The Twists And Turns Of The Evolution Of Life On Earth
In an evolutionary tree, neat branches link the paths of different species back through time. As you follow the forking paths, you can trace common ancestors, winding down the trunk to see the root organism in common.
Evolution in the real world is a little messier—full of dead ends and changes happening beneath the surface, even before new traits and species appear. And the research and science that gave us a better picture about how life evolved on Earth can just be just as complicated.
Evolutionary biologist Neil Shubin, author of Some Assembly Required: Decoding Four Billion Years of Life, from Ancient Fossils to DNA, explains how technology like DNA sequences has allowed scientists to fill in these gaps in the story of evolution. He talks about the scientists behind these discoveries, including Susunu Ohno, who stumbled on junk DNA by transforming genomes into music and paper cutouts.
Neil Shubin is the author of Some Assembly Required: Decoding Four Billion Years of Life, from Ancient Fossils to DNA (Pantheon, 2020). He’s an evolutionary biologist and professor of Anatomy at the University of Chicago in Chicago, Illinois.
IRA FLATOW: This is Science Friday. I’m Ira Flatow. You’ve probably seen an evolutionary tree with its neat branches linking the parts of different species. If you follow down the tree, you can trace back to common ancestors and wind down towards the trunk to see the root organism.
Evolution in the real world is a little messier, full of dead ends and changes happening beneath the surface even before new traits and species appeared. And the discoveries and scientists they gave us a better picture about how life evolved on Earth, well those stories could be just as complicated. Evolutionary biologist, Neil Shubin, writes about all these stories in his new book, Some Assembly Required– Decoding Four Billion Years Of Life From, Ancient Fossils To DNA. Producer Alexa Lim spoke with Dr. Shubin.
ALEXA LIM: Hi, Dr. Shubin. Welcome to Science Friday.
NEIL SHUBIN: Well, thanks for having me. It’s great to be here.
ALEXA LIM: Paleontologists have been digging up fossils that show evidence of changes in species for a long time. So how does the technology, like DNA sequencing, add to the evidence? What other connections or gaps does it allow you to fill in?
NEIL SHUBIN: We’ve witnessed and we’ve lived in the past several decades through a genetic revolution, where we now have genome projects [? the ?] complete genomes for many different kinds of species. And we [? can now ?] leverage that information to ask, what are the kinds of genetic differences that are associated with the major changes in evolution we see that in the billions of years of the history of life? I mean, paleontologists have gotten really good at finding new fossils they tell us about how great transformations happen.
Now we have this whole new data set to mine and it’s a really remarkable time. It was totally humbling for me because I was training to be a fossil hunter and this was the late 1980s when we were finding all kinds of new genes that tell us about how development, from egg to adult, happens. And it was showing a basic toolkit that builds animal bodies as different as flies, worms, and people. And that’s a game changer.
ALEXA LIM: Great. And your book does double duty. You outline the big discoveries in evolutionary research, but you also look at the people behind those discoveries. Did you go through footnotes or were there any interesting archives that you had to dig into to find some of these people?
NEIL SHUBIN: Yeah, well, some of them I knew about before. Others I happened upon through just serendipity in my own life. So let me give you one example.
I was the co-director of the Marine Biological Laboratory in Woods Hole, Massachusetts a few years ago. And I heard stories of a remarkable woman who had worked there in the 1800s by the name Julia Barlow Platt. And so I went to the library there and just hearing the buzz about her– people had talked about.
And I saw her story. And her story is science and overcoming challenges in a nutshell. This is a woman trying to do science in the 1800s– made a fabulous discovery, which is incredibly important for understanding evolution. Which for experts in the audience that she helped discover a new cell type called the neural crest, which is big in the [? origin ?] of vertebrate organisms.
But she found this discovery and nobody believed her because it ran against the current dogma. And she couldn’t find a job in science and ultimately quit science, but she became mayor of Pacific Grove, California, and ended up saving Monterey Bay. I mean, it doesn’t get better than that. I mean, it’s just amazing.
ALEXA LIM: And another really interesting person you talk about was a critic of Charles Darwin. Just his name alone is interesting– St. George Jackson Mivart, who in response to Darwin’s idea wrote a book called, On the Genesis of Species, and a dig at Darwin.
NEIL SHUBIN: Always a dig.
ALEXA LIM: So I mean, what was his main criticism of Darwin’s theory of evolution?
NEIL SHUBIN: Yeah, Mivart was a professional curmudgeon, honestly, and a brilliant one at that. I mean, he reputedly his Anglican faith and became Catholic but then couldn’t get into college so he studied natural history. He was a friend of Huxley and a Darwinist, who then turned on Darwin and later the Catholic church. And he was excommunicated by everybody.
