What It Is, What It Isn’t

and Why Scientists Like It So Darned Much

EVOLUTION

By Ben

Darwin, caught in the act of evolving from a monkey.

Evolution Is a Theory•In everyday language, “theory” has a kind of uncertain sound to it, like

something might work in theory, but it probably won’t work in reality.

•In science it is used a little differently. You might have noticed that. For

example, the theory of gravity. They call it a theory even though

scientists don’t really debate whether or not gravity exists.

•But every once in a while someone notices something that changes

how scientists describe gravity, or explain its causes. For example, the

old way of thinking about gravity was just that heavy things somehow

attracted matter, but in the 1900s physicists talk about how space is

curved by matter, which can make other matter sort of “roll towards it”.

(I don’t really understand physics, obviously. It’s just an example of how scientists view theories.) That was

gravity, PS

Evolution Is a TheoryReally, all scientific theories are like that. Some are a little more obvious to everybody than others, and some ideas that looked really promising at first and were talked about as theories ended up being wrong.

Nearly every scientist in the world believes that evolution is just such a theory1. Maybe ‘believes’ is the wrong word. On the first day of class, my genetics prof, Dr. Jonathan Dennis said “evolution isn’t something that you believe in or disbelieve in. You either study biology and see it happen every day, right there on your [petri] plates or you are shutting your eyes.”

1. Estimates vary between 95% scientific support (including non biology types) and 99.56%

True, a theory isn’t a fact, but that is because theories are better than facts. Don’t laugh now. A fact is something like “this bird has a beak that is an inch long.” Biologists accumulate millions of these facts, but that isn’t the point of science. That’s just stamp collecting. What scientists are interested in is why all these facts are, and what they tell us about the world we’re living in. That’s what a theory does. It is the explanation for all those millions of random facts. A good theory makes scientists go “Oooohhhhh. I get it!”

Evolution Is a Theory

Sorry about all that writing. Maybe to be clear, a summary would help.

•A theory tries to give the fundamental mechanism for all the weird stuff we see. In other words, it explains why.

•Just because it is called a theory does not make it unlikely or shaky: that isn’t what the word means in science.

•Evolution is one of those theories. It’s a scientific explanation for why life acts as it does.

This PowerPoint is boring. We need more pictures. Here are two

you’ll like. These are two very closely related subspecies of

tortoise. They can live a long time – there was one named Harriet that lived

to be 175 years old!

These fellas are from 2 different (but nearby) islands off South

America.

These islands are in the Galapagos.

Isabela Island

Española Island

Let’s zoom in on those lovely specimens!(Don’t click nothin’)

Turtle #2

Turtle #1

Pirates?

Yes, tortoises are pretty great, but there was secretly a point to all that. Here are a few observations.

Basically there is a sub-species of tortoise for each island, and even though tortoises can float and paddle huge distances (slowly, of course), it doesn’t seem like the tortoises visit each other’s islands very much.

There are tortoises on the mainland too – the coast of South America – but they aren’t as similar to Galapagos Tortoises as the Galapagos ones are to each other. The islanders are like 600 pounds and the ones on the coast are only like the size of a dinner plate.

The climate in the Galapagos is really strange for a tropical island chain right on the equator: compared to the coast of South America, it is quite a bit colder and dryer.

Even though the climates of the coast and the nearby islands are super different, the plants/animals you find on them are the same. But if you look at some islands that do have a really similar climate like the Cape de Verde Islands off of Africa, what lives there is totally different.

Galapagos

Cape de Verde

So. The Galapagos and the closest continent have animals and plants in common, but have pretty different conditions in terms of temperature and moisture.

Cape de Verde, on the other hand…

…is super far away, has the same climate, but totally different kinds of life.

Most biologists would have guessed that climate would be the most important thing in deciding whether a certain kind of animal will live somewhere. But apparently it’s

actually proximity! It almost looks like…

…the tortoises just have to be able to get to there, even if it is a different habitat and it isn’t much suited to it at all, to begin

with, and then it can eventually become suited to it.

