Scott Grafton's</a> book provides a few more.</p><p style="text-align: justify;"><br /></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgIY88bPB3m7-8EAZu6HE5cPyzOXC1yyd2c5-wkFuxG0vv-pAsQFybSATvGUXB-jmNDiABEJZqWmt18UJeLcLXmldYbmrS4w81IspBzJnAGqpZzFB-9iaL5BqNV8EMw-2FAqwofgye-Ct8/s450/9781524747329.jpg" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="450" data-original-width="298" height="320" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgIY88bPB3m7-8EAZu6HE5cPyzOXC1yyd2c5-wkFuxG0vv-pAsQFybSATvGUXB-jmNDiABEJZqWmt18UJeLcLXmldYbmrS4w81IspBzJnAGqpZzFB-9iaL5BqNV8EMw-2FAqwofgye-Ct8/s320/9781524747329.jpg" /></a></div><div style="text-align: center;">One human-centric interpretation of <a href="https://www.penguinrandomhouse.com/books/564652/physical-intelligence-by-scott-grafton/9781524747329">Physical Intelligence (by Scott Grafton)</a>.</div><p style="text-align: justify;">Metin brings up the example of the <a href="https://www.strandbeest.com/">Strandbeest</a>, which is a kinetic sculpture with no nervous system or centralized control. This is an example of a purely reactive system that also generates seemingly intelligent behavior. Closer to the human experience is the <a href="https://www.eucognition.org/index.php?page=passive-dynamic-walkers#:~:text=The%20passive%20dynamic%20walker%2C%20which%20goes%20back%20to,the%20robot%3B%20it%20is%20brainless%2C%20so%20to%20speak.">Passive Dynamic Walker</a>, which produces human-like bipedalism without a central nervous system. This is the essence of the physical: a particular physical configuration can exhibit reactive behavior independently of a central controller.</p><p style="text-align: justify;">While serving as part of the peripheral nervous system, and in fact being controlled by a central nervous system, muscles can also play a key role in physical intelligence. While muscle cells can be spontaneously active without being inputs by motor neurons, there is a elaborate coordination between the central nervous system and muscular control. Muscular control can produce both <a href="http://syntheticdaisies.blogspot.com/2012/01/evolution-and-neuromechanics-of-very.html">very fast</a> and <a href="http://syntheticdaisies.blogspot.com/2012/04/neuromechanics-and-evolution-of-very.html">very slow</a> adaptive movements. In addition, the overall shape of a body in relation to its muscles can constrain the behavior of the agent in question.</p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgXJLx1Z4ighLKH-Ax5MS0NgUMSzlXZYe9vWKOmqCs2-F-UNFlgcxU_ZtdD25nPATJjtjuUw8ixiHtodfV1JzLPPVq7zzZWwrE6CO4ozzWOIPvxMNjWKAjXE2w0zO4QzI38fNjdVZmmk5E/s420/dafee966f1be9c475518629285e9b3cd.gif" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="237" data-original-width="420" height="226" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgXJLx1Z4ighLKH-Ax5MS0NgUMSzlXZYe9vWKOmqCs2-F-UNFlgcxU_ZtdD25nPATJjtjuUw8ixiHtodfV1JzLPPVq7zzZWwrE6CO4ozzWOIPvxMNjWKAjXE2w0zO4QzI38fNjdVZmmk5E/w400-h226/dafee966f1be9c475518629285e9b3cd.gif" width="400" /></a></div><p style="text-align: left;"><span style="text-align: justify;">The main takeaway is that the brain, body, and environment all work interdependently to shape the behavior that emerges from this complex system. Even in cases where there is no brain (or neural network), the interactions between body and the environment are enough to generate reactive behaviors that appear to be intelligent. This is true for both individual morphologies and the collective behavior of many agents (e.g. </span><a href="https://en.wikipedia.org/wiki/Swarm_intelligence" style="text-align: justify;">swarm intelligence</a><span style="text-align: justify;">). In fact, the brain can be supplanted by </span><a href="https://en.wikipedia.org/wiki/Control_theory" style="text-align: justify;">control mechanisms</a><span style="text-align: justify;"> that regulate the conformity and response to physical forces in the environment. Future work should focus on the differences between "neural" and "physical" behavior, as well as the </span><a href="https://en.m.wikipedia.org/wiki/Necessity_and_sufficiency" style="text-align: justify;">necessity and sufficiency</a><span style="text-align: justify;"> of each component in the triad.</span></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiiGc7H915nBSwyrPi8sn8wOBEXPuxZtPvJbWCwhuchrzYig2LEynalOIv6V2qh8eTk2NtD9q69xwDnXk3nDiE8ArgAgW_hbokcwHeYA4rmnzNK1ZJKw8cFeBcqroIYS20qLLVxTlwplDk/s483/gr1.jpeg" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="483" data-original-width="356" height="320" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiiGc7H915nBSwyrPi8sn8wOBEXPuxZtPvJbWCwhuchrzYig2LEynalOIv6V2qh8eTk2NtD9q69xwDnXk3nDiE8ArgAgW_hbokcwHeYA4rmnzNK1ZJKw8cFeBcqroIYS20qLLVxTlwplDk/s320/gr1.jpeg" /></a></div><p style="text-align: center;">A diagrammatic example of this relationship (with a brain in the feedback loop) from <a href="https://www.cell.com/trends/neurosciences/fulltext/S0166-2236(97)01149-1">Chiel and Beer</a>, <i>Trends in Neuroscience</i>, 20(12), P553-P557.</p><p style="text-align: left;">In conclusion, <a href="https://www.darpa.mil/">DARPA</a> has also engaged in the idea of physical intelligence, and <a href="https://www.nextbigfuture.com/2009/06/physical-intelligence-follow-up.html">there was a proposer's conference in 2009</a>. This version of Physical Intelligence has a strong cybernetics flavor, particularly in incorporating the <a href="https://syntheticdaisies.blogspot.com/2015/09/reconsidering-model-as-unit-of.html">EGRT (Every Good Regulator Theorem)</a> into the mix.</p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj14M2LATDHDe1t84QVvJ8ZbDPOynM5xlvm8I6ySMLtEshAdnQDVtozw8oWeZAfYAjlB-dTFNEurC0C24UJTKbSIFNCHPMMwG4lndz30ka7MyIJrtj5LKbID9ZiqhUQcGz_9xli0DW9lmE/s730/cybernetics-1-730x430.jpeg" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="430" data-original-width="730" height="235" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj14M2LATDHDe1t84QVvJ8ZbDPOynM5xlvm8I6ySMLtEshAdnQDVtozw8oWeZAfYAjlB-dTFNEurC0C24UJTKbSIFNCHPMMwG4lndz30ka7MyIJrtj5LKbID9ZiqhUQcGz_9xli0DW9lmE/w400-h235/cybernetics-1-730x430.jpeg" width="400" /></a></div><br /><p style="text-align: center;">Cybernetics of the firm (deemphasizing the role of individual morphology). COURTESY: <a href="https://www.newworldencyclopedia.org/entry/Cybernetics">New World Encyclopedia</a>.</p><div style="text-align: center;"><br /></div>Bradly Aliceahttp://www.blogger.com/profile/06482487682656113637noreply@blogger.com1tag:blogger.com,1999:blog-1792896637814721350.post-7146163883706825372021-02-28T21:50:00.003-06:002021-02-28T22:21:09.521-06:00The Way of The Polymath<div style="text-align: center;">
