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Connor McShaffrey

@cmcshaff.bsky.social
256 followers 228 following 124 posts

CogSci / Bioengineering PhD, Previous NSF Graduate Research Fellow (he/him) sites.google.com/view/connor-mcshaf… Indiana University '26, Vassar '21 🎓 Modeling life and its limits with dynamical systems 🦠 microscopy for fun 🔬

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Reposted by Connor McShaffrey
Physical Review Letters @physrevlett.aps.org · 28/09/2026
To simplify multiscale systems, scientists often average out fast variables and focus on slow ones. New work shows how this method neglects complex, narrow pathways, or “singular funnels,” and misrepresents systems’ resilience to perturbations. More: go.aps.org/3Tp3dxZ
A color gradient contour plot illustrating a singular basin with a singular funnel. On the right, a large region shaded with an orange-yellow color gradient represents the basin of attraction. It contains a thick black vertical curve labeled ɣc (periodic rotation). This region narrows in the lower half, passing a point on the left edge labeled e2 (saddle equilibrium). In the upper half, the region curves around a white space that contains a black point labeled e1 (stable equilibrium). To the left of this region, five very narrow, deep orange vertical strips extend across white space.
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Ann-Sophie Barwich @smellosopher.bsky.social · 22/08/2026
"Sniffing, Physiology, and Search: Odor Navigation in Embodied Neural Networks" Extended paper published; soon Open Access. In the meantime, contact the principal scientist @gjseverino.bsky.social - who is on the market, btw- for access to his study. LINK TO PAPER: direct.mit.edu/artl/article...
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The Arthur C. Clarke Award @clarkeaward.bsky.social · 08/08/2026
We're backing Children of Time: The Roleplaying Game on @kickstarter.com www.kickstarter.com/projects/gsh... HAL says he wants to be GM... 😱
kickstarter.com
Children of Time: The Roleplaying Game
Create millennia-spanning sci-fi epics in this groundbreaking roleplaying game based on the award winning Children of Time novels.
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Ricard Solé @ricardsole.bsky.social · 02/08/2026
What separates life from death? What makes the cell on the left different from the one on the right? These are questions I explore in my new @princetonupress.bsky.social book. At the cell scale, death begins when the distinction between inside & outside collapses. press.princeton.edu/books/hardco...
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Connor McShaffrey @cmcshaff.bsky.social · 04/07/2026
This looks like it is going to be fascinating! One thing I have been fixated on in research is how important it is to seriously consider death if we want to better understand life, and this book looks like it will land right in that sweet spot!
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Sasha | Kai Dao 🔬 @kaidaoscience.bsky.social · 19/06/2026
8 hours. That’s all fish need to heal wounds 🐟⏱️ Why are they so fast compared to humans? I break down the science of rapid regeneration in a microscopy story 🔬 Watch here: youtu.be/Mt9f61adaP0 #FluorescenceFriday #Microscopy
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Connor McShaffrey @cmcshaff.bsky.social · 20/06/2026
Very excited to announce that the final version of our paper, "Matters of Life and Death in Computational Cell Biology," is now published through npj Systems Biology and Applications! www.nature.com/articles/s41... #Biology #CellBiology #ComputationalBiology #DynamicalSystems
nature.com
Matters of life and death in computational cell biology - npj Systems Biology and Applications
npj Systems Biology and Applications - Matters of life and death in computational cell biology
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Connor McShaffrey @cmcshaff.bsky.social · 02/04/2026
Very honored to have received the IU Cognitive Science Program's 2026 Outstanding Research award!
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Diverse Intelligences Summer Institute #DISI @divintelligence.bsky.social · 02/03/2026
📣📣📣 Applications for the 2026 Diverse Intelligences Summer Institute (DISI) are now open!! Are you interested in intelligence, mind, and cognition in all its forms? Early-career scholars from any discipline—and storytellers in any medium—are encouraged to apply! More info: disi.org
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Miguel Aguilera @maguilera.net · 20/02/2026
New paper out in PRL! With @artemyte.bsky.social and Sosuke Ito, we combine stochastic thermodynamics with nonequilibrium MaxEnt in large networks to infer entropy dissipation in high-dimensional systems from time series (up to 1000 variables!) journals.aps.org/prl/abstract...
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Annalee Newitz @annaleen.bsky.social · 03/02/2026
This deal is incredible & it's for the best cause! You can get ALL the fiction by me and @charliejane.bsky.social from @humblebundle.com for a low, low price -- and all sales benefit the Miss Major Alexander L. Lee Black Trans Justice Center. www.humblebundle.com/books/charli...
A picture of Annalee and Charlie Jane bundled up in their winter clothes, inside a tunnel made of twinkling LED lights. They are smiling and Annalee is sticking out their tongue. A friend is photobombing them in the background, popping up and smiling over Charlie Jane's shoulder.A picture of several novels by Charlie Jane Anders and Annalee Newitz. "Charlie Jane Anders and Annalee Newitz from Tor Books Supporting Miss Major Alexander L Lee TGIJP Black Trans Cultural Center" Book Bundle.
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Dr. Keith R. Brunt @profbrunt.bsky.social · 15/01/2026
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...
cell.com
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...
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Annalee Newitz @annaleen.bsky.social · 10/01/2026
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)
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Connor McShaffrey @cmcshaff.bsky.social · 01/01/2026
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!
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Connor McShaffrey @cmcshaff.bsky.social · 12/11/2025
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.
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Ricard Solé @ricardsole.bsky.social · 12/11/2025
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
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Connor McShaffrey @cmcshaff.bsky.social · 03/11/2025
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.)
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PessoaBrain @pessoabrain.bsky.social · 07/10/2025
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...
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Hiroki Sayama @hirokisayama.bsky.social · 06/10/2025
#ALIFE2025 #TONAL2025 satellite
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Connor McShaffrey @cmcshaff.bsky.social · 06/10/2025
