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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
Carl T. Bergstrom @carlbergstrom.com · 07/10/2026
Terry Tao @teorth.bsky.social: Indiscriminate brute-force application of AI to mathematics is depleting the field of good questions without renewing this resource or providing commensurate value. OpenAI: We hear you. Here's a .zip file with 377 hasty AI solutions to important open problems.
nytimes.com
OpenAI Releases Findings on 377 Math Problems, Further Roiling Field (Gift Article)
After a previous solution angered mathematicians, the company characterized the new release as being more responsive to concerns about A.I. disrupting research.
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Connor McShaffrey @cmcshaff.bsky.social · 30/09/2026
No that's fair. That experience of feeling out of the loop and just having it would be disappointing to me as well.
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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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Connor McShaffrey @cmcshaff.bsky.social · 24/09/2026
Do you really think it can solve any information theoretic question on its own? I have been talking to it about dynamics a little, and have found it to be better at applying well-documented concepts than it is at fleshing out new mathematical concepts. Not to say it is not powerful, even there
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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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Connor McShaffrey @cmcshaff.bsky.social · 09/08/2026
I have a Beer hivemind theory. I think he is establishing a homunculus in the mind of every person that works closely with him. Assuming we also become vectors for the spread, then the singularity may indeed be near, just not for the reason the AI-bros think ...this was almost my thesis topic
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Connor McShaffrey @cmcshaff.bsky.social · 09/08/2026
Ha! That section must have resonated with your own Randy homunculus... But if any of the writing is invoking that imagery, that is truly all I could ask for
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Connor McShaffrey @cmcshaff.bsky.social · 08/08/2026
@eforbes.bsky.social
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Connor McShaffrey @cmcshaff.bsky.social · 08/08/2026
He sure is lol I joke with him that at this point I have a little Randy homunculus that sits atop my brain and challenges me to keep making ideas a little more rigorous or communicate them clearer
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Connor McShaffrey @cmcshaff.bsky.social · 08/08/2026
I was just rereading this a couple months ago and thinking about how relevant it still is! Great book
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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 · 05/07/2026
To be honest, I had never personally made such a strong connection to Mary Shelley until I was reading the part of your book available for preview! Usually other literature pops into my mind for the life-death issue. I am excited to read the rest; our perspectives might be very complementary
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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
We also consider how these constraints intrinsically arise through the operation and regeneration of cellular systems, utilizing cellular automata as idealized case studies to guide our intuitions.
A schematic of the intrinsically generated viability constraint for a glider in Conway's Game of Life.
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Connor McShaffrey @cmcshaff.bsky.social · 20/06/2026
Far from a trivial inclusion, considering these geometries together results in a much richer geometry of fate outcomes which can be understood through viability space decomposition, which derives novel global organizing manifolds in dynamical systems with existential constraints.
A schematic of viability space decomposition being applied to a single-cell model with existential constraints.
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Connor McShaffrey @cmcshaff.bsky.social · 20/06/2026
While the idea of a cell's state unfolding in an abstract geometric space, such as a Waddington landscape, is relatively common, comparatively little attention is paid to geometry that bounds the range of states that a cell can physiologically exist in.
Two depictions of a bounded viability region which defines where in state space a cell can still be considered to exist.
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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 · 27/05/2026
No worries, I knew you would get to it when you got a chance! Thanks!
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Connor McShaffrey @cmcshaff.bsky.social · 27/05/2026
Congrats! Very exciting 🙂
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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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Connor McShaffrey @cmcshaff.bsky.social · 20/02/2026
She's earned it! My cat has attitude and the gremlin isn't even two years old yet
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Connor McShaffrey @cmcshaff.bsky.social · 20/02/2026
I always gave her so many belly rubs because I suspected she had mastery of the dark arts
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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 · 19/11/2025
It looks like if the mermaid's purse egg-capsule developed into a little person instead of hatching into a skate!
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Connor McShaffrey @cmcshaff.bsky.social · 19/11/2025
I was midway through sipping on my drink and almost choked when I read this. Absolute gold.
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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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Connor McShaffrey @cmcshaff.bsky.social · 27/10/2025
I've had an increasing number of people ask me why I do not have LLMs automate my paper writing/research for me. My first answer is always on principle. My second is that nothing I work on is so derivative of other work that it is that well-represented in the training set.
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Connor McShaffrey @cmcshaff.bsky.social · 26/10/2025
All I know is that it is uncorrupted by the blind use of LLMs. Ah, the joys of being illiterate.
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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 · 29/08/2025
Congrats Will!
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Connor McShaffrey @cmcshaff.bsky.social · 27/08/2025
🤫
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Connor McShaffrey @cmcshaff.bsky.social · 26/08/2025
You're tempting me lol
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Connor McShaffrey @cmcshaff.bsky.social · 26/08/2025
Going to change my dissertation proposal to this three days before the defense...
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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 · 17/08/2025
It was a pleasure, Tom :) very excited to see what comes next. Hope you are getting settled in your new home!
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