<div class="separator" style="clear: both; text-align: left;">This content is cross-posted to the <a href="https://medium.com/orel-group/way-of-the-polymath-db96a4478e57">Orthogonal Research and Education Lab Medium</a>.</div><div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjcjYcYtNWL8JaBMHrwpNXxop0hw6E9nKtZxaASSBwvfGNp2Wp3Koejy1VXtxcXXhqsj9gGHZRIx9LeklaEfgBefRuMG6x50ESpTW9UtkQiDbJpe7jAjB9uV-F1M5h6qEmGOj4k7yhvRZE/s1600/hedgehog-or-fox-direction.jpg" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="198" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjcjYcYtNWL8JaBMHrwpNXxop0hw6E9nKtZxaASSBwvfGNp2Wp3Koejy1VXtxcXXhqsj9gGHZRIx9LeklaEfgBefRuMG6x50ESpTW9UtkQiDbJpe7jAjB9uV-F1M5h6qEmGOj4k7yhvRZE/s400/hedgehog-or-fox-direction.jpg" width="400" /></a></div>
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What constitutes a polymath, and why are they so rare? Another way to ask this question is why are there so few <a href="https://en.wikipedia.org/wiki/The_Hedgehog_and_the_Fox">foxes relative to hedgehogs</a>? The occasional hyper-specialist would have you believe the term "polymath" is an epithet. However, there are a number of skills that the polymath possesses that translate into an advantage for advancing both theory and fundamental knowledge. Aside from the mastery of multiple intellectual areas, the most important of these is the ability to synthesize information from a number of sources. The advent of digital scholarship may enable this ability in the foxes among us [1].<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgHwY3QY8kAKRkFcSC-SmYlN_GINMvllBTE3Uxm8kLJb9euINiNUDLpd2L-ht5erpTc9d0QKbldWSSlrcE1j9fBhJX6p_dpQBePFyeDlsR_KaJs6ftsmhw1zQrlEKs_dO_s9unoCftPZ_g/s1600/download.jpe" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="320" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgHwY3QY8kAKRkFcSC-SmYlN_GINMvllBTE3Uxm8kLJb9euINiNUDLpd2L-ht5erpTc9d0QKbldWSSlrcE1j9fBhJX6p_dpQBePFyeDlsR_KaJs6ftsmhw1zQrlEKs_dO_s9unoCftPZ_g/s320/download.jpe" width="269" /></a></div>
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One depiction (late 19th, early 20th century) of a polymath.</div>
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<br /></div>Back in 2015, Nature Careers released a list of recommendations to combat the hyper-specialist tendencies of PhD programs [2], but many of these are simply window-dressing. One view is that improving the state of interdisciplinary thinking is to improve the infrastructure for collaboration and disseminating big ideas. However, a more fundamental (and harder-to- implement) change that can be made is to reconfigure the epistemic landscape of science [3]. One aspect of this indeed involves the training of scientific generalists, but generalist training does not equate polymathism.<br />
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The other factor involves the potential zero-sum nature of generalized knowledge [4]. There is a constant tradeoff between deep expertise in one area versus more shallow expertise in a number of areas simultaneously. Society tends to reward deep expertise, and synthesis is rather expensive knowledge-wise. In any case, there is a game-theoretic interpretation of this scenario, but that is a topic for another post. <br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhulKYC80TFjHpisJKvSMxZjCQHyVCKH2e_jz-2BQxDw4KkNiXIoUJJ_uCydHBB5DWg93Dxkn7QOSH_zAgUmilY9ZYqZUy4czLULrFNCcyHIPDsCY8bkpwqVveV2l38Xr25rnP9XK1Eb68/s1600/hedgehog1.jpg" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="266" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhulKYC80TFjHpisJKvSMxZjCQHyVCKH2e_jz-2BQxDw4KkNiXIoUJJ_uCydHBB5DWg93Dxkn7QOSH_zAgUmilY9ZYqZUy4czLULrFNCcyHIPDsCY8bkpwqVveV2l38Xr25rnP9XK1Eb68/s400/hedgehog1.jpg" width="400" /></a></div>
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Here is a semi-annotated reading list on singular (but multidisciplinary) academic activity:<br />
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Hossenfelder, S. <a href="http://backreaction.blogspot.com/2015/07/the-loneliness-of-my-notepad.html">The loneliness of my notepad</a>. <i>Backreaction blog</i>, July 8 (2015).<br />
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Issacson, W. <a href="https://medium.com/theaspenjournalofideas/themythofthelonegenius6a5146c7da10">Myth of the Lone Genius</a>. <i>Aspen Journal of Ideas</i>, July 24 (2015). <br />
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These articles critically examine the myth of the lone genius. The first article points out that tools enabling collaboration (e.g. internet, large-scale consortia) are finally starting to bear fruit. Proportion of single-author papers has gone down over last 20-30 years, but that does not mean lone efforts are in absolute decline. In fact, "isolation" is a myth, given the social networks and information-sharing culture in academia. <br />
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Bateman, T.S. and Hess, A.M. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4378433/">Different personal propensities among scientists relate to deeper vs. broader knowledge contributions</a>. <i>PNAS</i>, 112(12), 3653-3658. (2015).<br />
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Kirkegaard, E. <a href="https://emilkirkegaard.dk/en/2015/03/personality-correlates-of-breadth-vs-depth-of-research-scholarship/">Personality correlates of breadth vs. depth of research scholarship</a>. <i>Project Polymath blog</i>, March 6 (2015).<br />
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* relates style of scientific investigation to type of contributions (specialized studies vs. broad interdisciplinary synthesis) made by scientists. Survey methodology does not assume that contributions can be both deep and broad, despite setting this up as a dichotomy. Is "deeper" vs. "broader" a major dichotomy in scientific exploration.<br />
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* suggests that the difference between scientific generalists and specialists is epistemic, not economic as traditionally assumed (e.g. a certain strategy is more or less risky).<br />
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* views differences in types of scientists (e.g. polymathy) as a matter of personality, not epistemic bias.<br />
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Palla, G., Tibely, G., Mones, E., Pollner, P., and Vicsek, T. <a href="https://www.researchgate.net/publication/278733548_Hierarchical_networks_of_scientific_journals">Hierarchical networks of scientific journals</a>. <i>arXiv</i>, 1506.05661 (2015).<br />
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Presents a hierarchical network analysis of scientific journals and their relevance to measuring influence and the diffusion of ideas in specific scientific fields.<br />
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Muldoon, R. and Weisberg, M. <a href="https://link.springer.com/article/10.1007/s11229-010-9757-8">Robustness and idealization in models of cognitive labor</a>. <i>Synthese</i>, 183, 161-174 (2011).<br />