Gasp!

And that explains why on each island the tortoises look a little different: they have become suited to their own island since they got there. And that’s why they are sort of like the little

dinner plate-sized tortoises back on the mainland, but much less closely: they are the great, great, great, …, great

grandkids of those little mainland tortoises!

Charles Darwin

He noticed the same thing with

HMS Beagle.noticed this on his voyage on the

finches, iguanas,

and lava lizards

He couldn’t get the idea out of his head, once it had

occurred to him, and he spent the next 13 years

amassing huge volumes of evidence (the vast majority of which still stands today) and writing his thesis, The

Origin of Species.

I’ll sum all that up for you here though:

1. Life branches out, growing more and more unique all the time. It could have been like this from the beginning. If we were to follow it back far enough, we might eventually get back to the very first organism – all of life’s common ancestor. If you draw it out, it looks like a tree.

2. Animals change because sooner or later, nature will happen to reward some individuals because of their characteristics, and so those will pass on their traits for the next generation. This is natural selection. Species will keep growing and changing and trying to branch out, but natural selection will keep pruning off the bad branches, until the original branch has grown in a completely new way, leaving a new species.

Ok, that all happened really fast. It might have seemed like there was some trick there, or it might not seem really obvious, or just doesn’t look quite right to you.

For example: So what if the tortoises that live close to each other are more similar than the ones that are further away on the continent. That doesn’t prove evolution is right and creation is wrong.

Answer: That’s right. It doesn’t prove anything. All the examples I’ll bring up will be like that. They will be really suggestive and show over and over again that even if evolution turns out to be wrong (as I believe is technically possible), you can’t fault scientists because nature, in thousands and thousands of examples, sure makes it look like evolution is the right explanation for the facts.

Think it over a bit. Go back and go through the last few slides nice and slowly and come up with some objections you have to my reasoning. Remember. This doesn’t prove anything, but it should give you a flavour for the theory of evolution.

OK, so I’m not sure how good my explanation was.

•Evolution says that life can change. That it is dynamic, surprising, creative.

•In species, there is always variation. Not only is one species different from another, but even within a species, each organism is unique.

•In this variation, some differences are good and some are bad for the organism.

•Those with an advantageous variation (an adaptation) will be more likely to survive and reproduce. This is simply what the phrase “survival of the fittest” means.

•Slowly, slowly, gradually, bit by bit these changes add up. A bone becomes longer and longer over a hundred thousand years. A gene that encodes a fur colour is mutated and stops functioning. And eventually, if nature selects against the original, the species doesn’t look very much like what it did so long ago.

We’ve used tortoises as an example. Now let’s try a bird, the gull.

Gulls currently live in northern North America, northern Europe and northern Asia.

There are several species and subspecies of gulls, and if you figure out which can breed with each other and which can’t (and scientists have because they just

love finding things like that out), you might notice an interesting pattern.

An Example

Theses birds can interbreed.

So can these.

And these.

But not these!

Theses birds can interbreed.

So can these.

And these.

But not these!

Isn’t that interesting? OK, probably not, but stick with it for a bit

longer.All the gulls can breed with the populations right beside its own because they are not too different.

The only exception is in Europe, where the gulls can’t breed with those from Asia.

In fact, starting from Europe, as you go west, the gulls get more and more different.

These birds are an example of a ring species. They get that name because they make a complete ring around the earth at some given latitude.

It doesn’t take very much imagination to come up with an explanation for this. The species started out in Europe and grew and grew until a few of the gulls picked up and flew somewhere less crowded – North America. They are still pretty similar to their European ancestors (and that’s why they can still interbreed).

Theses birds can interbreed.

So can these.

And these.

But not these!

They spread across that continent, and kept spreading west into Asia. The ones that moved over are still pretty similar to those from North America. Spread, spread, spread and eventually the gulls, after a few million years, meet up with their great great (etc) ancestors that are still chilling in Europe. But because they’ve changed so many times on their journey around the Earth, they are too different to inter-breed.

