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This is probably more a physics/CS question than a biological one, but how far off are we from having physics simulators good enough to try the types of experim
by nomilk 2y ago
This is probably more a physics/CS question than a biological one, but how far off are we from having physics simulators good enough to try the types of experiments MIT did with the eye but for entire organisms? Presuming that will one-day be possible (i.e. the simulation takes earth's physics as inputs, and spits out organisms vaguely similar to those found on earth), then we could presumably enter the physics of exoplanets and find out what their creatures might be like.
- MVissers 2y agoHah, I'm creating something like this right now as a hobby. Will open source it soon: https://www.youtube.com/watch?v=PDePFvxj6Po https://www.youtube.com/watch?v=PDePFvxj6Po I think we're quite far off if you want to model full organism complexity. But if you want to answer a research question you can model simpler versions today. Like this research team did around how vision evolves. By the way– As of recently, we were able to model C Elegans (flatworm) in 3D with all neurons and neurotransmitters. It reacted to virtual stimuli just like a real worm (https://www.nature.com/articles/s43588-024-00738-w https://www.nature.com/articles/s43588-024-00738-w). So single-organisms is already possible. But the evolution of these entities in 3D will take us a bit more time is my guess: Also I'm not a CS person, just an enthusiast.
- bloomingkales 2y agoCan the virtual flatworm’s virtual actions be mapped to the physical sensors of a flatworm in the real world? Can we get the real world’s flatworm to control any part of the virtual one? Can these two things interface yet is the question (virtual to real bidirectional interface), especially since you are suggesting we have a clone of it. If we do this experiment, what does that say about something doing an experiment on humans (humans control humans inside video games). Sounds insane right? Why would we ever do this? Well … we have this perfect digital clone of a flatworm, what else are we going to do? There’s a lot of evidence that humans would absolutely go down this rabbit hole until it’s logical conclusion. One word: Teledildonics Anyway, the flatworm that is born into such an experiment would never know, or it would just be useless to know. :shrugs:
- utkarsh858 2y agoThat's quite a cool project, but as a thought can the simple rules you started from... Are they simple enough? Like the rule which states that offspring will carry the traits of parents, so exactly what traits they carry. how are they carried. Are these rules simple enough?
- MVissers 2y agoSo they carry neural nets and evolve using the NEAT algorithm, which introduces slight variations: new connections and new nodes. Over time this allows fish to develop basic behavior such as searching for food, navigation a maze, etc. The only other 'useful' gene right now is around herbivore/carnivore digestion (0 to 1), which allows them to extract more energy from either meat or plant-food. Most of the time they actually develop specific behavior according to this gene. I don't really code in what offspring need to do beyond having slight variations to both factors described above, it kind of evolves randomly into more complexity (neural net + behaviors). Also importantly– I need to program an energy decay system and death if they run out. So basically: Energy source, energy decay and evolving neural nets that can give an organism the possibility to survive and evolve if they get more energy. And voila– Life emerges. Working on plants now, and again simple rules: Neural nets in the plants to mimic evolution of complex biological systems that evolve from generation to generation. And a light-based energy source and light-based energy capture system (leaves). My current (preliminary) experiments show that the plants start to look like trees over time to maximize energy capturing compared to competing plants. Looking to publish this once I have it a bit more refined.
- utkarsh858 2y agoAmazing, looking forward for the plant to tree, simulation. One more question, sorry my knowledge of ML is not so profound, does NEAT algorithm mimic how natural selection works? And how.
- MVissers 2y agoSo the special thing about NEAT is that it allows the shape of the neural net to change. It can also do some sort of mix between two neural nets (like sexual reproduction), but I haven't implemented that. Natural selection in this sim just happens by itself, there is a limited amount of food and only the best adapted ones survive. So the best performing neural networks duplicate themselves and create small variations of themselves. This part is not connected to the NEAT algorithm, I've just seen that NEAT performs particularly good vs more fixed-structure neural networks.
- Douger 2y agoI'm looking forward to seeing the source! How long have you been working on it?
- asimpletune 2y agoVery cool channel. Thanks for sharing.
- harry-wood 2y agoSimulating physics of muscles/skeleton structures has been done many times over, and I feel like the focus on eyes and vision is what makes this one interesting. Anyway it's quite a fun category of youtube video: https://www.google.com/search?q=simulating+evolution+muscles https://www.google.com/search?q=simulating+evolution+muscles They tend to be two-dimensional or have other big simplifications. I guess trying to evolve a "real" organism explodes in complexity very quickly even if you ignore the "brain".
- djtango 2y ago10 years ago when I was still in academia, modelling more than 8 water molecules solvating an ion started to get computationally very expensive lol Depends how accurate you want your model. Pie in the sky thinking, we need quantum computing before I can imagine these kinds of simulations making sense
- crackalamoo 2y agoCan machine learning accomplish the same? See e.g. Microsoft MatterSim https://www.microsoft.com/en-us/research/blog/mattersim-a-deep-learning-model-for-materials-under-real-world-conditions/ https://www.microsoft.com/en-us/research/blog/mattersim-a-de...
- _kidlike 2y agoisn't that what Nvidia Omniverse is?
- crackalamoo 2y agoYeah, that's the ambition. More generally, ML is good at approximating many NP-hard problems efficiently, so I wonder if it will be a more practical alternative to quantum computing for things like molecular simulation.
- mathieuh 2y agoWell, from a philosophical point of view you might say that it's impossible. The idea of laws that can apply to e.g. mathematics might not apply to organisms because organisms are described in terms of teleology. The heart doesn't just happen to circulate blood, it beats in order to circulate blood to oxygenate the body and so on. And just because, for example, organisms that live in cold climates generally have thick hair, having thick hair doesn't imply cold climates. Some mammals fill niches filled by birds in other ecosystem, or by fish in others. Likewise in New Zealand they have birds filling niches that in other ecosystems are filled by mammals. I'm not sure biology can be a purely inductive science.
- adrianN 2y agoThe answer ranges from „we could do that in the eighties“ to „it’s literally impossible“ depending on the fidelity you wish the simulation to have.
- pinkmuffinere 2y agoThis is exactly it, _many_ such simulations and evolutions have been done already, all with incomplete/inaccurate world models, leading to predictions that _might_ be meaningful. I recall a coworker used reinforcement learning to teach a robot to walk — but instead it learned to abuse an error in the physics simulation and shuffle around in a ridiculous manner.
- dsign 2y agoSo I guess it will be very hard, in a pure Darwinian meaning, to evolve an organism from scratch. But relax that meaning a little by fixing some things and letting only some things evolve, and I suspect it's already possible.