Alan Garfinkel

The leading authority on nonlinear and oscillatory chemical reactions has got to be Irv Epstein at Brandeis, whom I'm sure you must know. some of his models might be relevant

Mike, are you familiar with the Eigen-Schuster Hypercycle models of what they call 'pre-biotic evolution'?

An image of the brain generated by ChatGPT which has mislabeled almost every brain structure and even invented new ones,

Screenshot of LLM offering to generate the image "Would you like a visual diagram of how the cerebellum interfaces with cortical prediction pathways in this framework?"

ChatGPT offered to make an image for me of how the cerebellum interacts with other brain predictive processing pathways and this amazingly confused diagram was the result--mislabeling almost every brain structure & even inventing new ones. 😱 Let's hope our future doctors aren't using LLMs to study!

#DynamicsClub in June: 𝗖𝗮𝘀𝗲𝘆 𝗔𝗱𝗮𝗺 from Purdue University will share her work on dynamic neuromodulation. www.nature.com/articles/s42...

June 12 (Thur) at 11am PT / 2pm ET
Join in person at UCLA or on Zoom: lingyunxiong.github.io/DynamicsClub/

Delighted to share that I will give a department seminar at UCSD 𝑺𝒉𝒖 𝑪𝒉𝒊𝒆𝒏 - 𝑮𝒆𝒏𝒆 𝑳𝒂𝒚 𝑫𝒆𝒑𝒂𝒓𝒕𝒎𝒆𝒏𝒕 𝒐𝒇 𝑩𝒊𝒐𝒆𝒏𝒈𝒊𝒏𝒆𝒆𝒓𝒊𝒏𝒈 on Friday, June 6th. be.ucsd.edu/seminar/2025...

Join us in La Jolla at 2pm in The FUNG Auditorium.

I have been selected by the UCLA Molecular Biology Institute for the 2025 Boyer/Parvin Posteoctoral Award. 🥳🥳🥳

Initiated by Paul Boyer since his Nobel Prize in 1997, this honor is now supported by the Parvin foundation to celebrate the legacy of Dr. Boyer, beyond ATP synthase and the sodium pump.

Best non-technical book on pattern formation is The Self-made Tapestry by @philipcball.bsky.social

that's not a bad video at all. Yes, pattern formation in PDEs is an incredibly beautiful and scientifically important phenomenon, and we've published a bunch of papers using it to mechanistically explain patterns in physiological systems

#DynamicsClub in May: 𝗡𝗮𝘁𝗮𝗹𝗶𝗲 𝗛𝗮𝘂𝗴𝗹𝘂𝗻𝗱 @ox.ac.uk will share her recent work on the glymphatic system during sleep. pubmed.ncbi.nlm.nih.gov/39788123/

May 7 (Wed) at 9am PT / 5pm BST
Join us on Zoom: lingyunxiong.github.io/DynamicsClub/

After the Genetic Paradigm: Why We Need a New Biology PHILIP BALL | One sign of this shift is that biology is becoming more ready to accept and to speak of concepts long considered taboo...

I'm aiming to get some thoughtful biologists together (there's no lack of them!) to discuss what kind of narratives might best reflect the nature of their field in the 21st century. Here's a preview of the goals; I'm excited and optimistic about it.
www.marginaliareviewofbooks.com/post/after-t...

Hi Bryan- yes, definitely applications to depressive disorders. search "depression" in Ivy's paper. you will find a discussion of a very interesting new theory of depression, way beyond the now-discredited "serotonin hypothesis". Also Google "depression rhythm" for things like circadian influences

Are physiological oscillations physiological? Abstract figure legend Mechanisms and functions of physiological oscillations.

My article with @agarfinkel.bsky.social titled "𝗔𝗿𝗲 𝗽𝗵𝘆𝘀𝗶𝗼𝗹𝗼𝗴𝗶𝗰𝗮𝗹 𝗼𝘀𝗰𝗶𝗹𝗹𝗮𝘁𝗶𝗼𝗻𝘀 𝙥𝙝𝙮𝙨𝙞𝙤𝙡𝙤𝙜𝙞𝙘𝙖𝙡?" has ranked as a Top Viewed Article by Wiley. Check it out if you haven't done so: onlinelibrary.wiley.com/doi/full/10.... #TopViewedArticle

Pleased to host 𝗗𝗿. 𝗔𝗹𝗶𝗰𝗶𝗮 𝗠𝗰𝗗𝗼𝗻𝗼𝘂𝗴𝗵 for the first IBP Departmental Seminar on Thursday, April 3rd. Join us in person at UCLA to find out the 𝘱𝘩𝘺𝘴𝘪𝘰𝘭𝘰𝘨𝘪𝘤𝘢𝘭 𝘣𝘦𝘯𝘦𝘧𝘪𝘵𝘴 𝘰𝘧 𝘵𝘩𝘦 𝘧𝘦𝘮𝘢𝘭𝘦 𝘬𝘪𝘥𝘯𝘦𝘺 and meet members of the Department of Integrative Biology and Physiology!

