Andrew Krause

With respect to biology, I feel we are still very much pre-Newtonian (ie we are still missing THE fundamental paradigm or theoretical framework ), and I really do not understand how people sincerely think we can get to the Moon in 10 years.

Really nice overview! I'll send this to a few colleagues in molecular developmental bio and other areas, and see if it helps our communication.

From genes to patterns: five key dynamical systems concepts to decode developmental regulatory mechanisms Summary: Dynamical systems theory provides a powerful quantitative and intuitive framework to understand developmental processes. This Primer brings key concepts of this framework to the ever-growing ...

5 dynamical systems concepts every developmental biologist needs to know! This came out of the 2023 Morphogenesis Program. @pauformosa.bsky.social ‪@perez-carrasco.bsky.social‬
journals.biologists.com/dev/article/...

MoDiS 2026 This is an ESI Workshop

Workshop on "Modelling Diffusive Systems: Theory and Applications" (MoDiS) @ Erwin Schrödinger Institute (ESI), Vienna, Austria

Dates: 26-30 Jan 2026. Apply before 15 September.

sites.google.com/view/modis20...

Vaguely related is one of my favorite relativistic objects: superluminal scissors.

math.ucr.edu/home/baez/ph...

This is coming partly from watching my own country ignite itself in a nationalistic fervor... Of course the details are different, but I've always found the inward-facing side of country's research and other interests to be detrimental to long-term good human impacts.

I like celebrating Turing himself, and I think his work in general had profound impacts across the sciences etc. But I find this, and the over-emphasis (IMO) of Turing's contributions to Enigma, a bit on the nationalistic side. Do we really need to put more money into defense-oriented research etc?

I always tell people at character creation to not select chronic illnesses. As I get older, I collect them like Pokémon. But I do not want to catch any much, much less catch them all...

🚨Job alert in theory/math devbio 🚨
I’m currently advertising postdoc positions to join my group. We’re building reaction-diffusion models to understand some of the crazy things embryos can do. We are based in a beautiful part of Scotland :). Please share! www.abdnjobs.co.uk/vacancy/rese...

As a field, we often fail to value diversity in many aspects of science and mathematics, from people to subjects. We should do more to embrace a multiplicity of approaches and ideas, rather than trying to give some partial ordering of "importance" or "value."

Stay safe Sarah. I'm sorry that we live in such "interesting times."

Cynical and analytical LKB are great, but wholesome LKB hits different. ❤️

This is where I spend quite a lot of my time these days, especially as there are vastly different cultures among experimentally-oriented scientists in different (even nearby) areas. Some areas have theoretical work in their core, but many do not, so one has very different problems of translation.

It is a crude psuedo-compressible form of Navier-Stokes (click f(x) to see/change the implementation) followed by the most naive possible numerics for a PDE: finite differences + forward Euler. The goal of the website is to solve rather 'general' PDEs, and this is one way to (crudely!) do fluids.

Interactive simulation | VisualPDE An interactive simulation of a partial differential equation, live in your browser with VisualPDE.

This is excellent!

You might enjoy this interactive simulation on @visualpde.com where you can click to introduce a cylinder into a flow. The accuracy is undoubtedly terrible, but it gives a roughly similar kind of flow!

visualpde.com/sim/?preset=...

Our review on dynamical systems of fate and form in development!

We argue that currently, the universalist approach dominates and creation of new models, which is inherent to pluralism, is not sufficiently emphasised. This brings us to, in Sections 6 Machine learning cannot replace modelling, 7 Are hybrid models the answer?, a discussion of how mathematical biology has responded with the rise of machine learning. We argue that ML, which emphasises prediction (activity 3), is ill-prepared to deal with complexity without incorporating some form of mechanistic model building. But we also, more controversially for those working in mathematical biology, emphasise how some of the responses to the rise of ML have fallen into the trap of making models of models (or fitting models to data generated by models) rather than innovating by creating new models of biology itself. We conclude that mathematical biology needs less unification and less analysis of existing models, and more creativity and more creation of new models. We should be creative without fear of them being wrong or producing ideas that are mathematically intractable, with an aim of providing a multitude of tools for better understanding of biological systems.

Instead, the radical definition of complex systems comes from, what is known as, critical complexity. Work by Paul Cilliers and Alicia Juarrero warned against aggrandising models (even supposedly complex systems models) [3], [4]. They emphasise the need to embrace the ambiguous, messy, fluid, non-determinable, contextual, and historical nature of complex systems. They describe complex phenomena as unfinalizible and inexhaustible, which means that we can never capture any given biological system entirety with models [5]. Fig. 1, adapted from Di Paolo et al. (2018), captures the interdependence, fluidly and interactivity of agents and environments in a complex system [2]. Complex systems are open-ended, which means there is no uncontested way of telling whether what we have included in a model is crucial or what we have omitted as irrelevant is indeed so. Models can, according to the critical complexity approach, be contradictory: we can accept two incompatible predictions as both describing the same system.

