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Simulating Natural Selection

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Nov 14, 2018

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Simulating Natural Selection
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  • - [Narrator] This video is about natural selection.
  • If you've watched the previous videos in this series,
  • you've seen these blob creatures live, die, and replicate.
  • But it's been a little bit artificial.
  • We just gave each type of creature a replication chance
  • and a death chance and we saw what happened.
  • With natural selection though,
  • we usually can't know precise replication
  • and death chances.
  • Instead, selection comes from interactions between
  • a creature's traits and it's environment.
  • So in this video,
  • we're going to make a real evolving system
  • by putting our blob creatures into a simple environment
  • and giving them traits.
  • Let's see what we can learn
  • by watching some actual natural selection happen.
  • All right, so what does our environment look like?
  • Creatures will live on this plane
  • and each morning, food appears on the plane,
  • and the blobs emerge from their homes around the edge
  • to go out and eat the food.
  • Here are the rules.
  • If a blob fails
  • to find any food before running out of energy,
  • it will die.
  • If a blob gets one piece of food
  • and manages to get back home to the edge,
  • it will live on to the next day.
  • And if a blob gets two pieces and gets home,
  • it will survive to the next day and also replicate,
  • adding another creature to the next day.
  • So that's the environment.
  • Before we talk about our creature's traits
  • and how they might vary,
  • let's just watch these creatures live their lives
  • for a few generations.
  • (suspenseful music)
  • So we see that these creatures can manage
  • to live over several generations in this environment.
  • And the number of creatures actually expanded over
  • the first few days and then leveled off.
  • So the population started out below the carrying capacity.
  • But once the population expanded to around 95,
  • the creatures really had
  • to compete with each other for food.
  • Once we allow mutations,
  • the variation will give some creatures an advantage
  • and we'll start seeing some natural selection of traits.
  • So let's turn on mutations and see what happens.
  • Let's start out with one trait variant, speed.
  • Each time a creature replicates,
  • there's a chance that a mutation will give the new creature
  • a slightly lower or slightly higher speed.
  • Speed is great because it allows you
  • to beat other creatures to the food.
  • But speed will also have a cost.
  • Moving quickly is less efficient.
  • If a creature's speed is doubled,
  • it will cover a distance in half the time
  • but use twice as much energy to go that distance.
  • Faster creatures can't forage over as much ground
  • as slower creatures.
  • So they might not find food before running out of energy.
  • If we un-pause this world with speed mutations turned on,
  • what would you predict?
  • When the faster creatures start appearing,
  • will they sprint to victory?
  • Or will the slower creatures prove the virtue of patience?
  • It could also turn out that
  • the current creatures have struck a good balance.
  • Or it could be that being fast and being slow
  • are both good strategies.
  • It's hard to say at this point.
  • We'll just have to un-pause and see what the nature
  • of the situation is.
  • And let's speed it up a bit so we can see more generations.
  • (suspenseful music)
  • All right, so it turns out
  • to be worth sacrificing efficiency for speed
  • in this environment.
  • Or, at least the initial speed value I picked
  • was slower than optimal.
  • This is our first example of natural selection.
  • We didn't know the best speed value going in,
  • but the creatures mutated
  • and somewhat randomly tried out different speed values,
  • and then through natural selection,
  • the population evolved to have
  • a higher average speed over time.
  • And I want to double down on that last point.
  • The population evolved.
  • As much as we all love Pokemon,
  • individuals don't evolve in
  • the biological sense of the word.
  • Populations evolve over generations.
  • One interesting thing to notice
  • is that as the average speed of the population went up,
  • the number of creatures in any given day tended
  • to go down.
  • The creatures now compete more fiercely
  • and are less efficient overall.
  • This is part of the meaning of the term selfish gene.
  • We'll talk more about genes
  • and the term selfish gene in the future videos,
  • but for now,
  • just notice that even though
  • we might call these creatures better
  • because they did better in the competition for survival,
  • the total population size actually went down.
  • Selection didn't happen for the good
  • of the species as a whole.
  • But again, more on that in future videos.
  • All right, now that we've gotten our feet wet
  • with one varying trait,
  • let's add two more.
  • Size and sense.
  • First, size.
  • Size scales the creature in all three dimensions.
  • The benefit of size is that it lets you eat other creatures
  • if you're at least 20% larger than them.
  • Getting an extra food source
  • is great if you can pull it off,
  • but being big costs a lot of energy.
  • The energy cost depends on the cube
  • of a creatures size value.
  • I could have picked any function
  • for the energy cost I suppose,
  • but I made it a cube because volume scales
  • as the cube of length,
  • and volume is closely linked to the mass
  • a creature has to carry around.
  • The total energy cost
  • of a creature's movement each time step
  • is equal to the cube of the creature's size
  • times the square of the creatures speed from before.
  • Which you might notice is reminiscent
  • of the formula for kinetic energy.
  • But anyway, it's especially costly
  • to be both big and fast.
  • And on top of this cost,
  • smaller creatures will actually run