I think it’s a pretty cool example, anyways, because you can literally follow one species changing into another

species over time, as that species spreads west and at the same time slowly evolve into something a little

different.

(PS: I put that picture in 3 times in a row because it took so long for me to colour it.)

There are thousands and thousands of examples everywhere on Earth. From viruses and bacteria to fish to butterflies to reptiles to mammals, from the poles to the equator under, over on and in land and sea. No, none of them prove beyond a shadow of a doubt that evolution is true. It’s still possible that God just made creation to look like evolution is the explanation.

OK, you say, it looks like one bird can evolve into a new kind of bird. But how could birds have evolved in the first place?

Meet Achaeopteryx (ark-ay-op-ter-icks)

Nevermind the fancy genetic evidence backing this up, you can actually see that this dinosaur had feather!

Of course this skeleton is super old, so the feathers themselves wouldn’t last, but their imprint in the silt-hardened-into-rock did. Click back a slide and see if you can pick out the feather prints on the big picture.

They’ve found 10 really good specimens in north eastern China. Just recently? Not so much. While the picture I showed you is of a recent (last few years) find, they dug up the first one back in… well, guess:

A) October 19th, 1990

B) 1914

C) 1860

D) 1492

Quick! You have 5 seconds!

5 4 3 21TIME UP!

Answer: C) 1860. Just one year after Darwin published The Origin of Species

Anti-evolution folk make a big deal out of “missing links” as if the absence of evidence was the evidence of absence.

Two comments:

1. You can’t reasonably expect any better. So many things have to be just right before a fossil can be formed, there are lots of things that can happen to destroy the fossil in the millions of years it sits there waiting to be dug up, and finally, there are so many places on Earth that we can’t dig, and even if we could, it would take hundreds of years to properly excavate even a small fraction of the ground under us.

2. There really aren’t that many so called missing links in the fossil record. You might be surprised to know that there is a very complete fossil history from primates to humans, from fish to tetrapods (things with 4 legs), from reptiles to mammals, from dinosaurs to birds (you just saw one important intermediate). Even, surprisingly enough, from hippos to whales!

Fishy Type Things

Lungfish

Tetrapods

Reptiles

Dinosaurs

Extinct Birds

Mammals Other Stuff

Primates

Humans

Other Fish

Hippos

Whales

Here’s a little diagram of some animals that made some pretty crazy “leaps”. In the next few slides, I’ll show you some fossils.

Fishy Type Things

Lungfish

Tetrapods

Reptiles

Dinosaurs

Extinct Birds

Mammals Other Stuff

Primates

Humans

Other Fish

Hippos

Whales

Fishy Type Things

Lungfish

Tetrapods

Lungfish Lungfish (still alive and kicking)(still alive and kicking)

Achanthostega

Tiktaalik

This is the first definitive tetrapod. It had lungs, 4 limbs (not fins) that

could basically do push ups, could turn its head (unlike fish with a gill cover), had teeth etc. It probably lived on land and water (called

amphibious).

Fishy Type Things

Lungfish

Tetrapods

Reptiles

Dinosaurs

Extinct Birds

Mammals Other Stuff

Primates

Humans

Other Fish

Hippos

Whales

Birds

Dinosaurs

We’ve already met Archaeopteryx, but here is the full skeleton

comparison, from dinosaur to pidgeon

Fishy Type Things

Lungfish

Tetrapods

Reptiles

Dinosaurs

Extinct Birds

Mammals Other Stuff

Primates

Humans

Other Fish

Hippos

Whales

Reptiles

Mammals

This one is tricky, because a lot of what

separates reptiles from mammals isn’t shown in just the fossil history (placentas!). Genetics

is what is relied on most, but that isn’t as obvious as seeing a

skeleton progress from one form to another.

However, early mammals do have

pretty different heads compared to their reptile ancestors.

Watch!

The important thing to have seen in that series was that the teeth became differentiated and multicusped, the lower jaw fused together and the ear bones moved up

to… where the ears are.