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* introduce us to an economic optimization model called the marginal contribution/reward (MCR).<br />
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* motivation of individuals or groups of scientists is accomplished either through self-interest or epistemic norms.<br />
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* MCR assumes that cognitive labor can be optimally distributed across collaborations to solve hard problems. The problem is stated as a constrained maximization of "success" and "return". Model does not provide good approximations of success, return, or epistemic norms, not does it distinguish amongst different scientific skill-sets (generalists vs. specialists vs. hyper-specialists).<br />
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Sarma, G.P. <a href="http://philsci-archive.pitt.edu/11060/1/training_scientific_generalists.pdf">Should we train scientific generalists?</a> <i>arXiv</i>, 1410.4422 (2014).<br />
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* how to introduce students to a vocabulary of multiple disciplines, and how this would encourage research breadth.<div><br /></div><div><br /></div><div>alexarje <a href="https://www.arj.no/2012/03/12/disciplinarities-2/">Disciplinarities: intra, cross, multi, inter, trans</a>. <i>Alexander Refsum Jensenius blog</i>, March 12. (2012).</div><div><br /><br />
<b>NOTES:</b><br />
<b>[1] </b>Alicea, B. "<a href="http://syntheticdaisies.blogspot.com/2011/09/academic-connectivity-revisited.html">Academic Connectivity and the Future of Scientific Ideas</a>". <i>Synthetic Daisies blog</i>, September 9 (2011).<br />
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[2] Nurse, P. <a href="https://www.nature.com/articles/nj7560-371a">To build a scientist</a>. <i>Nature</i>, 523, 371-373 (2015).<br />
<br />
[3] Weisberg, M. and Muldoon, R. <a href="https://www.jstor.org/stable/10.1086/644786?seq=1">Epistemic Landscapes and the Division of Cognitive Labor</a>. <i>Philosophy of Science,</i> 76(2), 225-252 (2009).<br /><br />
[4] Downey, G. <a href="http://uncoveringinformationlabor.blogspot.com/2006/03/interdisciplinarity-sub-disciplinarity.html">Interdisciplinarity, sub-disciplinarity, and inter-topicality</a>. <i>Uncovering Information Labor </i>blog, March 31 (2006).</div>Bradly Aliceahttp://www.blogger.com/profile/06482487682656113637noreply@blogger.com1tag:blogger.com,1999:blog-1792896637814721350.post-29509250293502781692021-02-12T16:31:00.005-06:002021-02-12T23:27:23.088-06:00Assorted Darwin Day Content<div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhultZ-cCXILruPev8kiIiLxHE-xc3JKUzXIeiE0Qldn2aQmfNdU6g8Ya-_lqBR18R4O_-cq_Sc_Sau3u12vmLHHlwlYV13FmU5lQhVJHIy6tpW03F0MEHvfWl2TyJY6zhQ8byMCXx8E74/s1155/Et-vvClVgAAGCKW.jpeg" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="1155" data-original-width="755" height="400" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhultZ-cCXILruPev8kiIiLxHE-xc3JKUzXIeiE0Qldn2aQmfNdU6g8Ya-_lqBR18R4O_-cq_Sc_Sau3u12vmLHHlwlYV13FmU5lQhVJHIy6tpW03F0MEHvfWl2TyJY6zhQ8byMCXx8E74/w261-h400/Et-vvClVgAAGCKW.jpeg" width="261" /></a></div><div class="separator" style="clear: both; text-align: center;"><br /></div><div class="separator" style="clear: both; text-align: left;">For <a href="https://syntheticdaisies.blogspot.com/search?q=darwin-day">this year's Darwin Day post</a>, I will highlight a number of items I have recently run across on Twitter. Some of these have been retweeted on the <a href="https://twitter.com/Orthogonal_Lab">Orthogonal Research and Education Lab Twitter feed</a>, other materials are related to discussions in our research group meetings.</div><div class="separator" style="clear: both; text-align: center;"><br /></div><div>To start things off, I will draw your attention to a new special issue of <i>Royal Society of London B</i> called "<a href="https://royalsocietypublishing.org/toc/rstb/2021/376/1821">Basal cognition: multicellularity, neurons and the cognitive lens</a>" that is worth checking out. The term "<a href="https://en.wikipedia.org/wiki/Basal_(phylogenetics)">basal</a>" refers to evolutionary origins in the context of <a href="http://tolweb.org/tree/">phylogeny (the tree of life)</a>. </div><div><br /></div><div>There are three papers of particular note for Darwin Day: "<a href="https://royalsocietypublishing.org/doi/10.1098/rstb.2019.0761">The chemical brain hypothesis for the origin of nervous systems</a>" by <a href="http://www.twitter.com/JekelyLab">Gaspar Jekely</a>, "<a href="https://royalsocietypublishing.org/doi/10.1098/rstb.2020.0347">Elementary Nervous Systems</a>" by <a href="http://www.twitter.com/wormduty">Detlev Arendt</a>, and "<a href="https://royalsocietypublishing.org/doi/10.1098/rstb.2020.0458">Uncovering cognitive similarities and differences, conservation and innovation</a>" by <a href="http://www.twitter.com/drmichaellevin">Michael Levin</a> and colleagues.</div><div><br /></div><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi5aR2MSpNbW6DLyhssyVFloSMnwXfPpq8rdIStPbTy17AXOiluL95jvSMUSZFuREf1s4caw3Quk4cMxJksUaIoTigB36uTYhrPtOpiy0NSBMCra5xN0BYG-1TzGttStD5zAzvZ2dIf0Ac/s1083/elementar-nervous-systems.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="1083" data-original-width="945" height="400" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi5aR2MSpNbW6DLyhssyVFloSMnwXfPpq8rdIStPbTy17AXOiluL95jvSMUSZFuREf1s4caw3Quk4cMxJksUaIoTigB36uTYhrPtOpiy0NSBMCra5xN0BYG-1TzGttStD5zAzvZ2dIf0Ac/w349-h400/elementar-nervous-systems.png" width="349" /></a></div><div style="text-align: center;">The new paper on elementary nervous systems in <i>Royal Society B </i>(click to enlarge, figure from paper). <b>COURTESY:</b> <a href="http://www.twitter.com/wormduty">Detlev Arendt</a>.</div><div><br /></div><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj-yRACsbUl9KiG7os8HhijJaCyzyQ9JZuoUdnd7pZ1sIfWKBgNLM7DbQWFnroSweQM2QhsROJjfDA908bPUclqgt9bfBmu0LosaaPSKHBvEMy_Uk4lWScVBhoETpNsDETuYHXXxHtBpGs/s1188/darwin-online.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="617" data-original-width="1188" height="208" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj-yRACsbUl9KiG7os8HhijJaCyzyQ9JZuoUdnd7pZ1sIfWKBgNLM7DbQWFnroSweQM2QhsROJjfDA908bPUclqgt9bfBmu0LosaaPSKHBvEMy_Uk4lWScVBhoETpNsDETuYHXXxHtBpGs/w400-h208/darwin-online.png" width="400" /></a></div><div style="text-align: center;">A pointer to the <a href="http://www.twitter.com/uk_darwin">Darwin Online repository</a>.</div><div style="text-align: center;"><br /></div><div style="text-align: left;">In terms of old drawings and other archival materials, check out the <a href="http://darwin-online.org.uk/contents.html">Darwin Online</a> project. This is a nice repository of Darwin-related historical and scientific works. This resource contains books, personal correspondence, and published materials. Speaking of history, let's turn to the deep history of life.....