But in the interim he was one of Darwin’s great critics. He was criticizing what would happen during the great transitions in evolution. [? He was like ?] what good is 5% of a wing in a bird? Can you really have your transitional stages that mean anything?
Moreover, he said, if you think about the number and different changes that have to happen in any great transition, whether it’s the arch of birds or first fish to walk on land, there are so many features that have to change in sync, that they’d be impossible. If you think about fish walking on land you have to have arms and legs and wrists. You have to have lungs, you have to have necks, and that’s just the tip of the iceberg.
And if you think about the origin of birds, same thing. If they have hollow bones, high metabolisms, feathers, wings, and so forth. If all those have to evolve at once, then evolution would stop in its tracks. But he brought out the best in Darwin.
So he brought these criticisms up after the Darwin’s first edition of The Origin of Species, in 1859. But then Darwin actually handed a whole chapter which responded largely to Mivart, in his sixth edition, which is considered the main one– most reliable one. And it was a remarkable thing that he did because he was in response and came up with one of those great ideas.
ALEXA LIM: Right. Yeah, and he really distilled it down into this one idea about a change of function.
NEIL SHUBIN: Yeah, exactly. What he said is much of evolution is not necessarily the origin of new features, but a change in function of features that already exist. That’s huge. Because what it means is evolution doesn’t have to wait for the origin and new features, you could just repurpose features for new functions.
And the example that Darwin actually started to use, and that was, if you look at the invasion of land by fish, when fish had to walk land you’d say, well, lungs they had to come about. The reality is they didn’t. That his lungs were present in fish for eons before the first fish took steps on land. Lungs originally arose in fish as an accessory respiratory organ, along with gills, to allow them to breathe air when the oxygen supply in the water just wouldn’t cut it.
And there are other creatures like them as well. If you think about feathers in birds, you naively associate that those are associated with flying. They arose to help the ancestors of birds fly.
But that’s not the case at all. They originally rose in therapod dinosaurs, which weren’t necessarily flying animals, but they were extensively reused for thermal regulation, some certain insulation, or a courtship displays or what have you. But it wasn’t flight. And so, if you think about– if you think that lungs arose to help creatures walk on land, legs arose to help creatures walk on land, or feathers arose to help creatures fly you’d be in good company, but you’d be entirely wrong. And we’ve known a lot of this since Darwin.
ALEXA LIM: And so when we think about evolution and natural selection, it’s about responding to the environment. But this happens on a smaller scale. You say that genomes are at war with themselves. What do you mean by that?
NEIL SHUBIN: Oh, yeah. I mean, there’s a war going on inside of us all the time. I mean, it’s pretty remarkable that there are– if you look in our genome– and this was discovered by another scientist, I just loved telling her stories, Barbara McClintock, who discovered jumping genes. Now there’s different kinds of them. But basically, what they do is they make copies of themselves and then jump around the genome. They’re almost a selfish kind of DNA that, left to their own devices, will make copies of themselves and just proliferate across the entire genome.
And if you look at our own human genome, about 2/3 of our genome are these jumping genes that have taken over. But the reality is we live in a balance with these jumping genes. That is there are mechanisms, some of them not very well understood, that our genomes and physiology use to limit their jumping. Otherwise, it would kill us. Because what happens is these genes can jump, and it all depends on where they land.
In some cases, they can land in the middle of another gene, in which case they would knock out its function and can be deadly or harmful to the organism. In other cases, and we’re seeing this again and again, is these genes can jump and then land in a place where they can activate genes in new ways that can itself be fuel for evolution. And we’re seeing that in the evolution of pregnancy for instance, and some of the aspects of pregnancy. So it turns out to be fuel for evolution.
ALEXA LIM: And one of the things that I was surprised to read, some of the fuel for these genomes are viruses. And like you said, viruses are involved in the development of human memory and pregnancy?
NEIL SHUBIN: Yeah. I mean, this is really surprising and most people don’t realize this because obviously we’re living in an age of viruses. But we have this very complex relationship with viruses over hundreds of millions of years. If you look at our own genome, only 2% of our genome is composed of our own genes– the part of our genome that encodes for proteins.
The rest, we know, has lots of different functions. It turns out that 8% of our genome– 8%, four times more than our own genes– are [? an ?] ancient viral genetic material that somehow entered our genome. It turns out some of this had been put to work. I mean, there was a [? thing ?] in a study out of the University of Utah by, Jason Shepherd the neurobiologist there.
Jason was working on a gene that serves in memory in mice and people. It’s called Arc. And he looked at the protein of Arc concocted under a microscope. And he looked at that and he says, I’ve seen that before.
Where he saw before it was in a microbiology class when he saw a slide of HIV, the virus that causes AIDS. In the building next store he said, I got a slide to show you. And he didn’t tell them what was on the slide. And they looked at it, and they were like, hey, that’s HIV, the virus that causes AIDS. And it’s like, yeah!