Early mammals were really tiny: mouse sized-ish, but other than that, I’m not sure what they would have looked

like.

The first one was a kind of reptile, a therapsid. The last one was what is called a “near-mammal”. It was just a couple steps away.

Fishy Type Things

Lungfish

Tetrapods

Reptiles

Dinosaurs

Extinct Birds

Other Stuff

Primates

Humans

Other Fish

Mammals

Hippos

Whales

Mammals

Hippos

Whales

Hippopotamus ancestor

Whales and Dolphins

Fishy Type Things

Lungfish

Tetrapods

Reptiles

Dinosaurs

Extinct Birds

Mammals Other Stuff

Other Fish

Hippos

Whales

Primates

Humans

Primates

Humans

Bam! Monkey Skulls!

And now for a brief interruption for silly animations.

OK? So fossils give us a clear progression between all major groups. It seems crazy when you first hear

it. But when palaeontologists dig, find a skeleton, dig a bit deeper (into older rock) and find a slightly

different skeleton, dig a little deeper and find another slightly different skeleton etc., you can see why they think it looks like an animal evolving from

one kind to another.

But, here’s a good question: how the heck is this actually happening?

The concept is simple. If a certain DNA sequence

is the genetic code for one animal (its

genome), and another animal has a different

genome, then to go from one animal to the other, you just have to

change the genome from one to the other.

The catch is, every step of the way has to

produce something that can survive and

reproduce.

You’ve seen this picture before, I’m sure. The green and red parts are the phosphates. In between each of those, you should be able to see a grey circle with a couple red things in it. Those are the sugars. The blue and grey things connecting the two wavy lines are the nucleotides, or base pairs, or just bases.

Changing even one base is called a mutation, and that can have a big effect.

Kinase: provide phosphates needed by 30% of our proteins.

DNA Polymerase: copies our DNAHaemoglobin: carries oxygen in our red blood cells.

We are made of proteins. Basically everything that’s going on inside of us is done by proteins. Proteins make other proteins, fold other proteins, they destroy other proteins. The proteins talk to each other, pass on messages, assemble into huge towers and then pull back apart just as quickly, like Lego

building itself and taking itself apart. It’s a complex, amazing and really, beautiful thing, this life business.

http://www.youtube.com/watch?v=BtZEqQ1cpmk

Take 3 minutes and see what I’m talking about:

I’m telling you all this genetics stuff not just because it’s the most fascinating thing ever and you know it, but because it is the behind the scenes explanation for how evolution actually

occurs.

When The Origin of Species was published, Darwin was the first to admit that he wasn’t sure how exactly species

evolved. He was only sure that they did.

He was so close to knowing the answer and giving biology a 34 year shortcut though. On his bookshelf, but unopened, was Gregor Mendel’s theory of the gene, which was not

discovered until 1900.

Gregor Johann MendelPriest, scientist, total hottie.

He was the first to show how inheritance worked:

1. Every trait (for example, eye colour) is associated with a certain gene.

2. When an organism produces gametes (sperm or egg), the copies of a gene separate. If the copies are different, one gamete will get one version of the gene (one allele) and the other will get a different allele.

3. Alleles can be dominant or recessive. For example, wrinkly pea pods are dominant over smooth pea pods.

4. Alleles sort themselves out independently. For example, in a pea plant, pea colour and flower colour aren’t related.

A pea plant like the one Mendel studied.

It is these alleles that are passed on from generation to generation, selected for and against, mutated by mistakes in copying the DNA or

chemicals or UV radiation and such. It is what happens to their genes that makes species change.

In the 40s, 50s and 60s geneticists and chemists figured out that these genes are stretches of DNA, that molecule I showed you 4 slides ago.

There are 4 different base pairs or bases: Cytosine, Guanine, Adenine and Thymidine.

They occur thousands of times in a bacterial chromosome and millions of times in a human chromosome, and what order they are in decides what kind of protein they will make (you see, we are back to those proteins I

ranted about earlier).

Now let’s bring it back to what those genes are made up of.

