foo52 is cool

I love this "community"

@@davidzaydullin yea

the bibites dev

@@josephvanhaaften7710 edited

Thank you for providing this interesting context!

Thank you for the support! Good luck with your project 😊

I watched the previous one yesterday and was pleasantly surprised to find out this video was uploaded. Also good luck!

Great observation! As with most ALIFE simulations, evolution tends to keep the population with within a somewhat narrow part of the solution space. I'm definitely going to continue exploring the parameters of the simulation and tinkering with features to see how a more diverse ecosystem can be maintained :)

The process of evolution is definitely NOT based on biology. It's based on replicating systems with differential reproductive success whatever the substrate or medium. The simulations we generate (whether it's in computers, or on paper) loosely arrive at those rules first through our grasp of the was it works in biological systems. Genetic change is heritable & essentially irreversible. To prove evolution wrong, you must show what can reach into the DNA of every member of the descendants which inherited some beneficial gene & remove that gene from each of those descendants or send info to each recipient as to which gene to remove. There is no other option. It is only plausibly reversible if it occurs to the original organism in which the change occurred. Once the gene has been passed to multiple offspring, the odds of reversing that mutation in all offspring goes from being off the chart to utterly impossible.

Thank you for your comment and your subscription! :) I agree that the project so far has only made small strides towards the ideas that I outlined at the top of the video. However, I do think that in the current version of the simulation, new/undesigned structures could potentially emerge as multicellular systems that compose the hard-coded six traits in novel ways. So indeed individual cells may only have limited functions, but together they may form something more interesting! If you check out my paper in the description, I go through a case-study from the simulation with a multicell structure that was able to self-replicate quite reliably! Also, I agree that only having six possible traits is limiting - and I would like to add more - I don't think adding any number of fixed traits would really change that picture! Anyways, that's what I was thinking of as my initial strides towards the problem - maybe you disagree? I would be curious to hear what direction you think I should head in next :)

​@@dylancope Thanks for the quick and detailed response. I totally agree with you about the emergent properties of multicellular life, there are certainly possibilities there. I don't know how I'd go about emergent traits, there are a few models I can think of but ultimately I'm starting to understand (thanks to what you wrote) they're what you have already on a different scale, picking a selection of traits that can interact at some scale to facilitate the simulation of evolution at a larger scale. I don't think it'd actually be any more useful as a model of real evolution to do that without going to something like an engine that can fully emulate some kind of molecular interactions with the possibility of emergent complexity which isn't guaranteed. That said I might consider the following changes to your designs to reduce the number of traits rather than increase them. Pressure -> if you can have directed osmosis with the environment you could have emergent muscle analogues, a tensed muscle being a one with a higher internal pressure (more round) and a relaxed muscle having lower pressure and so smaller size (more stretchy/deformable by macro structure), this could actually be done by 'simplifying' the existing phagocytes, have phagocyte be the trait and then have a size of chemical be the target, Water is very small, sugar is small, proteins are medium, chunks of dead creature are large to very large... you could even have these be reversible so emitting molecules rather than absorbing them, transferring to neighbouring cells etc. In real cell chemistry I think that each of these ports is dedicated to a given molecule and directional but I don't think your simulation is that granular yet, but if you did go that far then the evolution of pheromones and synapse are theoretically possible so rather than relying on direct data transmission between connected nodes the communication protocol between different cells could be negotiated and evolved, co-operatively. An I want sugar pheromone responded to with a sugar exchange for example, these pheromones might then be hackable by other organisms which isn't the case in the networked connections your nodes create. Stickiness -> a cell that can be selectively sticky to the environment rather than to co-operative cells would allow for something similar to grip, move, release, grip move release, maybe Mucocytes, but these might also be a possible adaptation of the 'simplified' phagocytes. The ability to release chemicals would necessitate being able to modify the cell membrane to be resistant to certain chemicals as well as similar for internal cell structures to contain toxic chemicals for release Simplification of flagella and the spikes, these could be the same structure, the spikes are stiff and the flagella are not, the spikes get longer with exertion the flagella flex with exertion. This could allow for other expressions with perhaps other functions to be emergent. Though I'm not seeing obvious uses for these yet, spikes that change direction might rip holes into cells? added length providing range but also making the spike less strong. While flagella that change in length might be able to interact as sensory appendages? especially if they're sensitive to chemicals in a different way than the cell membrane I think the photo receptors could be chemical in nature instead of nodal, if there's the possibility for the growth of chloroplasts then measuring the sugar levels in the cell is analogous to a none directional light sensor rather than an explicit trait. So internal sensors for temperature, pressure, salinity, glucose levels etc, gives the ability to develop more emergent macro properties. To have sensory directionality the lifeform must be multicellular to block a sense from one or more directions. Rather than sensor components being built into a cell's trait list, especially for light as no individual cell is really opaque to light. Even without chloroplasts any measurable reaction that is facilitated by photons could serve as a way to sense light without giving direct access to sight to cells. Single Cells can follow gradients towards or away from a stimulus but complex features like sight shouldn't be baked into the design, in order to follow those gradients having a working memory if only of the last few time steps is critical, I go in this direction the gradient is followed, go faster, I go in that direction the gradient is reversed, go slower/change direction. This only works if it's possible for the cell to compare the situation now to the situation a couple of timesteps before, the bigger the gradient the bigger the response.

