It's that time again -- time for the OpenWorm Annual meeting. Below are the slides I presented on progress and the latest activities in the DevoWorm group. If anything looks interesting to you, and you would like to contribute, please let me know. Click on any slide to enlarge.
November 30, 2023
May 2, 2021
DevoLearn (Open-source) Maintenance and Evangelism
2021 has been a busy year for the DevoLearn initiative. Not only has Mayukh Deb been busy maintaining and generating new versions of the DevoLearn pre-trained model, but I (Bradly Alicea) has been engaging in technology evangelism to advance awareness and involvement in the initiative. The DevoLearn pre-trained model software (for C. elegans embryogenesis) is now at version 0.3.0, and has garnered 12 contributors making 165 commits (largely since January 2021). Our involvement in Google Summer of Code has bolstered many of these contributions. While our popularity is currently limited, we are trying to spread the word.
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 (DevoLearn: Engaging learners with Computational Developmental Biology) is a flash talk given to the OSF Education Un-conference on Open Scholarship Practices in Education Research, held in February. The second presentation was a longer (15-minute) presentation to the INCF Assembly (DevoLearn: a platform for open Developmental Data Science, Machine Learning, and Education), held in April.
December 18, 2020
Observer-dependent Models @ the Philosopher's Web Cafe
I gave a talk called "Observer-dependent Models" to the Philosopher's Web Cafe on December 11. I have made the slides available here, and the recording is here. Thanks to Jesse Parent (Orthogonal Lab Manager) and Charlotte Guo (series host) for hosting. It will be almost like being there (almost).
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:
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.
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.
April 17, 2017
Breaking Out From the Tyranny of the PPT
Perhaps the failures of PowerPoint are not about varied styles of communication across different domains of knowledge (scientific, business, legal), but more about the relevance of ideas and their overall structure. Relevance theory (Dan Sperber and Deidre Wilson) suggests that are biased according to what seems relevant [3]. Some of this is mediated by the cognition of attentional resources, but there is also an underappreciated role of cultural preferences and constraints. In the realm of science communication, the narrowly-defined relevance of typical PowerPoint design practice might encourage some aspects of scientific practice (science as memorization of facts, still images, simple graphs) at the expense of others (experimentation, data exploration, theory-building).
The tyrrany of representational orthodoxy, PowerPoint style. On the other hand, this is actually pretty good in terms of available clip art. While perfectly suitable for business-oriented communication (e.g. team-building, simple storytelling), this may or may not be suitable for other domains of knowledge.
[2] Ralph, P. (2015). Why universities should get rid of PowerPoint and why they won’t. The Conversation, June 23.
[3] Sperber, D. and Wilson, D. (1995). Relevance: Communication and Cognition. Blackwell Publishers, Oxford, UK.
[4] Alicea, B. (2012). Moving the Still, courtesy of the .gifted. Synthetic Daisies blog, October 19.
[5] Greenberg, A. (2010). The Underground Art of PowerPoint. Forbes, May 11. Some examples of PowerPoint art (converted to YouTube videos) include:
a) "Infiltration" by Jeremiah Lee.
b) "Joiners" by blastoons.
February 21, 2017
New Orthogonal Laboratory Methods
[2] Brown, C.T. (2017). Topics and concepts I'm excited about (Paper of the Future). Living in an Ivory Basement blog, January 9.
[3] the very notion of "high-risk research" is biased toward a fear of failure. Considering what is usually thrown into that bucket, "high-risk research" is a statement of cultural values more than an inherent risk. Removing the industrial, one-size-fits-all aspect of research might be a way to mitigate risk.
[5] Perkel, J.M. (2017). How Scientists Use Slack. Nature, 541, 123-124.
[6] Washietl, S. (2016). 6 Ways to Streamline Communication in Your Research Group Using Slack. Paperpile blog, April 12.
October 22, 2015
Arriving at October 21, 2015...... and beyond
Billings, L. Time Travel Simulation Resolves "Grandfather Paradox". Scientific American, September 2 (2015).

.png)
.png)
.png)
.png)
.png)
.png)
.png)
.png)
.png)






