The base pairs, Cytosine, Guanine, Adenine and

Thymine, or C, G, A, and T, are like letters.

3 of these letters make an amino acid, which is like a word. There are

20 amino acids.

Note that for unimportant reasons, T = U in this part of the code

These amino acids are strung together to make proteins, which are like sentences. These sentences can be big long

ones, but they have to have the right grammar.

If the words are in the wrong order or the wrong words are used, it won’t make sense (if a mutation causes a protein to get the wrong amino acid, it is called a nonsense mutation –

for real.)

This is called something extremely important sounding, because it is like the MOST important thing in biology.

Ladies and gentlemen, I give you, THE CENTRAL DOGMA OF BIOLOGY

http://www.youtube.com/watch?v=GkdRdik73kU

Very dramatic. Here’s a sweet video of the DNA being transcribed into RNA (yellow), which is then translated, one amino acid (red) at a time, into a protein. BE FASCINATED.

You know complete proteins? For your body to be able to make any protein it wants, it needs to have all the amino

acids or it won’t know a word it needs to write the sentence and the protein won’t get made.

If we push the analogy a little further, then the thousands of proteins in our cells make up a book, unique to each

individual.

That is where the variation comes from.

That is what natural selection acts on.

That is how evolution happens.

Molecular biologyBiochemistryMicrobiology

Genetics

EVOLUTION

BotanyBiogeographyPalaeontology

Epidemiology, VirologyPopulation, Community ecology Anatomy, Comparative anatomy

Embryology, Developmental biologyMarine, Terrestrial, Freshwater biology

Biology

Evolution is the link between all the branches

of biology.

It explains the big stuff (bottom half), and is

explained by the small stuff (top half).

We saw how all the big stuff points to it in the first part of this (now 46 slide and counting) powerpoint. The fossils and the

distribution of species and all that.

Then we saw how the little stuff, like genetics and molecular biology turn out to provide the perfect model for how

evolution actually works.

Scientists think it’s too much of a coincidence that all of their specialities are perfectly connected by this one idea. No

wonder they all like it so much!

So that’s it! That’s all! That’s what evolution is, how it works, and a tiny sliver of some of the evidence for it. I only partially understand most of it, and I completely understand none of it. On top of that, I’m not that great at explaining things, so I’m

guessing there are gaps and problems and confusing things in this presentation.

For example, I know how much you hate genetics, so I rushed through that stuff as much as I could, so I’m sure there will be big gaps there that you might have trouble crossing. If so, I’ll

try to explain it better later.

As a kind of epilogue, I’ll talk about a few objections I often hear from anti-evolution folk.

Objection 1: The universe was only created a few thousand years ago so there wasn’t anywhere near enough time for evolution.

Well, actually, here are some dates that we know for a fact:•The universe is 13 billion years old. •Our solar system is about 4.5-5 billion years old (that includes Earth). •The first fossils are about 3.5 billion years old (they were just tiny single-cell things). •The first multicellular fossils are 600 million years old, •The Cambrian explosion, when the super slow growth of life suddenly burst out into millions of families was about 550 million years ago.

So you see, there has been lots and lots of time for evolution to have occurred.

How do we know for a fact?

We know the age of the solar system (and therefore Earth) and the age of the universe by a super obvious

idea.

We can see galaxies that are about 10 billion light years away.

So what?

Light takes a year to go one light year.

So what?

For us to see that light, it would have had to leave 10 billion years ago.

Therefore the universe has to be at least 10 billion years old.

OK, we can’t move on until we take a minute an look at stars.

Never mind. I found a lot of pictures online, and none of them did anything to me. Pictures were completely empty compared to the views we enjoyed those blissfully slow quiet nights at camp, or on the roof of the van somewhere off a highway to Boulder. Becca, I miss it.

Here is how we will look at the stars. Click once, then close your eyes.

OK, I hope that worked for you. Big breath. Let’s finish up this slideshow.

We know the age of the rocks and fossils on Earth by radiometric dating.

To be honest, in high school, I had a hard time convincing myself that this could work because I didn’t understand it. Maybe you have the same

issue.

