APS-DBIO Profile picture
5 Aug, 12 tweets, 5 min read
Hello, it's a gorgeous Thursday! Time for a #DBIOTweetorial. A special edition this week — an inaugural *Editweetorial* by your host today, Prof. Bill Bialek @wbialek. #DBIOEditweetorial Image
Biological systems are complicated. If we try to make “realistic” models we are led into a forest of parameters. If we are going to have a theoretical physicist’s understanding of life, we have to find principles that cut through this complexity.
Maybe a #DBIOEditweetorial provides just enough space to summarize different strategies in the search for principles. Links are to papers that illustrate these ideas, and of course are just a sampling. Please respond with your own favorites.
One possibility is that there is no shortcut. In this view, the interesting theoretical problems are the inference of highly parameterized models from limited data. sciencedirect.com/science/articl…
Even if there are no shortcuts, we do know that today’s organisms are related to their ancestors, and hence to one another. In this view, the interesting questions are about evolutionary dynamics. nature.com/articles/s4158…
Another possibility is that the functionally important behaviors of living systems are independent of parameters. In this view, the interesting question is how parameter-independence is possible. pnas.org/content/101/14… Image
Simplicity in our description of biological function could emerge from microscopic complexity via the renormalization group. In this view, the problem is to build an RG without symmetry or locality. journals.aps.org/prl/abstract/1…
Finally, parameters may have been selected to generate near-optimal performance at essential functions. In this view, interesting questions are the optimization problem itself and its connection to data. sciencedirect.com/science/articl…
It would take much more space to explain how each of these ideas plays out in problems across all scales from protein folding to ecology. Full discussion of candidate principles must be grounded in quantitative connections to experiment.
There are links among different approaches. In evolutionary dynamics, variation occurs at the micro scale, but selection acts at the macro scale. Is this like an RG flow with a loop that connects macro back to micro? One of many challenging questions.
The biological physics community has made compelling progress by focusing on particular systems, engaging with myriad details. But theoretical physics is not a collection of examples. We should continue to dream of unifying principles. Image
Thanks to many friends who have shaped my thinking, and especially to the #EngageDBIO team who made this possible. Signing off here, your #DBIOEditweetorial host today, Bill Bialek @wbialek.

• • •

Missing some Tweet in this thread? You can try to force a refresh
 

Keep Current with APS-DBIO

APS-DBIO Profile picture

Stay in touch and get notified when new unrolls are available from this author!

Read all threads

This Thread may be Removed Anytime!

PDF

Twitter may remove this content at anytime! Save it as PDF for later use!

Try unrolling a thread yourself!

how to unroll video
  1. Follow @ThreadReaderApp to mention us!

  2. From a Twitter thread mention us with a keyword "unroll"
@threadreaderapp unroll

Practice here first or read more on our help page!

More from @ApsDbio

7 Oct
Hello and welcome to this week’s #DBIOTweetorial by Prof. Madhusudhan Venkadesan @v_madhu. Let’s go! Image
Feet and fins are quite different in their anatomy. But both have to be stiff enough to withstand the forces of propulsion. Are there deeper connections between them?

Paper: dx.doi.org/10.1038/nature…
Video:
All land vertebrates, or tetrapods, evolved from aquatic ancestors over 370 million years ago. So we and all land vertebrates are fish, in a manner of speaking!

Limbs evolved from fins, but the earliest tetrapod probably used a fin to move on land.