@@johnydlamazing ideas. Something I was pondering. Modifying physical properties is really interesting. Alien project is simpler in many way but does have muscle connections which combine with multiple cells for swimming and other behaviour like potentially trapping food in a net. I think a lot of that may be programmed rather than evolved. You kind of want a ‘Turing complete’ physical world. But simulating such a thing at speed becomes hard. Systems like Core Wars and Avida try and simulate a more open ended world by using more general programming languages. It’s certainly a good goal to be open ended. So combining Avida in a more realistic physics engine looks to be a good direction. Hard stuff though

@@oystercatcher943 I don't claim all the credit, I've been thinking about this since reading permutation city a few years ago it had an "autoverse" with a whole new simplified chemistry (no fission/fusion) and evolution from a designed single celled life form. The thing was even in the story so complicated that running experiments with more than a handful of microbes was a super computer endeavour so HARD is just not sufficient, but Greg Egan is a genius. His route describes cellular automata as the underlying physics and the emergent atoms be on a scale sufficient that pixelation of reality has a negligible effect on chemistry. But we're talking a running quadrilions of cells for just a single atom, and probably that cubed for a single life form xD not at all feasible for 2024 computation even with supercomputer access.

Haha yeah that's true - the road to science is always messier (and longer) than simple stories like that😅

Got to show some love for the OG evo sim guy

Thank you Alexandre! I really enjoyed my visit to the lab - hope everyone is doing well :)

Haha now there are two videos I'm hoping that people realise that the project isn't dead, I'm just slow to edit videos 😅

Good question. To be honest, I kind of hacked together a solution to that problem. It's not a proper spring-based model. Each node in the graph repels neighbours that are too close and attracts ones that are far away. If I recall correctly, there are some edge cases to handle the nodes moving with the cells and attaching them to anchors on the surface nodes.

The GRNs can have arbitrary depth - they evolve using the NEAT algorithm. But yes you're right that multicellularity is a way to gain depth. Also, depth within a cell has latency. Secondly, the current adhesion system cannot be repositioned. Although connections can be broken and remade.

It’s a very hard thing to grapple with. However this simulation is totally able to generate evolutionary novel behaviours if not structures. But even then it could make interesting multicellular structures. I guess you have decide the level at which you wish to run the simulation. Evolution is going on at multiple levels, within cells and at the organism level. CoreWars and Avida may be more open-ended because they use more general programming languages but in a much less biologically inspired environment. Doing both would be great but very hard to do I think. Also Battle-of-the-clans on YT is interesting in this respect but still on a simpler grid based world. I think every style has its place. IMHO No one simulation can do everything without as you say being hopelessly complex and slow ❤

To be honest, I don't think that any of those languages would make a huge difference. Java is pretty performant if you don't abuse the GC too much, and it's easier to do multiprocessing that C (not sure about Rust). And that's the key issue for this program. Collision engines are hard to parallelise. The only way it would be significantly more performant is if I managed to find a better backend physics library, as I moved away from my own implementation. Ultimately as this is a side project, I don't have time to write everything from scratch so relying on physics engines and UI libraries has been very helpful.