</div><div><br /></div><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhi9gR0y97RRn7Z1HlXfH65kNaK0ySMMitmM8b41wUgQjKGlDF0MaYzu0ioTPGY3EU-V-H8SZaKx6B1C3h6A5EokQVfJTRVnGe0RwTC-SgNEfbdmP_QRFP7w-WKbtVbp7xp8w8O0wZDWwo/s1281/billion-year-plates.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="1281" data-original-width="1189" height="320" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhi9gR0y97RRn7Z1HlXfH65kNaK0ySMMitmM8b41wUgQjKGlDF0MaYzu0ioTPGY3EU-V-H8SZaKx6B1C3h6A5EokQVfJTRVnGe0RwTC-SgNEfbdmP_QRFP7w-WKbtVbp7xp8w8O0wZDWwo/s320/billion-year-plates.png" /></a></div><div style="text-align: center;">A billion years of continental drift as an <a href="https://twitter.com/hvymtlscience/status/1356708233893838849">animated gif</a>. Click to enlarge.</div><div style="text-align: center;"><br /></div><div style="text-align: left;">This next feature is a new paper on a billion years of plate tectonic dynamics: "<a href="https://www.sciencedirect.com/science/article/pii/S0012825220305237?dgcid=coauthor">Extending full-plate tectonic models into deep time: Linking the Neoproterozoic and the Phanerozoic</a>" by <a href="https://twitter.com/hvymtlscience/">Mike Tetley</a> and colleagues. Now published in <i>Earth Science Reviews</i>, it is something we recently discussed in the weekly <a href="https://devoworm.weebly.com/">DevoWorm</a> group meeting.</div><div><br /></div><div>Following up on the <a href="http://www.youtube.com/watch?v=4nWdAtezTHQ&t=56m0s">DevoWorm discussion</a>, which was about mapping the <a href="https://www.nationalgeographic.org/encyclopedia/continental-drift/">continental drift</a> animation to the most basal branches of the tree of life, is an attempt to map Mammalian phylogeny [1] to continental drift over the past 225 million years. This was created by <a href="https://scholar.google.com/citations?user=_6KmyBIAAAAJ&hl=en">Carlos E. Alvarez</a>. The numbers on the maps (top) correspond to the numbered clades (subtrees - bottom). This topic deserves a deeper dive into the latest Phylogeography research [2], which may be the subject of a future blog spot.</div><div><br /></div><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhHTdRbsw_QWyn2No-Ri40ERo4iWow_zyPexVeNJxuM4_DmIOOyRPLZx2CNzTn9i2EDzsO5zsx7uXmmxU8fk4urg-Do1PWjwuVNDf-PIEXoYckU5h_4AnId5ZOSvr0_yOToulkLAUyAo-I/s1480/EtTiOZsXIAALrOq.jpeg" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="1480" data-original-width="1141" height="400" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhHTdRbsw_QWyn2No-Ri40ERo4iWow_zyPexVeNJxuM4_DmIOOyRPLZx2CNzTn9i2EDzsO5zsx7uXmmxU8fk4urg-Do1PWjwuVNDf-PIEXoYckU5h_4AnId5ZOSvr0_yOToulkLAUyAo-I/w309-h400/EtTiOZsXIAALrOq.jpeg" width="309" /></a></div><div class="separator" style="clear: both; text-align: center;">An attempt at matching up the tree of life with continental drift (click to enlarge).<b> </b><b>COURTESY:</b> <a href="https://twitter.com/CarlosEAlvare17">Carlos E. Alvarez</a></div><br /><div style="text-align: left;">The next feature is a new paper on evolution of development (evo-devo) in nervous system anatomy called "<a href="https://www.sciencedirect.com/science/article/abs/pii/S0070215320301277">Evolution of new cell types at the lateral neural border</a>", now published in <i>Current Topics in Developmental Biology</i>. This study even uses converging evidence from genetic regulatory networks and anatomy to demonstrate common mechanisms shared between invertebrates and vertebrates.</div><div style="text-align: center;"><br /></div><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgfwn3-s394Cw2Et1VavT7KmSjVyKfwanR0xhYBIsiqQ9wAcGqUKdjF1b92mWERksLzsZZ_JwaNiS5NY-smxluKBE6JbpM6pFAkwoiTtsDBkbiVCIYR6ygbQ1PNGbAP61KF1MLPJD_eZyk/s1488/neural-evo-1.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="1488" data-original-width="948" height="400" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgfwn3-s394Cw2Et1VavT7KmSjVyKfwanR0xhYBIsiqQ9wAcGqUKdjF1b92mWERksLzsZZ_JwaNiS5NY-smxluKBE6JbpM6pFAkwoiTtsDBkbiVCIYR6ygbQ1PNGbAP61KF1MLPJD_eZyk/w255-h400/neural-evo-1.png" width="255" /></a></div><div class="separator" style="clear: both; text-align: center;">A new paper on the evolution of new neuronal cell types (click to enlarge).<b> COURTESY:</b> <a href="https://twitter.com/JanStundl">Jan Stundl (Caltech)</a>.</div><div class="separator" style="clear: both; text-align: center;"><br /></div><div class="separator" style="clear: both; text-align: left;">Not only is this Darwin Day, but also the 50th anniversary of a <i>Nature</i> paper by Kimura and Ohta [3] on the <a href="https://en.wikipedia.org/wiki/Neutral_theory_of_molecular_evolution">Neutral Theory of Molecular Evolution</a>. Neutral Theory postulates that most biological variation is expressed in selectively neutral genes, and so is random in nature [4]. This stands in opposition to the selectionist perspective of evolutionary change [5, 6].</div><div class="separator" style="clear: both; text-align: left;"><br /></div><div class="separator" style="clear: both; text-align: center;"><br /></div><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhiRHIEhcxhS6H8BEE9oSSMHQGTZNRUpj__H5UShoFkA5bA_8hOScicXVwv19fj6SgYrjUo3vdeKBgoAezQhWXjwRmrtUl9Q_kK2QB-v8ABlo2NcvkO4DfDLZIwyadTshIcTY8ACJijjE0/s1361/motoo-kimura-50.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="1361" data-original-width="1185" height="400" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhiRHIEhcxhS6H8BEE9oSSMHQGTZNRUpj__H5UShoFkA5bA_8hOScicXVwv19fj6SgYrjUo3vdeKBgoAezQhWXjwRmrtUl9Q_kK2QB-v8ABlo2NcvkO4DfDLZIwyadTshIcTY8ACJijjE0/w349-h400/motoo-kimura-50.png" width="349" /></a></div><br /><div class="separator" style="clear: both; text-align: center;">Fully-tweetable neutral theory of evolution. <b>COURTESY:</b> <a href="http://www.twitter.com/CrawfordAJ">Andrew J. Crawford</a>.</div><div class="separator" style="clear: both; text-align: center;"><br /></div><div class="separator" style="clear: both; text-align: left;">Finally, and returning to neuroevolution, there are several items of interest from the laboratory of <a href="https://twitter.com/redmakeda">Cassandra Extavour</a>. The first is a talk at the <a href="http://www.twitter.com/SICB_">Society of Integrative and Comparative Biology</a> meeting on the <a href="https://twitter.com/ProfKenField/status/1345794278811906049">evo-devo-eco-neuro-biology</a> of <i>Drosophila</i> learning and memory. For more evo-devo work from <a href="https://www.extavourlab.com/">Dr. Extavour's lab</a>, check out this recent work (with open data) on insect size and shape [7, 8].