Radiometric dating of a rock looks at its radioactive isotopes. That means an element with a weird mass that makes it

unstable.

Example of a radioactive

isotope: Carbon-14

These radioactive isotopes are the parent atoms. They decay and turn into daughter atoms at a fixed rate determined by their physical properties.

For every daughter atom in the sample, there must have been a parent atom when the sample was formed. By looking to see how many parent and daughter atoms of the radioactive isotope there are, and knowing how long it takes for a parent to turn

into a daughter atom, you can very easily find out how long ago the rock formed.

Objection 2: Evolution can’t be true because it says the universe is getting more orderly and complex but the 2nd law of thermodynamics says that the universe can only become more chaotic over time.

Answer: true, the universe is becoming more disordered, and all closed systems do the same thing, but they are missing an important point: Earth is not a closed system. Huge amounts of solar energy is poured in every second.

This is what drives the formation of all the complex molecules on earth, from the sugars that plants make by photosynthesis to the proteins we make in our bodies from small amino acids.

The entire universe is increasing in entropy, that is, becoming more chaotic. But life on Earth is the exception. It goes against the stream.

Objection 3: Nice try, smart guy, but mutations in DNA change or lose functions for organisms but they don’t magically give them new functions.

Answer: This is just not true. While not magical, there are several very common processes that increase the amount of DNA and cause new proteins with new functions to be made. Here are some examples just off the top of my head:

•Duplications occur frequently when large stretches of repetitive sequences are being replicated.•Transposons hop around changing functions, duplicating themselves, inverting DNA, activating genes etc. For a large class of them, every time they jump, DNA gets added.•Insertions by HFR’s, prophages, plasmids, vectors etc all increase the amount of DNA and number of genes.•F` plasmids involved in so called bacterial sex get duplicated and passed into other cells.•Since only 1.5% of our DNA actually codes for proteins (the rest is just built up duplications, promoters and junk DNA), even a deletion mutation can add a function by causing some junk DNA to get read as a new operon.

Objection 4: Monkeys peel bananas upside down.

Answer: Ummm, what?

Objection 5: Look at all these examples of molecules like flagella (little propellers on cells) that couldn’t have evolved because they are “irreducibly complex”, that is, if you take them apart, their parts don’t do anything, so there is no way that they would have been made and assembled on their own.

Answer: I hear this one quite a bit. Anti-evolutionists with a poor understanding of molecular biology continue to grab any molecule in the cell that has been understudied and yell “look you don’t know how this evolved so evolution is wrong!”. The molecules are then studied and the evolutionary path becomes obvious. Sometimes the molecules have already been well studied and the answers to the anti-evolutionists claims are already there, but research has either not been done or there is dishonesty on their part in ignoring the evidence. The example that they repeatedly embarrass themselves with is the flagella one. But in fact, all the parts of it have important functions in the cell, which we have known about for quite a while, and the mutation that caused them to be assembled has been followed in the prokaryotic lineage.

While the discovery of something truly irreducibly complex would mean the end of evolution as we know it, so far none have been found among the millions of structures studied. Therefore it seems awfully optimistic to hope one will be.

Objection 6: It’s just so hard to imagine how a crocodile could be a bird’s closest living relative and all the other weird stuff evolution claims.

Answer: This is true. What we call common sense, or intuition, works extremely well for things that we can see and touch. We can easily imagine how big a centimetre is, or how far a kilometre is or how much a litre is or how long a year is or whatever. But when we start talking about billions of years, or stars millions of lightyears away or DNA that is just a few nanometres wide, it isn’t surprising that we get lost trying to picture it and our intuition fails. We have no reference for it. It’s the same problem with trying to imagine the answers to questions about the nature of God. It’s just so much bigger than we experience in day to day life. It transcends our understanding of the world.

And so, everyone, even the greatest scientists, will at least partially lose the help of their intuition when thinking about our origins, and people not used to relying on logic and reason to understand something instead of “gut feelings” will have trouble believing these things.