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 🙂
oist.jp
ECSU - ALIFE
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Patch Thompson @patchthompson.bsky.social · 24/09/2025
Anyway, here is some actually incredible news www.bbc.co.uk/news/article...
bbc.co.uk
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.
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Connor McShaffrey @cmcshaff.bsky.social · 05/09/2025
I am super excited to read this paper! Viability, semantic information, and more :) journals.aps.org/prxlife/abst...
journals.aps.org
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...
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Connor McShaffrey @cmcshaff.bsky.social · 29/08/2025
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?
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Connor McShaffrey @cmcshaff.bsky.social · 17/08/2025
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!
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Connor McShaffrey @cmcshaff.bsky.social · 04/08/2025
This looks like a nice entry point for folks interested in the intersection of dynamical systems theory and cell biology!
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Quanta Magazine @quantamagazine.org · 02/08/2025
Forgotten studies from the early 20th century are helping scientists probe how and whether individual cells can learn and remember.
quantamagazine.org
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…
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Connor McShaffrey @cmcshaff.bsky.social · 12/07/2025
Very excited to see the final version of this paper out!
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Connor McShaffrey @cmcshaff.bsky.social · 24/06/2025
I have been following this work and it is really neat stuff! Excited to see this one
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Melanie Mitchell @melaniemitchell.bsky.social · 30/05/2025
Alison Gopnik, telling it like it is, at Johns Hopkins.
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PessoaBrain @pessoabrain.bsky.social · 05/05/2025
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.
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International Society of Artificial Life (ISAL) @isalofficial.bsky.social · 02/04/2025
🏆🏆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
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allen institute @alleninstitute.org · 25/02/2025
#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.
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Connor McShaffrey @cmcshaff.bsky.social · 24/02/2025
Thomas does some really cool work. I highly recommend taking a look!
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Arnaldo Rodriguez-Gonzalez @aghostinthefigures.bsky.social · 23/02/2025
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!
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ALIFE Conference 2025 @alife2025.bsky.social · 16/02/2025
‼️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)* 👇
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Connor McShaffrey @cmcshaff.bsky.social · 12/02/2025
This book has had a profound influence on me. I am so excited to see it in print!
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BWJones @bwjones.bsky.social · 27/01/2025
NIH and now NSF. Effectively the entirety of science funding in America is on hold.
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Robert Rosenbaum @robertrosenbaum.bsky.social · 27/01/2025
Somewhat old news here, but since I'm switching over from the other site: Happy to announce that my Computational Neuroscience textbook was published by MIT Press. The text and code is freely accessible: mitpress.mit.edu/978026254808... (click Open Access) drive.google.com/drive/folder... (1/n)
mitpress.mit.edu
Modeling Neural Circuits Made Simple with Python
An accessible undergraduate textbook in computational neuroscience that provides an introduction to the mathematical and computational modeling of neurons an...
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Connor McShaffrey @cmcshaff.bsky.social · 15/01/2025
A shot I got manipulating the light passing through a soil sample at 250x magnification 🙂
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Ricard Solé @ricardsole.bsky.social · 11/01/2025
Is cognition a universal feature of the living world? How can we define it? Is a nervous system needed? If so, why? If not, why not? Check this fascinating @royalsocietypublishing.org Theme Issue led by @drmichaellevin.bsky.social & co. on Basal Cognition royalsocietypublishing.org/doi/pdf/10.1...
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Gail McConnell @gailmcconnell.bsky.social · 10/01/2025
Our fully 3D-printed microscope is featured in @newscientist.bsky.social www.newscientist.com/article/2462...
newscientist.com
World’s first fully 3D-printed microscope made in under 3 hours
The microscope cost less than £50 to build using an open-source design and a common 3D printer
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Ricard Solé @ricardsole.bsky.social · 10/01/2025
How can we model the emergent complexity of microbial ecosystems? How do you do the maths & predict their dynamics, from the gut & the soil to the biosphere? Here's a great review paper in @natureecoevo.bsky.social. @vmaull.bsky.social @saramitri.bsky.social nature.com/articles/s41...
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Connor McShaffrey @cmcshaff.bsky.social · 08/01/2025
As I watched a small patch of snow melt on my microscope slide, I was able to manipulate the light to get some really beautiful structure. Editing the colors and overlaying some effects gave this picture, which I'm quite happy with 🙂
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Craig Reynolds @craigreynolds.bsky.social · 04/01/2025
ALIFE 2025 The 2025 Conference on Artificial Life 6-10 October, 2025 Kyoto, Japan #alife
ALIFE 2025
The 2025 Conference on Artificial Life
6-10 October, 2025
Kyoto, Japan
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Steven Strogatz @stevenstrogatz.com · 02/01/2025
My lectures are freely available on YouTube: www.youtube.com/playlist?lis...
youtube.com
Nonlinear Dynamics and Chaos - Steven Strogatz, Cornell University - YouTube
This course of 25 lectures, filmed at Cornell University in Spring 2014, is intended for newcomers to nonlinear dynamics and chaos. It closely follows Prof. ...
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Connor McShaffrey @cmcshaff.bsky.social · 02/01/2025
Some debris from plants and cells found in a water sample, made to look like they're in outer space
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Connor McShaffrey @cmcshaff.bsky.social · 31/12/2024
Spider plant leaf, post processing to improve contrast 🙂
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Ricard Solé @ricardsole.bsky.social · 29/12/2024
How can we model the complexity of agents interacting with their worlds? How can we represent individual autonomy in mathematical terms? Here's a classic paper by Randall Beer with a dynamical systems perspective core.ac.uk/download/pdf...
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