Simulating an Evolving Microcosmos | The Path to Multicellularity

In this video I showcase a program that I have been working on for simulating evolution by natural selection. I dive into various mechanisms of the simulation and go over some interesting real-life biology in the process. The key aim of this project is to evolve multicellular organisms, starting from single-celled protozoa-like creatures that must collect mass and energy from their surroundings in order to survive, grow and reproduce.

Chapters:
00:00 - Introduction
00:56 - Life of a protozoan
02:46 - The start of the simulation
05:57 - How the cells work
06:53 - Introducing multicellular colonies
08:33 - Understanding evolution
11:38 - Looking at data from the simulation
13:27 - Evolving epigenetics introduction
14:14 - Waddington's Landscape and cell specialisation
15:22 - The Central Dogma of Molecular Biology
16:05 - Gene Regulatory Networks
16:54 - Outro
17:30 - Watching the simulation

Find the project on GitHub:

Credits:

Tectonic plates animation: Scotese, C.R., 2016. Plate Tectonics, Paleogeography, and Ice Ages, (Modern World - 540Ma)

Gene expression and cell specialisation diagram: Prof. Dave Explains, 2017. The origin of multicellular life

Music by Vincent Rubinetti
Download the music on Bandcamp:
Stream the music on Spotify:

This video was made possible thanks to the fantastic mathematical animation software Manim Community, originally developed by @3blue1brown

Socials:

[farenhite]

One of the greatest problems I had with "evolution simulators" is that they are almost always limited to a few stats, perhaps a neural network, and left there. Only one other evolution simulator actually evolved body parts in a meaningful matter(The Life Engine), and even then not to the extent which you have. Well done.

[erli]

I've had a very similar idea for the longest time as I'm absolutely fascinated by artificial life simulations. Kudos for actually executing it!

[minerharry]

The complex molecules thing is brilliant! As other sims have shown, predation is hard - but in our world the number of vitamins we would really prefer to get from other organisms is way more than is usually simulated (as in, not at all). A brilliant addition.

[Nanorooms]

This is absolutely brilliant. As a fellow math/biol channel, I think this is one of the coolest youtube videos on evolution I’ve come across. Kudos!

[Kram]

this is brilliant. Closest thing to first-principles evolutionary sim I've seen thus far.
I could even see a point in your sim where it looked like your individual cells almost glued together into a stomach of sorts. They didn't hold out in that shape, but it was quite close.

[isudsu]

This video was top tier. Got really excited when you started mentioning allopatric speciation, I like this topic and seeing it in simulation is very nice) Keep up the good content

[Brazil-loves-you]

Loved it. Thanks! I do biotechnology and this is my favorite evolution simulator a have encountered (even at this very initial state) also I would love (I NEED) to see the evolution playout as you accompany the events. In this video you mostly explained how it works. Now I want to see it in action. Keep this amazing work!! The epigenetics will be a challenge

[gulktroktet]

I'm so glad YouTube showed me this. Please lean into your talent for making videos like this, and make more.

[Etrancical]

I've always wanted to create a life simulation, but I never knew how to start. I mean, I know how to code and program, but there are just too many factors in a simulation, and I wanted to create one entirely on my own.

Watching this helped me get a general idea of what things to focus on when starting my project. I will certainly try to work on it now.

[axospyeyes]

PLEASE upload more; this looks amazing! best evolution sim ive seen yet

[lucvergnes]

We need part 2! Absolutely amazing project

[countingstarch]

Projects and videos like these are what make me always come back to programming and learning about the relationship between chemistry and biology, thank you for making this :)

The music is so fitting too, I just stared at the screen like a hypnotized chicken the whole time

[sungvin]

I love biology + programming so much, but there's almost no videos on Youtube I haven't watched yet with that theme, thank you for your work!

[pedroparreiras]

Please, don't stop your work, this is amazing

[AuroraRaiju]

Found this vid a week ago and can not stop thinking about it. I don't often rewatch the same video but this one has me hooked on the presentation and concept of this cell evolution simulation.

[baileescott]

I've been wanting to find something like this for so long! and just now found it! I know you have thousands of potential fans waiting to see this, please keep making more videos! Your audience and subs will grow

[gergely]

You're definitely gonna be a "big" youtuber, or at least much bigger than what you are now. Like come on you have 400 subs and this video quality is just incredible. Great job!!!

[prhobo]

This video has reached a rather large audience for your channel, Congratulations! I found it very pleasing to watch and adding to the great network of YouTube evolution simulator videos and channels. One thing though that I think you might benefit from is something Michael from Vsauce said recently, and I'm going to paraphrase here, " you shouldn't underestimate your audiences comprehension of a subject matter, but instead their knowledge of the vocabulary". If you take this into account I think you will be able to reach a wider audience for your upcoming videos on this subject by spending a touch more time explaining each step of more complicated ideas, especially in future chapters similar to this video's "Understanding evolution", and "Looking at data from the simulation". Your use of 3B1B's Manim is excellent in a quest to teach the masses and your graphs are very helpful, though, perhaps easing viewers into the graphs by explaining the concepts they are showing before the graph instead of during. That will give them less of a distraction and allow from them to grasp the concepts better before going into the actual data. Lastly, one section I think you should be carful of is during your explanation of Pooled Standard Deviation (10:33 -ish), taking a bit more time to explain what that exactly is, with simpler diction, for general audience members who are not as math savvy. Obviously that should apply to any future math concepts covered by this series going forward.

I hope these pointers aren't taken as an attack on your work and instead merely as constructive criticisms that I noticed during my viewing experience. I also hope that this series will continue and that your channel will grow to an even wider audience. I look forward to seeing that become a reality.

[therockrancher]

holy shit i wish i could give a video multiple like this is the coolest thing i've ever seen

[AKfire]

This is brilliant work.. The animations are incredble..