Something Weird Happens When You Simulate Lifeless Molecules

If you want to know if someone really understands  evolution, just ask them this one weird question.

Why does poop smell bad?

Oh.

Oh gosh.

Because it has bacteria in it, I guess?

Microbiome probably.

Trash-

Yeah, trash from the gut.

... of the body.

The food we eat?

Because of the chemicals?

Farts don't always smell bad.

Yeah. Well, that's a different question  entirely. Do you think it objectively smells bad?

Yes, I think so.

Yes.

How do you think it smells to flies?

Like the fly?

Yeah- They like it.

They love it. They like it, yeah.

They love it.

Animals love stinky things.

Yeah. They're attracted to it.

Poop smells good to flies because  poop is full of nutrients.

They use it as food.

But it's also full of bacteria that  can be life-threatening to humans.

So the real reason poop  smells bad to us is because

if anyone ever thought it smelled good,

they would probably get really sick,  die, and not pass on their genes.

After all, it's about survival of the fittest.

But survival of the fittest what?

I mean, most people think of natural selection  

as being about the survival of  the fittest individual animal.

Individual.

Individuals.

Individual animal.

Animal. Okay, so it's like an individual.

Yeah.

Which makes sense.

I mean, individuals best adapted to their  environment have increased odds of survival,

and therefore a higher likelihood  of passing on their genes.

So it follows that each individual should do  everything it can to survive and reproduce.

That is, it should be selfish.

But if that's true, then how do you explain this?

Worker bees will sting  predators to protect the hive,

even though it might kill them in the process.

Female worker ants are sterile,

so they can't reproduce,

but regardless, they work for the colony  for their entire lives until they die.

Monkeys adopt orphans, wolves bring  meat to non-hunting members of the pack,

and squirrels can let out alarm calls  to warn others about nearby predators.

So if natural selection is  all about selfish individuals,

why do we observe so much altruism in nature?

The survival is of the species that can adapt.

I think generally the species.

For the survival of the species.

So it's the survival of the species.

Okay. Yeah, you're right. Okay.

But survival of the fittest species or  the fittest group also doesn't work.

I mean, think about what you need  for natural selection to occur.

You need something that replicates  itself many times over, creating copies,

and then you need a pruning process,

whereby some of those copies get eliminated and  some thrive to go on and create more copies.

The problem with groups or species is that  they don’t typically make copies of themselves.

So you almost never get copies of groups fighting  

other copies of groups to  see which groups win out.

So if it's not survival of the fittest individual  and it's not survival of the fittest group,

then what is it?

Well, to explain that, I want  to take you on a little journey,

all the way back to the beginnings of the Earth.

Where we are now, there is nothing.

Well, not really nothing, but nothing interesting.

There are only simple things, like these blobs.

This one might be a carbon dioxide  molecule, or it might be cyanide.

We don't know for sure what they are,

but we do know that these  compounds are very simple.

So for now, they'll just be  blobs floating around our void.

In fact, much of what we'll encounter  along our journey here are just hypotheses.

A lot of Earth's early history is still a mystery,

so keep that in mind.

Now, every so often, our  blobs get a surplus of energy,

maybe from a ray of UV light  or a nearby hot source.

This is the first major upgrade  to our void, excess energy,

as it allows our blobs to  interact with each other.

And most of the time, this  interaction leads to nothing,

but sometimes these blobs can combine  into more complicated compounds. 

Here's a simple simulated example,  where we only have four red blobs.

Right now, they are all individual particles,  but each time step we move forward,

let's say there's a 10% chance that all  four combine into one red mega-blob.

And now imagine this mega-blob isn't very stable.

For every time step it's alive,

it has a 95% chance of falling apart  back into the four smaller blobs.

If we add more of these red blobs into the mix,  you'll notice that they rarely ever come together.

On average, a mega-blob only  exists around 10% of the time.

But if we were to reduce the chances of  the mega-blobs dissolving to only 1%,

the void would suddenly be filled with them.

This fact hints at an important  law that governs our void,

the law of stability.

Unstable blobs fall apart and  vanish. Stable ones endure.

Now, watch what happens if we  speed this up dramatically,

maybe a couple of years per second,  maybe even a couple million.

You can see our blobs keep  getting random jolts of energy,

so they combine with others to  form more complex compounds.

Most attempts fail and fall  apart, but every so often,

by pure chance,

you get a compound that is more  stable than the blobs it's made of.

This doesn't happen because the blobs  want to build more complex structures.

It's just because these new configurations  happen to be more favorable in the environment.

