Connor McShaffrey
@cmcshaff.bsky.social
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 🔬
https://sites.google.com/view/connor-mcshaffrey/bio
Indiana University, Vassar '21 🎓
Modeling life and its limits with dynamical systems 🦠 microscopy for fun 🔬
Pinned
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!
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
Preprint: arxiv.org/pdf/2511.07847
November 12, 2025 at 6:36 PM
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
Preprint: arxiv.org/pdf/2511.07847
Reposted by Connor McShaffrey
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
@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
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
@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
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.)
Definitely worth checking out!
(Also, Eden is a pretty groovy guy; you should consider following him.)
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...
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
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.)
Definitely worth checking out!
(Also, Eden is a pretty groovy guy; you should consider following him.)
Reposted by Connor McShaffrey
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...
The one that i would emphasize the most:
jocnf.pubpub.org/pub/qag76ip8...
October 7, 2025 at 4:33 PM
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...
The one that i would emphasize the most:
jocnf.pubpub.org/pub/qag76ip8...
Reposted by Connor McShaffrey
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 🙂
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
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 🙂
Looking forward to speaking about our recent work again later on at #ALife2025! Paper to be posted soon 🙂
Reposted by Connor McShaffrey
Reposted by Connor McShaffrey
Wohoo: @gjseverino.bsky.social's paper is accepted w minor revs in Proceedings of the Royal Society B: Biological Sciences!
"Social Contingency in Embodied Neural Networks relies on Co-Constructed Dynamical Mechanisms"
Follow him + his insanely creative modeling research!
Link to paper forthcoming
"Social Contingency in Embodied Neural Networks relies on Co-Constructed Dynamical Mechanisms"
Follow him + his insanely creative modeling research!
Link to paper forthcoming
September 23, 2025 at 10:31 PM
Wohoo: @gjseverino.bsky.social's paper is accepted w minor revs in Proceedings of the Royal Society B: Biological Sciences!
"Social Contingency in Embodied Neural Networks relies on Co-Constructed Dynamical Mechanisms"
Follow him + his insanely creative modeling research!
Link to paper forthcoming
"Social Contingency in Embodied Neural Networks relies on Co-Constructed Dynamical Mechanisms"
Follow him + his insanely creative modeling research!
Link to paper forthcoming
I am super excited to read this paper! Viability, semantic information, and more :)
journals.aps.org/prxlife/abst...
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
I am super excited to read this paper! Viability, semantic information, and more :)
journals.aps.org/prxlife/abst...
journals.aps.org/prxlife/abst...
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
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?
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!
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....
It is available here: tgaul.gitlab.io/publications....
August 17, 2025 at 4:40 PM
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!
This looks like a nice entry point for folks interested in the intersection of dynamical systems theory and cell biology!
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/...
August 4, 2025 at 6:37 PM
This looks like a nice entry point for folks interested in the intersection of dynamical systems theory and cell biology!
Reposted by Connor McShaffrey
New paper from the lab:
"The Effect of Timescale Dependence on Dyadic Interactions"
GJ Severino, SL Winkler, AS Barwich
Proceedings of the Annual Meeting of the Cognitive Science Society 47
escholarship.org/uc/item/8h10...
"The Effect of Timescale Dependence on Dyadic Interactions"
GJ Severino, SL Winkler, AS Barwich
Proceedings of the Annual Meeting of the Cognitive Science Society 47
escholarship.org/uc/item/8h10...
The Effect of Timescale Dependence on Dyadic Interactions
Author(s): Severino, Gabriel Juliano; Winkler, Sasha L; Barwich, Ann-Sophie | Abstract: Interactions between agents are supported through a continuous process of detecting and responding to behaviors ...
escholarship.org
August 4, 2025 at 12:04 AM
New paper from the lab:
"The Effect of Timescale Dependence on Dyadic Interactions"
GJ Severino, SL Winkler, AS Barwich
Proceedings of the Annual Meeting of the Cognitive Science Society 47
escholarship.org/uc/item/8h10...
"The Effect of Timescale Dependence on Dyadic Interactions"
GJ Severino, SL Winkler, AS Barwich
Proceedings of the Annual Meeting of the Cognitive Science Society 47
escholarship.org/uc/item/8h10...
Reposted by Connor McShaffrey
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
Forgotten studies from the early 20th century are helping scientists probe how and whether individual cells can learn and remember.
Very excited to see the final version of this paper out!
Final version is out:
www.nature.com/articles/s42...