</div><div class="separator" style="clear: both; text-align: left;"><br /></div><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiuAN7s0MhZj75e6CRVDfVMaMDo-SSxGYDnupEUSnWciTh_gFlg_CwJDGviIO54yfjoxQXJ4ZG1V6AtHWEBzZC8Qe6dfLuCMW0TCeWMnpQytwE78pl_UXokO357ETvz1dJh-mMgH98yuXY/s1374/evo-SICB-2.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="1374" data-original-width="1180" height="400" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiuAN7s0MhZj75e6CRVDfVMaMDo-SSxGYDnupEUSnWciTh_gFlg_CwJDGviIO54yfjoxQXJ4ZG1V6AtHWEBzZC8Qe6dfLuCMW0TCeWMnpQytwE78pl_UXokO357ETvz1dJh-mMgH98yuXY/w344-h400/evo-SICB-2.png" width="344" /></a></div><div class="separator" style="clear: both; text-align: center;">Original artwork from <a href="http://www.twitter.com/SICB_">SICB Twitter Account</a>, commentary from <a href="http://www.twitter.com/ProfKenField">Ken A. Field.</a></div><div class="separator" style="clear: both; text-align: center;"><br /></div><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjoB4YHeU83VDZkdaNaTyRVF1N8_XTtVNVdNuvlOTxAnA59Dpcnhmmcmtb6Eg9yCzfXdSsc-YhB7QnE8YrirbkXVfydLo0GUEaWNdU0savhMT0KJ6Ab2TljhwyrsDwWYipw91AvWkiiQf8/s1412/evolution-SICB.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="1412" data-original-width="952" height="400" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjoB4YHeU83VDZkdaNaTyRVF1N8_XTtVNVdNuvlOTxAnA59Dpcnhmmcmtb6Eg9yCzfXdSsc-YhB7QnE8YrirbkXVfydLo0GUEaWNdU0savhMT0KJ6Ab2TljhwyrsDwWYipw91AvWkiiQf8/w270-h400/evolution-SICB.png" width="270" /></a></div><div class="separator" style="clear: both; text-align: center;">Hand-drawn notes on the SICB plenary talk. COURTESY: <a href="http://www.twitter.com/AjnaRivera">Dr. Ajna Rivera</a>.</div><div class="separator" style="clear: both; text-align: center;"><br /></div><p style="text-align: left;"><b>NOTES:</b></p><p>[1] Foley N.M., Springer M.S. and Teeling E.C. (2016). <a href="https://royalsocietypublishing.org/doi/10.1098/rstb.2015.0140">Mammal madness: is the mammal tree of life not yet resolved</a>? <i>Philosophical Transactions of the Royal Society B</i>, 37120150140. doi:10.1098/ rstb.2015.0140.</p><p>[2] Avise, J.C. (2000). <a href="https://books.google.com/books?id=lA7YWH4M8FUC&printsec=frontcover&source=gbs_ge_summary_r&cad=0#v=onepage&q&f=false">Phylogeography: the history and formation of species</a>. Harvard University Press, Cambridge, MA.</p><p>[3] Kimura, M. and Ohta, T. (1971). <a href="https://www.nature.com/articles/229467a0">Protein Polymorphism as a Phase of Molecular Evolution</a>. <i>Nature</i>, 229, 467–469.</p><p>[4] Kimura, M. (1983). <a href="https://books.google.com/books/about/The_Neutral_Theory_of_Molecular_Evolutio.html?id=olIoSumPevYC&printsec=frontcover&source=kp_read_button&newbks=1&newbks_redir=0#v=onepage&q&f=false">The Neutral Theory of Molecular Evolution</a>. Cambridge University Press, Cambridge, UK.</p><p>[5] Nei, M. (2005). <a href="https://academic.oup.com/mbe/article/22/12/2318/1009566">Selectionism and Neutralism in Molecular Evolution</a>. <i>Molecular Biology and Evolution</i>, 22(12), 2318–2342. doi:10.1093/molbev/msi242.</p><p>[6] There are other critiques of selectionism from other perspectives. Here is one in the area of brain function: Fernando, C., Szathmary, E., and Husbands, P. (2012). <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3337445/">Selectionist and Evolutionary Approaches to Brain Function: A Critical </a><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3337445/">Appraisal</a>. <i>Frontiers in Computational Neuroscience</i>, 6, 24. doi:10.3389/ fncom.2012.00024.</p><p>[7] Church, S.H., Donoughe, S., de Medeiros, B.A.S., and Extavour, C.G. (2019). <a href="https://www.nature.com/articles/s41586-019-1302-4">Insect egg size and shape evolve with ecology but not developmental rate</a>. <i>Nature</i>, 571, 58–62.</p><p>[8] Church, S.H., Donoughe, S., de Medeiros, B.A.S., and Extavour, C.G. (2019). <a href="https://www.nature.com/articles/s41597-019-0049-y">A dataset of egg size and shape from more than 6,700 insect species</a>. <i>Scientific Data</i>, 6, 104.</p>Bradly Aliceahttp://www.blogger.com/profile/06482487682656113637noreply@blogger.com1tag:blogger.com,1999:blog-1792896637814721350.post-69799972654245076372021-01-22T09:50:00.002-06:002021-01-22T09:50:38.382-06:00OREL and DevoWorm Review of 2020<p style="text-align: center;"></p><div class="separator" style="clear: both; text-align: left;">As part of our preparations for the New Year, I prepared a set of presentations for my two research groups: <a href="https://representational-brains-phenotypes.weebly.com/">Representational Brains and Phenotypes</a> and <a href="https://devoworm.weebly.com/">DevoWorm</a>. I have posted the slides below, and if you see something interesting that you would like to participate in, <a href="mailto:bradly.alicea@outlook.com">please contact me</a>. If you are interested in learning more, please join the <a href="https://launchpass.com/orthogonal-research">Orthogonal Research and Education Lab</a> or <a href="https://launchpass.com/openworm">OpenWorm</a> Slack. You can also attend our weekly meetings: 3pm UTC Saturdays for Saturday Morning NeuroSim (<a href="https://representational-brains-phenotypes.weebly.com/saturday-morning-neurosim.html">more info</a>), or 3pm UTC Mondays for DevoWorm (<a href="https://devoworm.weebly.com/schedulejoin.html">more info</a>).</div><div class="separator" style="clear: both; text-align: left;"><br /></div><div class="separator" style="clear: both; text-align: left;"><br /></div><div class="separator" style="clear: both; text-align: left;">Saturday Morning NeuroSim presentation, with a focus on the <a href="https://representational-brains-phenotypes.weebly.com/">Representational Brains and Phenotypes</a> group (click slides to enlarge).</div><div class="separator" style="clear: both; text-align: left;"><br /></div><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjn9I-qgG9p9t-Vj9RnGRdnOyQD-qNL1k5flg1PaSg9V_S-KeVVTRwz49OyYogfDIukkfsNXtRD13Sk5LRjeJ262B4VyE6q6eEbp-7dX2wVPfh4t23Obng6xLY3E1Hpwb7UhC5HYmdylrQ/" style="margin-left: 1em; margin-right: 1em;"><img alt="" data-original-height="180" data-original-width="320" height="225" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjn9I-qgG9p9t-Vj9RnGRdnOyQD-qNL1k5flg1PaSg9V_S-KeVVTRwz49OyYogfDIukkfsNXtRD13Sk5LRjeJ262B4VyE6q6eEbp-7dX2wVPfh4t23Obng6xLY3E1Hpwb7UhC5HYmdylrQ/w400-h225/image.png" width="400" /></a></div><div class="separator" style="clear: both; text-align: center;"><br /></div><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiHak6w7bINx10f1OjGu3ynB_Q8N3jxEowYOM1wU6A9H_iit57Hpa8E9-YX24xI1mzsIcC9qUasijznKWWWEsNwuE4yi_UYU7b2IIcFoYmkflmudK6iGnBg_Wii6yRGqzWZ-44xmwLsaZo/" style="margin-left: 1em; margin-right: 1em;"><img alt="" data-original-height="225" data-original-width="400" height="225" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiHak6w7bINx10f1OjGu3ynB_Q8N3jxEowYOM1wU6A9H_iit57Hpa8E9-YX24xI1mzsIcC9qUasijznKWWWEsNwuE4yi_UYU7b2IIcFoYmkflmudK6iGnBg_Wii6yRGqzWZ-44xmwLsaZo/w400-h225/image.png" width="400" /></a></div><div