And now when these complicated  compounds become abundant enough,

they too get a chance to combine,

making our void increasingly complex.

And one day, by accident,

this causes an extremely unique shape to form,

one with a special property.

See, the blobs it's made of just happen to attract  similar blobs from the surrounding environment.

This red blob always attracts green blobs,

and this purple blob always attracts yellow ones,

and piece by piece, all these  blobs attract their opposites

until their counterparts suddenly snap  into position next to the original shape.

Now, this shape goes on to do the same thing.

Its green blobs attract red ones

and yellow ones attract the purple until  another shape yet again snaps into position.

This new shape looks exactly like the original.

What just happened fully  spontaneously is replication.

One shape became two.

This marks the birth of the first replicator.

We don't know exactly what  this replicator looked like.

It might've been a single standalone molecule  

or a group of molecules that  worked together to replicate.

There's a lot of debate on this today,

so instead, let's represent  the replicator as a character.

How about this one here?

Perfect.

Keep in mind it's still just a lifeless  molecule, one without any intent or purpose.

Now, you might think that the chances for the  replicator to form were extremely unlikely,

but in our void, where we have hundreds  of millions of years to play with,

what might seem impossible to  us becomes virtually inevitable.

And the thing is, the replicator  only has to arise once.

Once it's here,

it can take the simpler compounds available in the  environment to copy itself at a much faster pace.

And so it does that,

until it entirely fills our void.

At least, that's what you'd expect,

but there is a flaw in the process.

See, during the replicator's conquest of the void,

one of its copies makes a mistake.

Perhaps a stray ray of UV light hits  it during the replication process,

or the replicator uses a building  block it wasn't supposed to.

As a result, what we're left with is a new shape,

which is slightly different from its parent,

and so its properties might  be slightly different too.

This error might be harmful.

For example, it might make the copy less stable.

It could be beneficial, making  the copy better at replicating,

or it could be neutral,

not changing the replicator in any meaningful way.

This marks the final milestone in our void,

mutation.

Many species of replicators now occupy the void,

and what they do is they replicate themselves.

The problem is they all need  the same limited resources,

and so our void turns into a battleground.

So which replicator will win? What  kind of properties will the void favor?

Well, let's try to simulate what happens.

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Thanks to Hostinger for sponsoring this part  of the video, and now back to our simulation.

To simulate what a replicator  battle might look like,

let's assign simplified traits to each of  the replicators, starting with the first one.

This replicator is special,

since it's the only one that can form  spontaneously from smaller building blocks.

So we'll give it a spawn rate.

This should be quite rare,

so let's set the chance of  formation to 1% per time step.

Just keep in mind we're just making these numbers  up. The simulation is purely illustrative.

Now, once the replicator spawns,

let's say it's governed by three key traits.

First, a death rate,

the chance of it falling apart or  being destroyed with each time step.

Let's set that to be, say, 2%.

Second, a replication rate,

the chance to copy itself with each time step.

Let's say 4%.

And finally, a mutation rate,

the chance a copy comes out mutated.

If it's 4%, roughly one in  25 copies will be a mutation.

So every time a new mutation spawns,

it will inherit the replication death  and mutation stats from its parent,

but slightly randomized.

Notice that we won't give any of these  secondary replicators a spawn rate.

They'll only be able to form as  mutations from previous generations.

So if all of their copies die  out, they'll be gone for good.

Now, before we run the simulation,

I want to quickly shout out  the YouTube channel Primer.

Our setup was inspired by his amazing  in-depth simulations on evolutionary biology.

You should really check him out.

Okay, let's run it.

The graph on the right will  show how the populations grow,

and this box on the left will  show a slice of the void,

with all the winning replicators  and the correct ratios.

You can see how the first replicator  appears and then immediately disappears,

because it just happened to die  before it got the chance to replicate.

But that's okay.

The original replicator can be created from  smaller blobs, so it'll come back at some point.

This time, it's starting to take off.

You can also see that it spawns some  mutations, but they're struggling to keep up.

Eventually, though, superior mutations pop up  and start to replicate faster than the original.

But you can see almost all of them are  growing exponentially, which is unrealistic.

That's because we're missing the  final piece of our simulation,

limited resources.

The building blocks should eventually run out.

We can simulate this effect by introducing a sort  

of resource factor to each  species' replication rate.

This factor should depend on the total  number of replicators in the void, N,

which will also divide with an  arbitrary crowding factor, C.

C lets us define the maximum number of  replicators we'll allow into the void.

Say C is 10,000.