This approach views a model as a snapshot of a system and no single snapshot tells the whole story. For modelling the human body, for example, “a portrait of a person, a store mannequin, and a pig can all be models” [6]. None is a perfect representation, but each can be the best model for a human, depending on whether one wants to remember an old friend, to buy clothes, or to study anatomy. The critical complexity view suggests that theoreticians should avoid specialising in any one modelling approach and try to find the right set of models to understand a particular system in a given context. There can, of course, be more than one definition of complex systems. Indeed, Cilliers and Juarrero’s approach to complexity encourages a plurality of definitions (after all, there is no single view of a system). We would, though, emphasise that it is the radical definition of complexity – in which systems always resist a complete description, are open and unfinalizable – which is least well understood by mathematical biologists today. It is therefore important to investigate how complexity should be approached in the study of biological systems.

from a 2022 paper with @gyllingberg.bsky.social & @soccermatics.bsky.social

The lost art of mathematical modelling www.sciencedirect.com/science/arti...

The fact that trans people are a tiny minority asking for mostly incredibly cheap and unobtrusive accommodations must be utterly obfuscated in the UK. There's well placed people in our media and political class whose self image as liberal and tolerant cannot survive acknowledging this basic reality.

Unlike other tools to aid our conceptualization of different phenomena however, outside of philosophy we rarely approach metaphor with the careful nuance it deserves. Statistics courses are replete with caveats, but we don't teach metaphor with the same admission of caveats/nuance in its use.

James Murray's book on Mathematical Biology has a nice chapter on the "Use and abuse of fractals in biology" which I enjoyed immensely. I think this terminology "use and abuse" can apply to many powerful (but limited!) human tools such as metaphors, power laws, stylistic models, etc.

“Maybe we need to treat more diabetes with cooking classes, not just throwing insulin at people,” FDA Commissioner Marty Makary said on Fox News’ Sunday Futures. “You know, scientists have been waving the flag for years, saying you’ve got to look at this body of scientific data, and the modern medical establishment really has been disconnected.”

As the parent of a type-I diabetic, I would like to invite the ignorant piece of shit currently directing the FDA to kiss my ass.

New paper out in @pnas.org

We followed cells migrating along signalling gradients in 3D, and found they collectively behave as a living droplet - a self-propelling fluid that grows.

www.pnas.org/doi/10.1073/...

In this endearing 1923 caricature by his mother, 11-year-old Alan Turing gazes at daisies instead of playing hockey. Decades later, he’d explore phyllotaxis—the spiral patterns in plants—using a 'digital computer', in one of his final works, cut short by his untimely death in 1954.

Program and application instructions for the 2025 Mechanobiology of tissue morphogenesis and disease workshop in Baeza, Spain, October 21-23. Apply at https://www.unia.es/estudios-y-acceso/oferta-academica/formacion-continua/workshop-mechanobiology-of-tissue-morphogenesis-and-disease

Interested in Developmental Mechanics??? We are organizing a mechanobiology workshop in Baeza, Spain, October 21-23, 2025. Come join us (and please help us spread the word)!!!

We’re advertising an @iapetusdtp.bsky.social undergraduate summer research experience project on ‘Ecosystem Resilience in a Changing Climate’, with me, @blindmath.bsky.social, Denis Patterson & @tjohnwainwright.bsky.social. Please share with your undergrads! iapetus2.ac.uk/wp-content/u...

REP Scheme Summer Research Experience placements for current undergraduate students.Applications for 2025 are now open. Please see our list of projects and How to Apply, below, to start your application. Ov...

Undergrad in the life sciences? Want to do a research placement over the summer but also need a job - NERC are running the REP scheme again, paid summer research placements to widen participation in the life sciences. Details here iapetus2.ac.uk/new-rep-sche...

This very cool paper, and Carl's very nice short thread describing the value of basic research in biology, may be of interest to @thecopperdoctor.bsky.social @oneofmanychris.bsky.social and others.

12 examples of how developmental biology research led to fundamental discoveries for biomedical research. There are many more! Download ppt & jpg versions on @socdevbio.bsky.social website. Use & modify as needed. Poster formats are also posted to print & hang in your lab!

I hope you both stay safe and take care of yourselves. It's looking very strange from the outside...

Teaching Dynamics to Biology Undergraduates: the UCLA Experience - Bulletin of Mathematical Biology There is a growing realization that traditional “Calculus for Life Sciences” courses do not show their applicability to the Life Sciences and discourage student interest. There have been calls from th...

Not really what you're asking for, but I've really appreciated approaches like this more generally for "modernising" our approaches to teaching this material. In particular, I've always liked biological dynamics as a major motivator for many of these topics.

link.springer.com/article/10.1...