YouTube video by UVA - School of Medicine Jeff Saucerman, PhD, uses computational and experimental methods to find new drugs for heart disease

Quick video summary of my research: We develop computational and experimental methods to discover drugs for heart disease 🧪
youtu.be/nmpFDiE4GSg

🚨Our latest preprint: "Continuation methods as a tool for parameter inference in electrophysiology modeling" by @MattJOwen_
and me: doi.org/10.48550/arX...

You fitting models to data related to limit cycles?

Tweetorial follows... 🧵 1/9

How Life Really Works Just as I uncovered a new way to understand life, I got news about my own.

Eight years ago, I worked on mathematical modeling of gene regulation. Always, thought why the relevant literature and lessons from this field are not present in popular science. Well, now here it is. A moving piece by @philipcball.bsky.social
#biology #gene #emergence
nautil.us/how-life-rea...

What unique insights can modeling approaches capture about the immune system? The immune system, optimized by evolution to maintain health and prevent disease, is remarkably good at what it does. It detects pathogens and monitors physiological stresses with a sensitivity and selectivity that far surpasses that of man-made biosensors. It then mounts potent yet precise responses, enabling the body to maintain homeostasis amid varying internal milieu and external threats.

Thoughts from leaders of systems #immunology how mechanistic models can leverage omics/ML for deeper understanding of how our immune system works #sysbio @cp-cellsystems.bsky.social
www.cell.com/cell-systems...

His Dynamics: the Geometry of Behavior (with Chris Shaw) told the story of nonlinear dynamics in a picture-centric comic-book style. We and many others are currently drawing heavily on these ideas to teach dynamics to undergraduates, in our case to UCLA Life Science freshmen.

Ralph himself also had a major revelation: these high-level geometric and topological concepts of vector field, trajectory, etc. were also the perfect pedagogical tool to introduce students to the dynamics that are inherent in non-linear diff eqs.

The book replaces the vague and outdated concept of a differential equation by the rigorous notion of a vector field, a cross-section of the tangent bundle of a differentiable manifold. The fundamental concepts go back to Poincare’s work on the equations of the 3-Body Problem.

The math world lost a giant in September, with the death of Ralph Abraham. Ralph’s paradigm-changing Foundations of Mechanics (with Jerry Marsden) laid out the differential geometric and topological foundations of global analysis. (1/n)

Something that's been bugging me for a while in bioinformatics data analysis is this overreliance on packages, workflows and what's been called "cargo cult science".

Can we have more conceptual thinking, more theory?
Asking for what we really want to achieve and what we need to do gets us there.

This is priceless! tylervigen.com has long been a wonderful source for spurious correlations, but now it has added these totally bs "explanations" generated by AI!

Wild!

thanks for doing this, Jeff. please add me!

A common pathway to cancer: Oncogenic mutations abolish p53 oscillations The tumor suppressor p53 oscillates in response to DNA double-strand breaks, a behavior that has been suggested to be essential to its anti-cancer fun…

thrilled that Ivy Xiong’s poster was chosen to represent basic science at UCLA Dept of Medicine’s annual Research Day: intravital imaging (thanks, Natalie Porat-Shliom!) and mathematical modeling to identify key sex differences in kidney function.
connect.uclahealth.org/dom/2024/10/...

Are physiological oscillations physiological? Abstract figure legend Mechanisms and functions of physiological oscillations.

Delighted to post this article (open access), which takes direct aim at the doctrine of homeostasis, and argues for the fundamental role of oscillatory processes. Also discusses the math needed to understand the mechanisms of oscillatory processes, which is nonlinear dynamics.

Can you add me to the list? thanks!

@agarfinkel.bsky.social

Why is there no bookmark feature here? It would be really useful to save insightful posts, for our own learning and to refer to when challenging misleading claims and narratives especially those peddled by the ruling class. It’s an essential tool for accountability.