Then once there are 10,000 replicators,

the two terms cancel out and drive  the replication rate down to zero,

meaning none of the replicators will be able to  make copies until the population drops again. 

So let's see how this changes our simulation.

Okay.

Like the last time, the original  replicator starts to grow,

after which it's quickly  taken over by its mutations,

but this time, most of these mutation  populations start to decline.

Because of the scarce resources,  the new best population,

the lime one,

actually starts stealing  resources from the others.

After that, a few more mutations pop  up, even more powerful than the lime.

Ultimately, the purple replicator takes over,

occupying around 9,000 of  the 10,000 available spaces.

It completely curbs all the other populations.

It goes without saying that the environment  plays a massive role in which replicator wins.

If you change the environment,  you likely change the outcome.

But let's look at the stats of the  replicator that came out on top this time.

That winning species has  a replication rate of 20%,

compared to the 17% average  across all populations.

Obviously, being able to  replicate quickly pays off here.

Its death rate is below average.

Replicators that fall apart less  quickly can make more copies.

And finally, it has a 1% mutation  rate, compared to the average of 3.73%.

Although mutations help by injecting diversity,

for any single species,

fewer mutations mean more faithful copies.

If we rerun the simulation, you'll notice  the outcomes are always slightly different,

but the winning species consistently have high  replication and low death and mutation rates.

Now, in the real void, things  wouldn't have been as simple.

Instead of just tweaking these three stats,

the replicators would have to mutate all  sorts of different ways to gain an advantage.

For example, one replicator might mutate a  trait that lets it destroy other individuals

and then use their building blocks  to make more copies of itself.

This looks like strategy,

but it's really just chemistry  that gets copied over and over  

because it helps the replicator survive.

Naturally, a risk of offense would  likely favor mutations that result in defense.

So an opposing replicator might  stumble upon a mutation that helps  

it form protective barriers from nearby materials,

letting it endure those attacks.

These barriers would also help protect the  fragile replicators from environmental damage,

like UV light.

This marks an important threshold.

The replicator's traits aren't limited to just  

determining the properties  of the molecules themselves.

They can also shape the environment.

So by chance,

the replicators inevitably mutate in  ways that build scaffolding around  

themselves to increase the  chances of their survival.

They stumble upon ways of making  structures to propel themselves around.

They develop senses and ways of storing energy.

They even mix, exchange, and  steal traits from each other.

Through billions of years of trial and error,  this scaffolding gets more and more complex,

and as a result,

the replicator's interactions with  the void become exceedingly indirect.

They build complex survival  machines for themselves,

machines whose sole purpose is to  protect the replicators inside.

These machines became such experts at surviving,

they're still around some 4 billion years later.

They are the bacteria,

plants,

fungi,

and animals all around you.

Everything alive,

including you,

was built as a survival  vessel for these replicators.

But today, you'd barely  recognize them as replicators.

Now we just call them genes.

They're hidden deep within every living creature,

strands of DNA made from the sequences  of A, T, G, and C nucleotides.

Now, one of the leading theories is that those  

earliest replicators were actually  something closer to RNA molecules,

but then over time,

this must have evolved into a more  stable system of storing information,

the DNA and proteins we use today.

They are the code that shapes our traits.

We’re taught that these traits are  here solely to help ensure our survival

the survival of the individual or the species.

But do we have this the wrong way around?

When you have a child, what do you  pass on? The DNA. The DNA, the genes.

Yeah, the genes. Genes.

Okay yeah.

These tiny replicators are still fighting the  same battle that started billions of years ago,

and the logic behind them hasn't changed.

The traits just become more convoluted.

Replicators that produce traits poorly suited  to their environment tend to become less common,

while those that produce advantageous traits  become more numerous in the population.

So it's not about the fittest individual or group,

it's fundamentally about the  survival of the fittest genes.

They are the core unit of natural selection.

But why would natural selection  care exactly for the gene?

Why not something smaller or something bigger?

Well, for something to undergo selection,

it needs to have three characteristics.

First, it needs to be able to make  near identical copies of itself.

Second, it needs to exhibit traits that affect  its interaction with the environment which,

third, affect the probability of survival  and reproduction of the replicator.

Something small like a single  nucleotide doesn't work, because,

sure, it'll make identical copies of itself,

but alone,

it doesn't exhibit a trait  that could be selected for.

What about something bigger, like a chromosome?

Well, each chromosome affects  potentially thousands of traits  

that could influence its survival,

but when most creatures reproduce,

sections of chromosomes get swapped around.