Ref: jstor.org/stable/j.ctt16…
Read 13 tweets
17 Jun
Have you seen images of bacteria and wondered, “How do they form such strange shapes?” or “Why do they all look so different?” Join us for today's #DBIOTweetorial as we dive into how and why bacteria adopt the shapes they do! #EngageDBIO @goleylab @jordanmbarrows
As Kevin Young eloquently put it, “To be brutally honest, few people care that bacteria have different shapes. Which is a shame, because the bacteria seem to care very much.” Check out how diverse bacterial shapes can be! tinyurl.com/6d93vce4 tinyurl.com/uvbtwvs3
Bacterial shape is largely determined by the peptidoglycan (PG) cell wall, a large macromolecule that surrounds cells and provides structure and support. PG is necessary to maintain cell shape - cells burst when treated with drugs that target PG!
tinyurl.com/m4dys6hb
Read 12 tweets
10 Jun
Are the screaming BroodX cicadas driving you nuts? Wonder how such tiny insects even make such a racket? You’ve come to the right place! I study how insects make and hear sound. By the end of this I hope I can show what biophysical marvels they are! #DBIOTweetorial @NatashaMhatre
So what is sound? It’s a disturbance in a medium, generated by a moving object. In this cool gif, by @drussellpsu, you can you see a grey bar moving back and forth within a pipe. The air in the pipe is pushed around, and the disturbance within it (sound) travels through the air.
So anything that moves makes a sound?

Yup, pretty much! The world is full of it: the wind shakes leaves, they rustle; tires vibrate because of friction, and they rumble.

But how ‘loud’ the sound is depends on quite a few things!

frontiersin.org/articles/10.33…
Read 12 tweets
3 Jun
It's #DBIOtweetorial time, with your host @gibbological from @isbsci. Today, you'll get some facts about the ~10^13 microbes that call your gut home. By the end, I hope that you'll see yourself as much more than a mere human. You are an ecosystem! #EngageDBIO #microbiome 💩🦠🧑‍🔬
In the womb, we are sterile (obgyn.onlinelibrary.wiley.com/doi/abs/10.111…). At birth, our mothers (and surrounding environment) act as our 'sour-dough starter culture,' inoculating us with hundreds-to-thousands of species. The exact composition of this 'microbiome' is as unique to us as our genome.
Topologically speaking, humans are doughnuts. The entire outside of this doughnut is *covered* in microbes (mostly bacteria). Most of our microbes live in the colon. There are about 3*10^13 human cells and 4*10^13 bacterial cells in the body (doi.org/10.1371/journa…).
Read 12 tweets
27 May
It's #DBIOtweetorial time! Your host is Saad Bhamla @BhamlaLab. Today we'll learn about 10 ultrafast movements in organisms - from single cells to multicellular beasts. We hope to get you thinking engg+bio+physics of extreme movements.
#EngageDBIO #UltrafastOrganisms.
Contrary to common perception, cheetahs and falcons are not the fastest animals. Mantis shrimps for example can use a saddle-shaped spring to hammer at ~100,000 m/s^2. This is so blazing fast, it cavitates surrounding fluid. nature.com/articles/42881…
Trap jaw ants use their spring-loaded jaws to jump at faster acceleration of 10^6 m/s^2 in 0.06 ms. Faster than the blink of an eye or a bullet from a gun !! How to build robots at this scale and speed remains an open challenge. pnas.org/content/103/34…
Read 11 tweets
20 May
It's #DBIOtweetorial time! Your host, Wallace Marshall. Welcome to 10 Crazy Things Cells Do. We hope to get you thinking about the complexity of cells + challenges in learning physical principles that underly cell behavior. Let's get started!
#EngageDBIO #XtremeCellBiology.
Cells can be really big. Many cells are small, but some are gigantic. Each little "plant" in this picture is a single algal cell, Acetabularia, more than 10 cm long. What determines the size of cells? bmcbiol.biomedcentral.com/articles/10.11…
Cells can walk. You think of cells creeping along on a glass slide, but cells can move in more complex ways. @BEuplotes studies cells that can walk using 14 tiny feet. biorxiv.org/content/10.110…
Read 12 tweets

Did Thread Reader help you today?

Support us! We are indie developers!


This site is made by just two indie developers on a laptop doing marketing, support and development! Read more about the story.

Become a Premium Member ($3/month or $30/year) and get exclusive features!

Become Premium

Too expensive? Make a small donation by buying us coffee ($5) or help with server cost ($10)

Donate via Paypal Become our Patreon

Thank you for your support!

Follow Us on Twitter!

:(