Connor McShaffrey
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cmcshaff.bsky.social
Connor McShaffrey
@cmcshaff.bsky.social
250 followers 220 following 110 posts
CogSci / Bioengineering PhD Candidate, NSF Graduate Research Fellow (he/him)

https://sites.google.com/view/connor-mcshaffrey/bio

Indiana University, Vassar '21 🎓

Modeling life and its limits with dynamical systems 🦠 microscopy for fun 🔬
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cmcshaff.bsky.social
Connor McShaffrey @cmcshaff.bsky.social · Nov 13
Hello! Given all the new faces, I wanted to make an introduction post. I am a PhD student supervised by Randall Beer at Indiana University. My interests are in analyzing models of agent-environment dynamics to predict whether an agent will persist or perish under particular conditions. Papers below!
Reposted by Connor McShaffrey
profbrunt.bsky.social
Epstein-Barr Virus #EBV was linked to #MultipleSclerosis - now a plausible cause has been found, misidentification by longterm memory T-cells that pick on the wrong protein, ANO2, instead of the EBV-antigen. Massive inflection towards the elimination of MS!!!
🧪🧠Cell www.cell.com/cell/fulltex...
Anoctamin-2-specific T cells link Epstein-Barr virus to multiple sclerosis
Researchers identified anoctamin-2 (ANO2) as a frequent autoimmune target in multiple sclerosis, with T cell responses against ANO2 occurring in over half of patients. These ANO2-specific T cells shar...
www.cell.com
January 15, 2026 at 1:41 AM
Reposted by Connor McShaffrey
annaleen.bsky.social
Need an antidote to the horror and paralysis? See you tomorrow at 11 pacific time. citylights.com/events/panel...
Saturday Jan 10, 11 am PST Virtual panel discussion: speculative stories about political protest, resistance, and hope. Karen Lord, Annalee Newitz, and Malka Older. Free! Registration required (see link in post)
January 10, 2026 at 1:26 AM
cmcshaff.bsky.social
The last piece of microscope art I did in 2025 :) reflected light off a surface of a bubble and magnified by 100x, manipulated to give a planet-like effect

Wishing all a great start to 2026!
January 1, 2026 at 7:42 PM
cmcshaff.bsky.social
Where does the life-death boundary come from, and how will a cell's dynamics unfold relative to it? Myself, Eran Agmon, and Randy Beer argue for a theory of cellular viability, with new global organizing principles for cell fate.

Preprint: arxiv.org/pdf/2511.07847
A schematic of a death event in a multicellular system, where the loss of one cell results in a collapse in the dimensionality of the system. Each cell's essential variables have their ranges capped by viability constraints.
November 12, 2025 at 6:36 PM
Reposted by Connor McShaffrey
ricardsole.bsky.social
How “intelligent” is a slime mold? When it solves mazes, it might not be thinking:it’s obeying physics. Our new paper with
@jordiplam.bsky.social shows how it follows a least action principle,letting physics do the job arxiv.org/pdf/2511.08531
@drmichaellevin.bsky.social @docteur-drey.bsky.social
November 12, 2025 at 4:17 AM
cmcshaff.bsky.social
This is some really interesting work at the intersection of animal behavior, agent-environment modeling, and dynamical systems analysis.

Definitely worth checking out!

(Also, Eden is a pretty groovy guy; you should consider following him.)
eforbes.bsky.social Eden Forbes @eforbes.bsky.social · Nov 3
Happy to say one of my dissertation projects was accepted for publication in Movement Ecology!

We evolved small neural controllers to show how forager perception (visual v. tactile) and target signals generate different movement patterns during pursuit.

Pre-print: www.biorxiv.org/content/10.1...
November 3, 2025 at 7:46 PM
Reposted by Connor McShaffrey
pessoabrain.bsky.social
Do you review papers? Check out Earl's @earlkmiller.bsky.social recommendations.
The one that i would emphasize the most:

jocnf.pubpub.org/pub/qag76ip8...
October 7, 2025 at 4:33 PM
Reposted by Connor McShaffrey
hirokisayama.bsky.social
#ALIFE2025 #TONAL2025 satellite
October 6, 2025 at 12:45 AM
cmcshaff.bsky.social
It was an honor to be invited to speak at the TONAL workshop on the role of noise in Artificial Life! www.oist.jp/research/res...

Looking forward to speaking about our recent work again later on at #ALife2025! Paper to be posted soon 🙂
ECSU - ALIFE
www.oist.jp
October 6, 2025 at 7:46 PM
Reposted by Connor McShaffrey
patchthompson.bsky.social
Anyway, here is some actually incredible news

www.bbc.co.uk/news/article...
Huntington's disease successfully treated for first time
One of the most devastating diseases finally has a treatment that can slow its progression and transform lives, tearful doctors tell BBC.
www.bbc.co.uk
September 24, 2025 at 12:24 PM
cmcshaff.bsky.social
I am super excited to read this paper! Viability, semantic information, and more :)

journals.aps.org/prxlife/abst...
Physics of Life: Exploring Information as a Distinctive Feature of Living Systems
Living systems are defined by their active acquisition and use of information. This Roadmap surveys current research on life's information processes and their importance for the search for life beyond...
journals.aps.org
September 5, 2025 at 1:45 AM
cmcshaff.bsky.social
Hello friends of bluesky! I am finishing my PhD this academic year, and am looking for postdocs and faculty applications in the realm of nonlinear dynamics, biology, complex systems, and CogSci. Any recommendations for places I should be looking at?
August 29, 2025 at 3:51 PM
cmcshaff.bsky.social
Anyone interested in autopoiesis and Randall Beer's formalization of it in Conway's Game of Life would probably enjoy looking at Tom's undergrad thesis, where he extends the ideas to the "Larger than Life" and "Real Life" family of cellular automata!
tomgaul.bsky.social Tom Gaul @tomgaul.bsky.social · Aug 13
This spring I completed my senior honors thesis in Cognitive Science at IU! I extended Randall Beer's formalization of autopoiesis in the Game of Life to a continuous space limit called RealLife.