So a chromosome doesn't stay together  as a cohesive replicating unit,

and therefore it can't be selected for.

But a gene is somewhere in the middle.

It's a long enough stretch of DNA that  it can independently influence a trait,

but it's also short and stable enough to be  faithfully copied over into future generations.

This is why the gene is the  unit of natural selection.

This perspective led to one of the most powerful  and controversial ways of seeing evolution,

one popularized by Richard Dawkins  in his book The Selfish Gene.

Based on the work of evolutionary  biologists in the 1960s and 1970s.

And as a response against the, then very popular,

group selection theory.

Dawkins argued that just about every trait,

from animals helping each other  to being completely selfish,

is a strategy that helps their  genes survive and replicate.

Genes that maximize their own survival  are the genes that propagate best,

even if they do so at the expense of others.

Or in Dawkins' words,

we are survival machines,

robot vehicles blindly programmed to preserve  the selfish molecules known as genes.

Now, you might think this framework  isn't all that groundbreaking.

I mean, take the emperor penguins  in Antarctica for example.

They hesitate to jump into the water until  they are sure there are no seals around.

So what kind of genes could help a  penguin survive in this environment?

Well, if the penguin’s set of genes  make it more likely to be timid,

the penguin might stay back until  someone braver tests the water.

That way, the penguin is at  a lower risk of being eaten,

and has a better chance to survive,  reproduce and pass on its ‘timid’ genes.

Here, you can think about this either  as ‘the timid genes help the penguin’

or ‘the penguin helps the timid genes’.

Either way works.

So is there any real benefit to viewing  things from the gene's perspective?

Well, look at what happens when you use these  two frameworks to explain altruistic behavior,

which appears in a lot of places in nature.

Take California ground squirrels for example.

Females will let out alarm  calls if they spot a predator,

like a fox or a hawk,

to warn other nearby squirrels, even  though this puts her survival at risk.

The genes influencing this behavior  surely don’t help the squirrel.

But can the squirrel still help the genes?

I think this is a bit more  clear if you think about the  

fact that most living things reproduce sexually.

Right.

So a squirrel will get half its DNA  from its mom and half from its dad.

So it's actually sharing half  its genes with each parent.

But also, any child that it has,

it's also going to share half of its genes  with the child, but also any siblings.

But then if you take a step out to an uncle or up  to a grandparent, then it's sharing one-quarter,

and then another step out is one-eighth.

All to say, you share a lot of  genes with your immediate family.

And California ground squirrels, females  in particular, they live around family.

So if a squirrel has a set of genes that  make her call out when it spots a predator,

there is a very good chance that the  squirrels that hear her warning call

also carry those genes.

Now, as a result of her alarm call,

let's say the squirrel attracts a predator  her way, and it ends up getting eaten.

This action cost the ‘call’ genes  the chance to pass themselves on  

to any future offspring of that squirrel.

But, if the warning call saved  at least 2 copies of those genes

in two of the squirrel’s relatives…

well then, in total, these  2 squirrels have a better

chance of passing on the genes through their  offspring than the single squirrel did.

From the gene's perspective,  this could be a good trade-off.

It doesn’t matter which individual  helps the genes replicate,

only that as many copies as possible survive.

This principle, that altruistically helping your  close relatives helps preserve your own genes,

is known as kin selection.

And the payoff behind any altruistic  gesture under kin selection

depends heavily on how related you  are to the individuals you're helping,

because the less related you are,

the smaller the chances that you will share  that particular gene with another individual.

And you can see this in nature.

Male squirrels that don't live near relatives  almost never give out warning calls.

Now, there is a big question this  gene-centric view still has to address.

If selection really favors  genes that replicate well,

then why would sex ever evolve  as a means of replication,

if it throws away roughly half the genes?

Most animals reproduce sexually.

So why do it, when some organisms,

like certain plants and fungi,

get to pass on all of their genes  through asexual reproduction?

From a gene's perspective, this  seems like a much better deal.

When it comes to sexual  reproduction, people like to say,

"Okay. Well, it mixes up the genes.  It's like shuffling a deck of cards,

and isn't that better for creating more  variation? And clearly, that's advantageous."

Another way this has been explained  is if the genes that regulate sexual  

reproduction benefit from replicating sexually,

then they're going to keep  pushing for these genes.

Right.

Even if it's a net negative to  all the other genes in the genome.

Yeah.

So if it benefits them,  they'll keep pushing for it.

So are there any problems with how The  Selfish Gene explains natural selection?

Well, yes. I mean, it turns out the  framework comes with a lot of controversy.