class="separator" style="clear: both; text-align: center;"><br /></div><div class="separator" style="clear: both; text-align: center;"><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhxrFIe6d9K1gOl7vEUiGg0NmQILm-YaynI_d_vO1Gx-ryhFoQZnEe9hluJk1BayTMO1AHQrlcZdgIybK98FpH_cqJdtc2k-vhyphenhyphene0hpIIdZtLy3A9SChIeJds2TcOUG3-LVZ_A2GvAAugM/" style="margin-left: 1em; margin-right: 1em;"><img alt="" data-original-height="225" data-original-width="400" height="225" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhxrFIe6d9K1gOl7vEUiGg0NmQILm-YaynI_d_vO1Gx-ryhFoQZnEe9hluJk1BayTMO1AHQrlcZdgIybK98FpH_cqJdtc2k-vhyphenhyphene0hpIIdZtLy3A9SChIeJds2TcOUG3-LVZ_A2GvAAugM/w400-h225/image.png" width="400" /></a></div></div><div class="separator" style="clear: both; text-align: center;"><br /></div><p style="text-align: center;"></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEju7eY6cAY1kq44tD_OA47VLAprZjU8ewrE4QjkVXdECm-ZtYbRsvpXgCSx7e1iHVlicUGUPJKMku4fgLZ6nuUr9RGW3vyi9TQKeoHTOpJ7Lk1hxnEJ8AW6kIclapoMXskWdnVav2BssqU/" style="margin-left: 1em; margin-right: 1em;"><img alt="" data-original-height="225" data-original-width="400" height="225" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEju7eY6cAY1kq44tD_OA47VLAprZjU8ewrE4QjkVXdECm-ZtYbRsvpXgCSx7e1iHVlicUGUPJKMku4fgLZ6nuUr9RGW3vyi9TQKeoHTOpJ7Lk1hxnEJ8AW6kIclapoMXskWdnVav2BssqU/w400-h225/image.png" width="400" /></a></div><br /><p></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhvhZpdJTO9ETBs8NPGwxuW6nD1SsHNoK8XmxwnO-OnS3H0dZT-zUFZtwV1SomgM-gFxSRgMRnJYXpEev51G49VTW7aBDIxU8ostqmbDuEydznCbDrDG4i2f3tXI5CR77G7ubNdx8HcoEo/" style="margin-left: 1em; margin-right: 1em;"><img alt="" data-original-height="225" data-original-width="400" height="225" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhvhZpdJTO9ETBs8NPGwxuW6nD1SsHNoK8XmxwnO-OnS3H0dZT-zUFZtwV1SomgM-gFxSRgMRnJYXpEev51G49VTW7aBDIxU8ostqmbDuEydznCbDrDG4i2f3tXI5CR77G7ubNdx8HcoEo/w400-h225/image.png" width="400" /></a></div> <p></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhF89nsNGRH41vdIW_a2PbiC90LYh449sFztaoh0nWZ8LM2mCqgPMIzkhxLFaQP7KULy_Q5OUCW07Eb-UQZKSIJGYyPmQ4BXi8fKvSFtFhHycDvHsdJhlmv64wTX3foRlVyJbpdqH6v8pM/s960/Slide-6-5.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="540" data-original-width="960" height="225" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhF89nsNGRH41vdIW_a2PbiC90LYh449sFztaoh0nWZ8LM2mCqgPMIzkhxLFaQP7KULy_Q5OUCW07Eb-UQZKSIJGYyPmQ4BXi8fKvSFtFhHycDvHsdJhlmv64wTX3foRlVyJbpdqH6v8pM/w400-h225/Slide-6-5.png" width="400" /></a></div><br /><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiffQUgkfHr7sKvx-5hBrsjOjt6p4mldSNIxs-paCqiHgN_ndFFKmW26ggPQl8V25OQVW499fp2sTBzhnQeKnHiMxNOi2YoYWcUxxOwsEQnxAcYiBzYDm3BQrzUotZns-6FsmwswiMFRHE/s960/Slide-6-75.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="540" data-original-width="960" height="225" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiffQUgkfHr7sKvx-5hBrsjOjt6p4mldSNIxs-paCqiHgN_ndFFKmW26ggPQl8V25OQVW499fp2sTBzhnQeKnHiMxNOi2YoYWcUxxOwsEQnxAcYiBzYDm3BQrzUotZns-6FsmwswiMFRHE/w400-h225/Slide-6-75.png" width="400" /></a></div><p style="text-align: center;"><br /></p><p style="text-align: center;"></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgsGDqOsO4gAV4raXSFjuz0qqbm67IE0e0tKmXaJvO_NcQLx_WlmgV0tCxvv4-pQCayzty_dGaosxG2E6bXTd5lAk-qTfXePFzW0wBSivcFARZTACunX-vQTt_H2QPifZpV53qPp0z0eDQ/s960/Slide6.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="540" data-original-width="960" height="225" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgsGDqOsO4gAV4raXSFjuz0qqbm67IE0e0tKmXaJvO_NcQLx_WlmgV0tCxvv4-pQCayzty_dGaosxG2E6bXTd5lAk-qTfXePFzW0wBSivcFARZTACunX-vQTt_H2QPifZpV53qPp0z0eDQ/w400-h225/Slide6.png" width="400" /></a></div><div class="separator" style="clear: both; text-align: center;"><br /></div><div class="separator" style="clear: both; text-align: center;"><br /></div><div class="separator" style="clear: both; text-align: left;">DevoWorm weekly meeting presentation, with a focus on the <a href="https://devoworm.weebly.com/">DevoWorm</a> group (click slides to enlarge).</div><div class="separator" style="clear: both; text-align: left;"><br /></div><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgSF-ZPVBLRqZxZu_sA2wmPyK6ScNc1dr_Nykx_MH5tnmgrIrzDkD9WzC-oTIcQnhbp5jrTVXl2NUXyel_PFeuStQi0mBJ2u8P2s0tcERZQABLGWKgitYwB1AmE9QZzwBo7hADYwFbzkzA/s720/Growing+into+2021.001.jpeg" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="405" data-original-width="720" height="225" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgSF-ZPVBLRqZxZu_sA2wmPyK6ScNc1dr_Nykx_MH5tnmgrIrzDkD9WzC-oTIcQnhbp5jrTVXl2NUXyel_PFeuStQi0mBJ2u8P2s0tcERZQABLGWKgitYwB1AmE9QZzwBo7hADYwFbzkzA/w400-h225/Growing+into+2021.001.jpeg" width="400" /></a></div><div class="separator" style="clear: both; text-align: center;"><br /></div><br /><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhEb1yN-SX5m34GystJpHks0PyQfJ2yyeEf1b6_wq5IxRqEjrNqai_zAzvyg9khdGBxCFTdFb167cCtSXSkdLS-tqc3wrMRJszAZN0lDXC_gf1c-zJUHTdt8o8yyMiLPA9gpnEUBnYtKc8/s720/Growing+into+2021.002.jpeg" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="405" data-original-width="720" height="225" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhEb1yN-SX5m34GystJpHks0PyQfJ2yyeEf1b6_wq5IxRqEjrNqai_zAzvyg9khdGBxCFTdFb167cCtSXSkdLS-tqc3wrMRJszAZN0lDXC_gf1c-zJUHTdt8o8yyMiLPA9gpnEUBnYtKc8/w400-h225/Growing+into+2021.002.jpeg" width="400" /></a></div><div class="separator" style="clear: both; text-align: center;"><br /></div><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiYObwt0G9bQLLN5WSC_TA0iqL2MUyNHUWVhl_Mu7tOgR1Jxx9pZZ-vImexyJ9ic85F3szVDGkMvFaTOugKEQLHcC54jISMuGn2oa9UZQZ53jlE2gM0jrzVRT-Z7SkZEh1IvjOb-r1U58g/s720/Growing+into+2021.003.jpeg" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="405" data-original-width="720" height="225" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiYObwt0G9bQLLN5WSC_TA0iqL2MUyNHUWVhl_Mu7tOgR1Jxx9pZZ-vImexyJ9ic85F3szVDGkMvFaTOugKEQLHcC54jISMuGn2oa9UZQZ53jlE2gM0jrzVRT-Z7SkZEh1IvjOb-r1U58g/w400-h225/Growing+into+2021.003.jpeg" width="400" /></a></div><div class="separator" style="clear: both; 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margin-right: 1em;"><img border="0" data-original-height="405" data-original-width="720" height="225" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgBmMjPaJUVHDfMmfigJTi_XeCjS3US28PxfA9Y7djJ3Uf_ykPqTZ9EaBLrvEXlT9JKj-_ptViJdWHs85efzTu-Q-m1V8gU-Fc4Njazz7blcTuljVvAzR6SurGnrCJaJtd-j9ghVvn_8qM/w400-h225/Growing+into+2021.005.jpeg" width="400" /></a></div><br /><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgxsbJ0xYDD0wQhqMqPVHOrZdDL7NJBJvneKKWU4KlRA0g1UO1mr5GjSdH6n9o61lKHcS8RHemkXOvkrInYpiv22zaKciGC9t0zGOdpoMYdsRLyegMQnR9NM9Tsb8QW7TTdDAxwmhoXgQg/s720/Growing+into+2021.006.jpeg" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="405" data-original-width="720" height="225" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgxsbJ0xYDD0wQhqMqPVHOrZdDL7NJBJvneKKWU4KlRA0g1UO1mr5GjSdH6n9o61lKHcS8RHemkXOvkrInYpiv22zaKciGC9t0zGOdpoMYdsRLyegMQnR9NM9Tsb8QW7TTdDAxwmhoXgQg/w400-h225/Growing+into+2021.006.jpeg" width="400" /></a></div><br /><div class="separator" style="clear: both; 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text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEizNt_EEHEZNY31AMWr8FIUz1Y8N7E843giyR1vsozoj_6bW9vbQMoBXaaTFLmdOu_dmFxC4Y7yqSNTvOUdbaykekwsnlRkZBIJpOBcomJb5p5fIvDox3c_lAzR8_ZdhqL2bEbQPjYkAdo/s720/Growing+into+2021.009.jpeg" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="405" data-original-width="720" height="225" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEizNt_EEHEZNY31AMWr8FIUz1Y8N7E843giyR1vsozoj_6bW9vbQMoBXaaTFLmdOu_dmFxC4Y7yqSNTvOUdbaykekwsnlRkZBIJpOBcomJb5p5fIvDox3c_lAzR8_ZdhqL2bEbQPjYkAdo/w400-h225/Growing+into+2021.009.jpeg" width="400" /></a></div><br /><div class="separator" style="clear: both; text-align: center;"><br /></div><div class="separator" style="clear: both; text-align: center;"><br /></div><br /><div class="separator" style="clear: both; text-align: center;"><br /></div><br /><p></p>Bradly Aliceahttp://www.blogger.com/profile/06482487682656113637noreply@blogger.com1tag:blogger.com,1999:blog-1792896637814721350.post-84484462810484823932020-12-23T02:57:00.000-06:002020-12-23T02:57:25.521-06:00Synthetic Daisies Summary for 2020<p style="text-align: center;"></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEidSGazaV0kx6symGsqAF5TD8n-FNNGqiPP50Jl1EJQMbkEkuSf5Jopdq5LRnTpTmcj6hxEC1D3M2CEEMJJA3CRpUSdSAhZoUy0SUNlxEG38H7e2FQkJ65RCN8aCelVzvOTudK5OgKEtG0/s1080/AdobeStock_362915790-1080x675.jpeg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="675" data-original-width="1080" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEidSGazaV0kx6symGsqAF5TD8n-FNNGqiPP50Jl1EJQMbkEkuSf5Jopdq5LRnTpTmcj6hxEC1D3M2CEEMJJA3CRpUSdSAhZoUy0SUNlxEG38H7e2FQkJ65RCN8aCelVzvOTudK5OgKEtG0/w320-h200/AdobeStock_362915790-1080x675.jpeg" width="320" /></a></div><div style="text-align: center;"><br /></div><div style="text-align: left;">It has been awhile since I've done a readership post. But as 2020 comes to a close, let's do a Top 10 review of posts and pages for the past 12 months, ranked by readership. </div><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiiAcBfZJz3kFtt3-OnIB6qzuGly22nhTLfy4YheeKiwCDrsVmVc0kM_TB7PMvS4XNuRvpiNxhiRIsuNgAoFt3QYP_9-CyFKMBZXyOo-EYk5g3sTFq56MV7olwKPz_RDOVQJCcB6b_9n6k/s988/top-10-posts-2020.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="725" data-original-width="988" height="294" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiiAcBfZJz3kFtt3-OnIB6qzuGly22nhTLfy4YheeKiwCDrsVmVc0kM_TB7PMvS4XNuRvpiNxhiRIsuNgAoFt3QYP_9-CyFKMBZXyOo-EYk5g3sTFq56MV7olwKPz_RDOVQJCcB6b_9n6k/w400-h294/top-10-posts-2020.png" width="400" /></a></div><div class="separator" style="clear: both; text-align: center;">Top 10 posts for 2020 (by readership). Click to enlarge.</div><div class="separator" style="clear: both; text-align: center;"><br /></div><div class="separator" style="clear: both; text-align: left;">The Carnival of Evolution posts (<a href="https://syntheticdaisies.blogspot.com/2012/04/carnival-of-evolution-number-46-tree.html">#46</a> and <a href="https://syntheticdaisies.blogspot.com/2013/04/carnival-of-evolution-58-visions-of.html">#58</a>) and "<a href="https://syntheticdaisies.blogspot.com/2014/05/playing-long-game-of-human-biological.html">Playing the Long Game of Human Biological Variation</a>" are the top three posts of all time. "<a href="https://syntheticdaisies.blogspot.com/2013/02/ratchets-in-nature-short-review.html">Ratchets in Nature</a>" is the only blog post to be formally cited (<a href="https://scholar.google.com/scholar?hl=en&as_sdt=0,14&cluster=16465967404546461587">2 times according to Google Scholar</a>). Readership seems to be down from years past. Only two of the top 10 posts for the year were actually written this year ("<a href="https://syntheticdaisies.blogspot.com/2020/05/welcome-summer-of-coders-2020.html">Welcome, Summer of Coders</a>" and "<a href="https://syntheticdaisies.blogspot.com/2020/03/silver-linings-of-covid-19.html">Silver Linings of COVID19</a>"). Another post that made the 11 spot (nearly making the list) was another post from 2020, the post on the <a href="http://syntheticdaisies.blogspot.com/2020/10/asapbio-session-on-past-present-and.html">ASAPBio Preprint Symposium</a> from September. </div><div class="separator" style="clear: both; text-align: center;"><br /></div><p></p><div class="separator" style="clear: both; text-align: center;"><div class="separator" style="clear: both;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjbUv-cnFrWbiWE_sjXDYsP2QfXJ-OMdWeMGM344P967BDth0dTpMBiO1GfpsAYgRMa1akQrSisyFVGQqp6wfq-B1GGSTRa-ADZA5b8CNZRFg5RX-sscGZtYj284pK36JtgDTYWjBmTV5c/s1007/ASAP-bio-post.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="455" data-original-width="1007" height="181" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjbUv-cnFrWbiWE_sjXDYsP2QfXJ-OMdWeMGM344P967BDth0dTpMBiO1GfpsAYgRMa1akQrSisyFVGQqp6wfq-B1GGSTRa-ADZA5b8CNZRFg5RX-sscGZtYj284pK36JtgDTYWjBmTV5c/w400-h181/ASAP-bio-post.png" width="400" /></a></div><br /><div class="separator" style="clear: both;">Post on the <a href="http://syntheticdaisies.blogspot.com/2020/10/asapbio-session-on-past-present-and.html">ASAPBio Session on the "Past, Present, and Future of Preprints"</a> (Post #11 for 2020 by readership). Click to enlarge.</div></div><p style="text-align: center;"></p><div class="separator" style="clear: both; text-align: left;">I have also posted a view of the top 10 pages viewed in 2020. The pages were created several years ago, and are not typically updated as much as I would like. The top view was on the "<a href="http://syntheticdaisies.blogspot.com/p/htde-workshop-2012.html">Hard to Define Events Workshop</a>", a session from 2012 hosted at that year's Artificial Life conference. We never followed up on this workshop (it's been eight years!), but might be an interesting thing to create a virtual presence around. A meaning of the blog name, a list of favorite blogs, and various presentations round out the top 10. One more page of note is the "<a href="http://syntheticdaisies.blogspot.com/p/popular-algorithmics.html">Popular Algorithmics</a>" page, which is an accessible presentation of various algorithms. This is something that might be moved to the <a href="https://github.com/synthetic-daisies">Synthetic Daisies Github organization</a> as an open-source collection where people can contribute their own entries (a sort of Wikipedia of algorithms).