March 31, 2022

Updates on Open Source Community Tools

All hail the Guidance (and Attribution) Tree!

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 19-minute tour of a guidance tree based on the Rokwire Community.


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.

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 Authorship Tree, an idea I worked on circa 2017 in the Orthogonal Research and Education Lab. 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.


Recombining your Technical Stack
During the month of March 2021, we considered how we might strive for a Full Stack community. 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. 

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? 


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 Jitsi platform is a good example of this. Jitsi instances can be started through a web browser or mobile app, and Jitsi servers can be customized by specific organizations


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 whiteboard (Jamboard) and file sharing (Ignite RealTime) tools also work well with this shift. Doing a series of contingency tests based on common use cases may help. Adopting OBS 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. 

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 visualize Github tasks and milestones (ZenHub) is one example of a tool with multiple dependencies.

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.

February 15, 2022

Gyrification of the Tree of Mammals

For this year's Darwin Day post, I will be reviewing the evolutionary origins and developmental emergence of gyrification of the Mammalian brain. Gyrification occurs when the neocortex, or six layered cortex on the dorsal surface of Mammalian brains, exhibits wrinkles and folds rather than a smooth surface (lissencephaly). Gyrification is measured using the gyrification index (or GI). GI can range from 5.6 in Pilot whales (Globicephala) to 3.8 in Elephants (Loxodonta) and 2.6 in Humans (Homo) [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. 


Figure 1. A phylogeny of primate brain evolution (with Mammalian outgroups), with a focus on the origin of traits found in the human brain. COURTESY [2].

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. 

Figure 2. Allometric scaling across select Mammalian brain, showing an increase in gyrification for larger brains. COURTESY [4].

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.

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. 




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. COURTESY [6].

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]. 

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.


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). COURTESY [10].

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. 

Once again, an evolutionary conundrum. Happy evolutioning!

NOTES:

[1] Johnson, S. Number and Complexity of Cortical Gyrii. Center for Academic Research and Training in Anthropogeny. La Jolla, CA. Accessed: February 13, 2022. 

[2] Franchini, L.F. (2021). Genetic Mechanisms Underlying Cortical Evolution in Mammals. Frontiers in Cell and Developmental Biology, 9, 591017.

[3] Striedter, G. (2005). Principles of brain evolution. Sinauer, Sunderland, MA.

[4] Tallinen, T., Chung, J.Y. , Biggins, J.S., and Mahadevan, L. (2014). Gyrification from constrained cortical expansion. PNAS, 111(35), 12667-12672.

[5] Shingleton, A. (2010) Allometry: The Study of Biological Scaling. Nature Education Knowledge, 3(10), 2.

[6] Tallinen, T., Chung, J.Y., Rousseau, F., Girard, N., Lefevre, J., and Mahadevan, L. (2016). On the growth and form of cortical convolutions. Nature Physics, 12, 588–593.

[7] Zilles, K., Palomero-Gallagher, N., and Amunts, K. (2013). Development of cortical folding during evolution and ontogeny. Trends in Neurosciences, 36(5), 275-284. 

[8] Jayaraman, D., Bae, B-I., and Walsh, C.A. (2018). The Genetics of Primary Microcephaly. Annual Review of Genomics and Human Genetics, 19, 177-200.

[9] Heuer, K., Gulban, O.F., Bazin, P-L., Osoianu, A., Valabregue, R., Santin, M., Herbin, M., and Toro, R. (2019). Evolution of neocortical folding: A phylogenetic comparative analysis of MRI from 34 primate species. Cortex, 118, 275-291.

[10] Kelava, I., Lewitus, E., and Huttner, W.B. (2013). The secondary loss of gyrencephaly as an example of evolutionary phenotypical reversalFrontiers in Neuroanatomy, 7, 16.


December 3, 2021

MAIN and Neuromatch Conference Presentations


The Orthogonal Research and Education Lab is on the virtual move! We have been featured at two conferences this week. The first conference is MAIN (Montreal Artificial Intelligence-Neuroscience) conference, a hybrid conference that focused on cutting-edge research in Neuro-AI. Our submission (Developmental Embodied NeuroSimulation) is a group effort and summarizes our work in this area over the past few years. The graphical abstract can be found below.



We also had a presence at Neuromatch 4, 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. 


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 "The Universal Theory of Switching", 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. 

Another talk is on "Allostatic Kinds". 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 CEEALAR (Center for Enabling EA Learning and Research), an academic hostel located in Blackpool, UK.

Daniela Cialfi has built upon the lab's work on Meta-brain Models to develop "Economic Meta-brains", 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. 

Finally, our presentation on "Gibsonian Information" comes with a preprint. Gibsonian Information is the information content of direct perceptual processing (sensu 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.



Graphical abstract for the Gibsonian Information paper/presentation (direct perception as information content).


November 3, 2021

Ten years of "Virtual Reality in Neuroscience Research and Therapy"

Ten years ago today (November 3), me and co-authors Corey Bohil and Frank Biocca published the paper "Virtual Reality in Neuroscience Research and Therapy" in Nature Reviews Neuroscience. Happy Birthday, paper!

Click to enlarge.

This article made the issue cover of the containing issue. A closeup of the cover art (below) is entitled "Virtual Reality Reaches New Heights" by Kirsten Lee. Great image of a digital mountain range.

Click to enlarge.

After 10 years, this publication has been cited 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. 

COURTESY: Google Scholar. Click to enlarge.

About four years later, I single-authored a paper at F1000 Research called "Animal-oriented virtual environments: illusion, dilation, and discovery", 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.

October 25, 2021

Opening Access, Virtual, Distributed Lab Edition


Welcome to Open Access Week 2021! This year's theme is building structural equity. In the Orthogonal Research and Education Lab and the DevoWorm group, 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.


Figure 1. From the short film "What is Open Access" (PhD Comics, 2012).

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 Google Summer of Code and Neuromatch Academy.

Figure 2. The global reach (physical and virtual) of the Orthogonal Lab.

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.

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.

            

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 "Building a Distributed Virtual Laboratory Adjacent to Academia". 

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 contact us. Additionally, be sure to check out the #OAWeek hashtag for this blog (Synthetic Daisies), as we have content going back to 2016 on a variety of topics. 


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