It is available here: tgaul.gitlab.io/publications....
Author: Thomas M. Gaul Title: Biological Organisation and Viability: A Theory of Autopoiesis in Cellular and Euclidean Automata Abstract: Increasingly, biologists are emphasising the cell as the most fundamental unit of life, and importantly, a view of the cell as an emergent, dynamic object irreducible to its molecular composition — “greater than the sum of its parts.” But what makes a cell itself living? Most answers to this question are unsatisfactory: lists of properties or behaviours that always have exceptions. Moreover, there is a lack of consensus that does not appear to be near resolution. The theory of autopoiesis offers a potential solution here, providing an operational definition of the organisation of a cell, independent of what molecules compose it. Autopoietic theory allows us to answer questions about when a cell dies, and how it can behave. However, for it to realise this utility, rigorous theories need to be developed for specific models of emergent individuals. Beer (2020b) has previously used the Game of Life cellular automaton as one such model, and developed a mathematical theory of autopoiesis that can predict the behaviour and death of an emergent individual (Beer, McShaffrey, & Gaul, 2024). This thesis extends and reformulates this work to a broader class of cellular automata, called Larger than Life (LtL) (Evans, 1996). I then further extend the LtL theory to a Euclidean automata, called RealLife (Pivato, 2007), and provide evidence of the convergence of autopoiesis in LtL to RealLife. I also introduce a method for deriving automata rules from the organisation of an individual. Finally, I discuss the implications autopoietic theory has for our understanding of life and cognition, including a reevaluation of the relation between autopoiesis and the enactive approach to cognition (Di Paolo, 2005; Varela et al., 2017).
August 17, 2025 at 4:40 PM
cmcshaff.bsky.social
This looks like a nice entry point for folks interested in the intersection of dynamical systems theory and cell biology!
pauformosa.bsky.social Pau Formosa-Jordan @pauformosa.bsky.social · Aug 4
Introducing five concepts from dynamical systems to decode developmental regulatory mechanisms, have a read! @perez-carrasco.bsky.social‬ @roederlab.bsky.social @mpipz.bsky.social This effort started in a morphogenesis meeting @kitp-ucsb.bsky.social‬ in 2023. journals.biologists.com/dev/article/...
Adapted from Fig. 1 from Kadiyala et al 2025.
August 4, 2025 at 6:37 PM
Reposted by Connor McShaffrey
quantamagazine.bsky.social
Forgotten studies from the early 20th century are helping scientists probe how and whether individual cells can learn and remember.
What Can a Cell Remember? | Quanta Magazine
A small but enthusiastic group of neuroscientists is exhuming overlooked experiments and performing new ones to explore whether cells record past experiences — fundamentally challenging what memory…
www.quantamagazine.org
August 1, 2025 at 11:18 PM
cmcshaff.bsky.social
Very excited to see the final version of this paper out!
July 12, 2025 at 3:55 PM
cmcshaff.bsky.social
I have been following this work and it is really neat stuff! Excited to see this one
June 24, 2025 at 9:34 PM
Reposted by Connor McShaffrey
melaniemitchell.bsky.social
Alison Gopnik, telling it like it is, at Johns Hopkins.
May 29, 2025 at 11:38 PM
Reposted by Connor McShaffrey
pessoabrain.bsky.social
Principles of Biological Autonomy by Francisco Varela, new edition

Now that biology is finally catching up with Varela (eg agency is commonplace and teleology not scary) the book is probably more timely than ever. Here's my physical version!

The commentary by Di Paolo and E. Thompson very helpful.
May 5, 2025 at 5:21 PM
Reposted by Connor McShaffrey
isalofficial.bsky.social
🏆🏆AWARD SEASON🏆🏆

The International Society for Artificial Life is seeking nominations for our annual awards, recognising the efforts of our community.

We have 7 award categories to choose from. We welcome all nominations (& self-nominations). The specific awards are as follows:

👇

#ALIFE
April 2, 2025 at 6:00 AM
Reposted by Connor McShaffrey
alleninstitute.org
#Neuroskyence students! We're brainstorming ways to support your development over this summer break, esp. given the changes in summer intern programs across our fields. What other opportunities would you like to see?

Some ideas: undergrad-focused webinars, self-paced courses, challenges, etc.
February 25, 2025 at 5:01 PM
cmcshaff.bsky.social
Thomas does some really cool work. I highly recommend taking a look!
thosvarley.bsky.social Thomas F. Varley @thosvarley.bsky.social · Feb 23
If anyone in the complex systems/computational neuroscience field in Europe is looking to poach an American scientist, I'm interested in what might be out there.
My scholar profile: scholar.google.com/citations?hl...
February 24, 2025 at 12:55 AM
Reposted by Connor McShaffrey
aghostinthefigures.bsky.social
Getting back in the habit of making math/physics animations in my spare time. Here's an old favorite of mine; the formation of a homoclinic tangle!

I'm hoping to upload the code for a few of these on GitHub, once I feel it's polished enough for public viewing. Hopefully won't take too long!
February 23, 2025 at 4:34 PM