alt Hacker NewsI wish there's some breakthrough in cell simulation that would allow us to create simulations that are similarly useful to molecular dynamics but feasible on modern supercomputers. Not being able to see what's happening inside cells seems like the main blocker to biological research.
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Simulating the real world at increasingly accurate scales is not that useful, because in biology - more than any other field - our assumptions are incorrect/flawed most of the time. The most useful thing simulations allow us to do is directly test those assumptions and in these cases, the simpler the model the better. Jeremy Gunawardena wrote a great piece on this: https://bmcbiol.biomedcentral.com/articles/10.1186/1741-7007...
The folks at Arc are trying to build this! https://arcinstitute.org/news/virtual-cell-model-state
You may enjoy this, from a top-down experimental perspective (https://www.nikonsmallworld.com/galleries/small-world-in-mot...). Only a few entries so far show intracellular dynamics (like this one: https://www.nikonsmallworld.com/galleries/2024-small-world-i...), but I always enjoy the wide variety of dynamics some groups have been able to capture, like nervous system development (https://www.nikonsmallworld.com/galleries/2018-small-world-i...); absolutely incredible.
It's a main aim at DeepMind. I hope they succeed as it could be very useful.
'Seeing' inside cells/tissues/organs/organisms is pretty much most modern biological research.
What's missing feels like the equivalent of a "fast-forward" button for cell-scale dynamics
I believe this is where quantum computing comes in but could be a decade out, but AI acceleration is hard to predict
I wish there were more interest in general in building true deterministic simulations than black boxes that hallucinate and can't show their work.
Molecular dynamics describes very short, very small dynamics, like on the scale of nanoseconds and angstroms (.1nm)
What you’re describing is more like whole cell simulation. Whole cells are thousands of times larger than a protein and cellular processes can take days to finish. Cells contain millions of individual proteins.
So that means that we just can’t simulate all the individual proteins, it’s way too costly and might permanently remain that way.
The problem is that biology is insanely tightly coupled across scales. Cancer is the prototypical example. A single mutated letter in DNA in a single cell can cause a tumor that kills a blue whale. And it works the other way too. Big changes like changing your diet gets funneled down to epigenetic molecular changes to your DNA.
Basically, we have to at least consider molecular detail when simulating things as large as a whole cell. With machine learning tools and enough data we can learn some common patterns, but I think both physical and machine learned models are always going to smooth over interesting emergent behavior.
Also you’re absolutely correct about not being able to “see” inside cells. But, the models can only really see as far as the data lets them. So better microscopes and sequencing methods are going to drive better models as much as (or more than) better algorithms or more GPUs.