</div><div class="separator" style="clear: both; text-align: center;"><br /></div><div class="separator" style="clear: both; text-align: center;"><br /></div><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEii3bLM0LftbS6UKuBUJdMLf64be0zEOk1qZR7uogxJuNEhRGaCeNysEtcRXxeHeZCMl0kVyCTaMzhp_cwI9ETtQGV91XDCGdaKcaHcm2wLCq62c3ONbKY54X5CWFLj2jIeJdftMYsL57c/s989/top-10-pages-2020.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="720" data-original-width="989" height="291" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEii3bLM0LftbS6UKuBUJdMLf64be0zEOk1qZR7uogxJuNEhRGaCeNysEtcRXxeHeZCMl0kVyCTaMzhp_cwI9ETtQGV91XDCGdaKcaHcm2wLCq62c3ONbKY54X5CWFLj2jIeJdftMYsL57c/w400-h291/top-10-pages-2020.png" width="400" /></a></div><div class="separator" style="clear: both; text-align: center;">Top 10 pages for 2020 (by readership). Click to enlarge.</div><div class="separator" style="clear: both; text-align: center;"><br /></div><div class="separator" style="clear: both; text-align: left;">Aside from code and open-source content related to specific blog posts, the <a href="https://github.com/synthetic-daisies">Synthetic Daisies Github organization</a> also hosts the <a href="https://synthetic-daisies.github.io/">Synthetic Daisies meta-blog</a>. This is meant to be a collection of more substantial content from the original blog, organized thematically and presented in a manner similar to an <a href="https://en.wikipedia.org/wiki/Overlay_journal">overlay journal</a>. This includes featured posts and thematic collections, such as posts on Evolution or Models, Philosophy of Science, and Representation.</div><div class="separator" style="clear: both; text-align: center;"><br /></div><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiq2wcFLXaNrvT7yCPH0gU8UW6jko-Xj1KVhBb0-VxjnKz7j4MzNRSUVQerCn-GF9nGv36rIGlWkPeh11iEK3d8ePn18Wf-e7B4jPEgEnRYs8a20CeZGkGKWNzVuNETRW-Qr7kgKEMiet4/s1901/meta-blog.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="897" data-original-width="1901" height="189" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiq2wcFLXaNrvT7yCPH0gU8UW6jko-Xj1KVhBb0-VxjnKz7j4MzNRSUVQerCn-GF9nGv36rIGlWkPeh11iEK3d8ePn18Wf-e7B4jPEgEnRYs8a20CeZGkGKWNzVuNETRW-Qr7kgKEMiet4/w400-h189/meta-blog.png" width="400" /></a></div><div class="separator" style="clear: both; text-align: center;">Check out the <a href="https://synthetic-daisies.github.io/">Synthetic Daisies meta-blog</a>. Click to enlarge.</div><p></p><p style="text-align: left;">That's all for this year. Check us out in 2021 with a whole new set of posts!</p>Bradly Aliceahttp://www.blogger.com/profile/06482487682656113637noreply@blogger.com0tag:blogger.com,1999:blog-1792896637814721350.post-45515130056396614852020-12-18T15:40:00.001-06:002020-12-24T16:08:42.845-06:00Observer-dependent Models @ the Philosopher's Web Cafe<p style="text-align: center;"> </p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjZKvKrR0iYoYL2uJttS7N2io112vi8hL4e3R0lWMrGATs8PoMBGWBoln_7-egEleBjxYN4YqGD2d9sxp2hjIFA5kUH8uwYM4bA_qLeFcloon95swJMm1KkvBWv87UbpLWq9dn1Fz2jy-I/s567/PWC.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="400" data-original-width="567" height="283" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjZKvKrR0iYoYL2uJttS7N2io112vi8hL4e3R0lWMrGATs8PoMBGWBoln_7-egEleBjxYN4YqGD2d9sxp2hjIFA5kUH8uwYM4bA_qLeFcloon95swJMm1KkvBWv87UbpLWq9dn1Fz2jy-I/w400-h283/PWC.png" width="400" /></a></div><br /><p></p><p>I gave a talk called "Observer-dependent Models" to the Philosopher's Web Cafe on December 11. I have made the <a href="https://figshare.com/articles/presentation/Observer-dependent_Models/13340306">slides available here</a>, and the <a href="https://youtu.be/uLCAGpqLMA8">recording is here</a>. Thanks to Jesse Parent (Orthogonal Lab Manager) and Charlotte Guo (series host) for hosting. It will be almost like <a href="https://hbr.org/2020/04/how-to-elevate-your-presence-in-a-virtual-meeting">being there</a> (almost). </p><p>The talk involved reviewing and redefining the role of observers in empirical and simulated systems. "Observer" refers mostly to computational agents (agent-based simulation and AI), although many of the ideas introduced here may apply to the analysis of empirical observations (experiments). Here is the abstract:</p><p style="text-align: left;"><span id="docs-internal-guid-aeacd606-7fff-061c-3f5f-77bf587524d1"><span style="font-variant-east-asian: normal; font-variant-numeric: normal; vertical-align: baseline; white-space: pre-wrap;"><span style="font-family: times;"></span></span></span></p><blockquote style="text-align: justify;"><span style="font-family: times;">In many areas of science and philosophy, observers are seen as an integral part of understanding the natural world. Aside from a pedagogical role, observers are seen as less important in computational forms of inquiry. In this talk, I will reconsider a role for the observer in computational models as fully integrated with the agent. perhaps more fundamentally, causal outcomes and system dynamics are seen to be contingent on observers, while empirical observations themselves are dependent upon the actions of observers. As this is an article of faith in some interpretations of quantum mechanics, we extend this to algorithmic systems with a combinatorial solution space. The role for observers in computational and empirical investigations is established superficially using a number of concepts, including cybernetics, embodiment, and perceptual information processing. Then we will be introduced to more concrete examples of observer-oriented computational agents, such as observer-emitter systems and viewpoint networks. Finally, we will discuss how this approach goes beyond constructivism to consider multiple observers, multiple perspectives (relativism), and how they affect the interpretation of results.</span></blockquote><p><span style="font-family: times;">There is a lot to follow up on from this talk, including a number of themes to explore within the topic of agent-based observers, with more to come in the new year. </span></p><div class="separator" style="clear: both; text-align: center;"><span style="font-family: times;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj_t1cco8gjJ5t1VnK7cheU0zbgsFMpEUZncz0uyYsDPNvz_Ko9YTPvspwiWj9hn9rHhMnn5zwscgjR81P1S7g2-wsqqKOBAKbgel81eBtpDPs_dN2zr4JwZyXC4Pftsz81FjpSi2jwYCI/s960/Observer-dependent+Models.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="540" data-original-width="960" height="225" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj_t1cco8gjJ5t1VnK7cheU0zbgsFMpEUZncz0uyYsDPNvz_Ko9YTPvspwiWj9hn9rHhMnn5zwscgjR81P1S7g2-wsqqKOBAKbgel81eBtpDPs_dN2zr4JwZyXC4Pftsz81FjpSi2jwYCI/w400-h225/Observer-dependent+Models.png" width="400" /></a></span></div><span style="font-family: times;"><br /><p style="text-align: center;"><br /></p></span><p></p>Bradly Aliceahttp://www.blogger.com/profile/06482487682656113637noreply@blogger.com1