  • from creatures big enough to eat them.
  • So to benefit from being big,
  • you need at least some speed.
  • Long story short,
  • being big is high risk and high reward.
  • The third trait is sense.
  • Each creature has a certain sensing distance
  • at which it can sense food or other creatures.
  • Once a creature sees food or a smaller creature,
  • it can move straight toward it.
  • Or, if it sees a bigger creature, it can run away.
  • This sensing distance gets larger
  • as a creature's sense trait goes up.
  • Allowing it to avoid danger and be more efficient
  • with it's movements.
  • Each time step a creature pays a movement energy cost
  • which depends on it's size and speed
  • and a sensing energy cost
  • which is just equal to it's sense trait.
  • All right, so now that we have three traits,
  • let's rewind to before we turned on speed mutations
  • and instead turn on mutations for all three traits.
  • To keep track of what's happening
  • to all three traits at once,
  • we're going to use this three dimensional graph.
  • Each dot in the graph represents one creature.
  • And the position of the dot depends on the speed,
  • size, and sense values for that creature.
  • All right, let's see how it goes.
  • (suspenseful music)
  • So what can we say about the results?
  • The first thing I noticed is that the average speed
  • is significantly different from what it was
  • when only speed was allowed to vary.
  • Which is a little bit surprising
  • because we didn't explicitly change anything
  • about how speed works.
  • But, with sense and size able to vary,
  • different creatures were able to appear.
  • A creature's environment includes all
  • the creatures around it.
  • And for whatever reason,
  • speed just wasn't as valuable this time around.
  • And there's one other thing I noticed.
  • When I first ran the simulation,
  • I thought there would be a pretty intense selection
  • toward creatures with higher sense.
  • Because sense informs everything else the creature does
  • and it doesn't cost very much.
  • But instead, sense is fairly spread out
  • and centered roughly around the starting value.
  • That's the thing about natural selection.
  • It doesn't care what I or anyone thinks is best.
  • It just does what it does.
  • All right, one last simulation.
  • Let's see what happens if we change
  • the environment more explicitly.
  • Let's go to 10 food each day.
  • It's pretty clear that this won't be able
  • to support the population
  • of about 50 creatures we currently have.
  • So the number of creatures will go down.
  • But what else will happen?
  • I don't know, we'll just have to see.
  • (suspenseful music)
  • Hm, okay, well apparently the creatures
  • that thrived with 100 food
  • just aren't able to cut it with only 10.
  • Even though there should be enough
  • for say five to 10 creatures.
  • So it looks like if it's going to be possible
  • to survive with only 10 food,
  • there's going to have to be some time
  • for the population to adjust.
  • So instead let's do this.
  • We'll rewind to before we reduced the food
  • and then every two days we'll put out one less piece
  • of food until eventually we're only putting out
  • 10 pieces of food each day.
  • (suspenseful music)
  • All right.
  • So it's not too surprising that in a lower food environment,
  • things aren't just crowded
  • and being big just isn't worth it any more.
  • Sense, on the other hand,
  • became super valuable now that a low sense creature
  • can easily go a whole day without seeing anything and die.
  • And now speed is actually really valuable again.
  • This surprised me actually.
  • I thought in this sparse environment
  • that efficiency would be king,
  • making both size and speed go down.
  • But, apparently speed is actually more valuable now.
  • So again, I can't predict it.
  • So other than reiterating the fact
  • that I don't know what's going to happen,
  • what can this teach us?
  • Well, to put it plainly,
  • the environment matters, a lot.
  • Reducing the amount of food didn't just reduce
  • the number of creatures,
  • it totally changed which creatures exist.
  • You'll often see evolution depicted
  • as this march toward more and more advanced
  • or complex or higher creatures,
  • but that's not how it is at all.
  • The only thing that matters is how well
  • a creature is adapted to it's environment.
  • Okay, so, before we go, let's do a quick recap.
  • Even with this relatively simple environment we created,
  • we were able to see some important principles in action.
  • But we're not done yet.
  • In the next few videos,
  • we'll keep exploring natural selection
  • by trying to see how some more complicated
  • and even counter-intuitive traits can be favored.
  • See you then.
  • (suspenseful music)

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Description

In this video, we avoid telling the creatures what their survival chances are and let them figure it out themselves. This is the fifth in the series on evolution.

Made with Blender and python.
Github: https://github.com/Helpsypoo/primer

A few places to learn more about evolution and natural selection:
https://evolution.berkeley.edu/evolibrary/misconceptions_faq.php
https://www.khanacademy.org/science/biology/her
Any intro biology text you might have access to.

Special thanks to supporters on Patreon, especially:
Jordan Scales
Eric Helps
Ben Kamens
Ben Komalo
Christy Serbus
Sean Barker

Support Primer on Patreon:
https://www.patreon.com/primerlearning

Come over to the subreddit for deeper discussions of the concepts, sims, or anything else.
https://www.reddit.com/r/primerlearning

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License information:
Creative Commons 4.0 (CC-BY-NC). More info at https://creativecommons.org/licenses/by-nc/4.0/

Speaking of attribution:

The music is "Investigations" by Kevin MacLeod, distributed under a CC-BY license via incompetech.com.

Several other inputs into the graphics are from public domain contributions to https://www.blendswap.com.

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