One of the biggest criticisms against The  Selfish Gene is that it leaves little to chance.

It implies that every gene present in the genome  is there because it actively got selected for,

by natural selection, over many generations.

But many genes are actually  invisible to natural selection,

because they don't really exhibit  meaningful traits in the population.

Yet, they can still evolve over time.

Imagine 20 blind cave fish,

10 with green eyes and 10 with blue.

Since they’re blind,

we’ll assume that their eye color traits  make no difference to their survival

so they get passed down purely by chance.

Now, to form the next generation,

randomly “pick” any fish from  the first group and replicate it.

If you repeat this 20 times,  you get a 2nd generation.

By chance alone, one color will probably  appear more often than the other.

And if you repeat this  process over many generations,

one color might eventually completely take over.

Not because it’s better,

but purely due to random sampling.

This shift in the frequency of gene  variants is called genetic drift.

It’s most apparent in small populations and for  

traits that aren't pruned  for by natural selection.

But it doesn’t only apply to silent genes.

Even when genes exhibit meaningful traits,  

there is a chance that genetic  drift overrides natural selection,

and a less fit gene will spread  through the population just by chance.

Look back at our replicator battle.

If we run our simulation enough times,

sometimes the winning gene won’t be the one  with the traits that maximize its own survival.

Here, you can see that the winning population  actually has a higher than average mutation rate,

just by chance.

And the average mutation rate is  also higher than the starting value.

These are simplified examples,  but there is an ongoing argument  

about how much of evolution was  actually due to natural selection

and how much of it was up to chance.

Another major criticism of  The Selfish Gene is about the  

unavoidable implication behind the word selfish.

It seems to imply that genes have agency,

like they know what they're doing  and they understand the consequences,

but it's only a metaphor,

just as portraying them as characters was a  way for us to make the story more engaging.

Of course, molecules don't  know what they're doing.

They don't decide to replicate or  conspire to out-compete others.

They just react according to the laws of physics.

So what may look like intention

is just simple chemistry that  happens to work well and propagates.

But perhaps the most obvious and  easiest to understand criticism is  

that the whole framework is an oversimplification,

and that's true.

Genes are much more complicated than we thought.

It's not as simple as one gene equals one trait.

One gene can influence many traits, and  one trait can be influenced by many genes.

There are genes that are wholly  contained within other genes.

There are genes that inhibit or activate others,

and then there are even genes that  seem to not encode for anything,

the so-called non-coding DNA.

All to say, we still have  a lot to learn about genes.

Not to mention that the environment itself,

like whether it's hot or cold,

or how much food there is,

also affects how different genes get expressed.

Genes are much less deterministic  than they might seem!

So you might think that a single gene  would rarely have a large enough effect  

that natural selection can directly impact it,

but it doesn't matter how  convoluted the pathway is.

If a gene has a measurable effect  on its own survival and replication,

it will be subject to some  amount of natural selection.

And surely, the whole theory is a simplification,  but any theory or framework of nature is.

And what we're covering in this video is an  even more simplified picture of that framework,

but that doesn't take away the fact  that viewing the world through this  

lens has an incredible power to help  us understand the process of evolution.

It helps us understand why we see such a  range of different behaviors in our world

because fundamentally,

those traits tend to cause the increasing  prevalence of the genes they are associated with.

It's like the whole point  is figure out what's true.

Get to the truth.

And this, to me, is the  baseline truth of evolution.

This is what I love about making Veritasium,

is that we get to sort of  unpack and dig under the hood.

And it's what I loved about  reading The Selfish Gene book,

is that it really opened my eyes to this.

Previously, I'd always just probably  thought at the level of the individual,

but it makes more sense to  think at the level of the gene.

The feeling that you and every other  living organism is being driven by some  

molecules deep in every cell  is fundamentally unsettling,

and seems to remove agency from you as  an acting, thinking being in the world.

Yeah, it's pretty grim.

But whether or not you agree with the fact that  

we might be controlled by our genes  and we're simply their flesh robots,

I think it's kind of unreasonable  and unrealistic to go through life  

thinking that every decision is governed by this.

It doesn't really do you any good,

because we perceive the world as individuals.

So I think it's very beneficial to see  yourself as your own thing, as your own unit.

I want to give a big shout-out to Joe Hanson  from BeSmart for helping us out with this video,

and another shout-out to Primer for letting us  adapt his simulation on the first replicators.

I have put links to their  channels down in the description,

so please check them out.

And finally, I want to say  a huge shout-out to you.

Thank you for watching.