"Associative conditioning in gene regulatory network models increases integrative causal emergence". 🧪
Described here:
thoughtforms.life/learning-to-...
www.nature.com/articles/s42...
"Associative conditioning in gene regulatory network models increases integrative causal emergence". 🧪
Described here:
thoughtforms.life/learning-to-...
Forms of life, forms of mind | Dr. Michael Levin | Learning to Be: how learning strengthens the emergent nature of collective intelligence in a minimal agent
A description of our findings in a recent preprint on effects of training on causal emergence in a model of gene-regulatory networks
thoughtforms.life
July 12, 2025 at 3:55 PM
Very excited to see the final version of this paper out!
I have been following this work and it is really neat stuff! Excited to see this one
Our paper on single-cell learning is now published in
@currentbiology.bsky.social!
@wallaceucsf.bsky.social
sciencedirect.com/science/arti...
@currentbiology.bsky.social!
@wallaceucsf.bsky.social
sciencedirect.com/science/arti...
June 24, 2025 at 9:34 PM
I have been following this work and it is really neat stuff! Excited to see this one
Reposted by Connor McShaffrey
Alison Gopnik, telling it like it is, at Johns Hopkins.
May 29, 2025 at 11:38 PM
Alison Gopnik, telling it like it is, at Johns Hopkins.
Reposted by Connor McShaffrey
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.
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
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.
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.
Reposted by Connor McShaffrey
🏆🏆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
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
🏆🏆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
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
Reposted by Connor McShaffrey
#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.
Some ideas: undergrad-focused webinars, self-paced courses, challenges, etc.
February 25, 2025 at 5:01 PM
#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.
Some ideas: undergrad-focused webinars, self-paced courses, challenges, etc.
Thomas does some really cool work. I highly recommend taking a look!
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...
My scholar profile: scholar.google.com/citations?hl...
February 24, 2025 at 12:55 AM
Thomas does some really cool work. I highly recommend taking a look!
Reposted by Connor McShaffrey
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!
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
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!
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!
Reposted by Connor McShaffrey
‼️FYI.
The deadline for paper contributions is May 4th 2025*.
Our submission platform will open shortly.
Note: This year looks a bit different to previous years. We'll be inviting 3 types of contributions:
Full papers (3-8 pages)
Summaries (2 pages) ✨️new!✨️
Late Breaking Abstracts (2 pages)*
👇
The deadline for paper contributions is May 4th 2025*.
Our submission platform will open shortly.
Note: This year looks a bit different to previous years. We'll be inviting 3 types of contributions:
Full papers (3-8 pages)
Summaries (2 pages) ✨️new!✨️
Late Breaking Abstracts (2 pages)*
👇
February 16, 2025 at 8:39 AM
‼️FYI.
The deadline for paper contributions is May 4th 2025*.
Our submission platform will open shortly.
Note: This year looks a bit different to previous years. We'll be inviting 3 types of contributions:
Full papers (3-8 pages)
Summaries (2 pages) ✨️new!✨️
Late Breaking Abstracts (2 pages)*
👇
The deadline for paper contributions is May 4th 2025*.
Our submission platform will open shortly.
Note: This year looks a bit different to previous years. We'll be inviting 3 types of contributions:
Full papers (3-8 pages)
Summaries (2 pages) ✨️new!✨️
Late Breaking Abstracts (2 pages)*
👇
This book has had a profound influence on me. I am so excited to see it in print!
"Can a book be ahead of its time by 50 years?! The answer is a definitive ‘yes’ in the case of this phenomenal book by Francisco Varela. A real gem of a book about the philosophical foundations of biology and so much more." - Luiz Pessoa @pessoabrain.bsky.social mitpress.mit.edu/978026255140...
Principles of Biological Autonomy
Francisco Varela’s Principles of Biological Autonomy was a groundbreaking text when it was first published in 1979, putting forth a novel theory of how...
mitpress.mit.edu
February 12, 2025 at 8:23 PM
This book has had a profound influence on me. I am so excited to see it in print!
Reposted by Connor McShaffrey
NIH and now NSF.
Effectively the entirety of science funding in America is on hold.
Effectively the entirety of science funding in America is on hold.
I’m an NSF panel reviewer that was scheduled to meet today. Just got notice that all NSF panels were canceled today. I reviewed some innovative proposals in support of students. Devastating if these scholars don’t get to do this work. For the love of science & students I hope this is just a delay.💔
January 27, 2025 at 5:34 PM
NIH and now NSF.
Effectively the entirety of science funding in America is on hold.
Effectively the entirety of science funding in America is on hold.