And so they got to work on it. It turns out that parts of Arc are a repurposed virus. And what happens is– so when HIV, the virus that causes AIDS, moves from cell to cell, it makes [? Taxol, ?] which protects the genetic material, which facilitates the safe travel of the genetic material from cell to cell, it’s how it does its work.
Well, Arc does the same thing. It forms a capsule, much like HIV. It’s using that, and it moves from cell to cell to do its normal function. So it turns out that this viral function was [? being ?] put to good use in repurposing for a memory gene for it to allow its material to move from cell to cell.
ALEXA LIM: Wow! That’s amazing.
NEIL SHUBIN: It’s amazing.
ALEXA LIM: And mind blowing.
NEIL SHUBIN: It is mind blowing. And there’s a protein, or it’s a set of proteins, involved in pregnancy in the placenta that these are also repurposed viruses. The hypothesis is that sometime in the distant past in one of our distant ancestors, there was a virus that invaded the genome, and that somehow that virus instead of infecting, it was later repurposed, was domesticated if you will, to a new function. So rather than harm, to help and to put to a new use. So viruses can be fuel for evolution, and that’s one of the more remarkable recent discoveries of molecular biology.
ALEXA LIM: And some of the researchers had some really interesting and beautiful ways to try and understand these questions. One of them that popped out for me was, Susumu Ohno used paper cutouts of chromosomes and translated chains in the music. How did he do that?
NEIL SHUBIN: Yeah, Ohno was a genius. And Ohno is famous for the theory that the way new genes can evolve, one of the main ways new genes can evolve, is through duplication copy. So one of the big mistakes that can happen during when cells divide is you can end up with extra copies of genes.
And so he said, well, that could be a major mechanism of evolution because you get extra copies of genes, you had all that redundancy. Genes can evolve new functions in new ways. And he turned out to be profoundly right.
But the way he got to this, he wasn’t working at a time of high technology, he was trying to understand how– what’s the genetic material? And how much genetic material exists in different species? So to do that as he had pictures of the chromosomes of different species, that he took under a microscope, and he would blow those pictures up to the correct scale and then cut them out and weigh them. So he’d weigh all the chromosomes, his cardboard cut outs of the chromosomes– they had a rhinoceros– he’d weigh them and compare them to cardboard cut outs of the chromosomes of say a salamander.
And you find, wow, the salamander has much more genetic material inside its cells than big rhinos or other creatures. Turned out to be a really profound set of experiments. I mean, here he’s making a paper doll equivalents of the chromosome.
But what he discovered was that the complexity of an animal does not relate to how much genetic material it has inside the cell. Which at the time he was working, in the ’50s it was a pretty big deal– the ’50s and ’60s that’s a big deal.
And that’s something that’s only later confirmed by the genome projects, since 2000 where we find that creatures– we humans have about 20,000 genes. There are some creatures like lilies, and frogs, and salamanders which are much more genetic material. So the complexity of an animal doesn’t necessarily correspond to the amount of genetic material in itself and the insights into that were first seen when Ohno cut out cardboard chromosomes [INAUDIBLE].
But he had another hobby. He was a musician. And so what he did is he looked at the amino acid structure of proteins, which was becoming known in the 1960s. He put a different note for a different– for each amino acid inside the genome. And he compared the scores he would get for proteins of different species.
So he’d get the score of a protein in a mouse and compare it to the protein in the salamander and he’d have these tunes that you could listen to. They’re on YouTube. You can listen to them.
ALEXA LIM: Really?
NEIL SHUBIN: Well, yeah, you can’t listen to them for long. [LAUGHS] They’re not very [? tonal. ?]
ALEXA LIM: Right. I think I’d be more inclined to have 23andMe done if I got a paper cut out of my genome.
NEIL SHUBIN: There go go. Me too. Me too. [? Definitely. ?]
ALEXA LIM: What I like about these biographies is that some of these scientists were very wrong in their ideas, but they were just as fervent adamant about their ideas. I mean, why are the wrong turns so important?
NEIL SHUBIN: Wrong turns are so important in science. When people put an idea out there that builds based on new data that gets us to think in new ways, that propels science off in whether it’s right or wrong. And we’ve been propelled as scientists by wrong ideas.
You think about Mivart, with this wrong idea. Well, that propelled Darwin to greatness. And so, it’s not about being necessarily always being right, it’s about using evidence to move the field forward. And oftentimes, the fields move forward by wrong ideas that have propelled other scientists in opposition to do much better.
And we see that unfolding in real time with the coronavirus research, which every day you find new research that’s some of it’s conflicting. But truth will out. Evidence will win the day. But sometimes wrong ideas do [? make the ?] [? field ?] very importantly.
So that’s why some of the people that I talked about in the book were wrong, but they were right at the time. They were right with the evidence that they had. And so they thought about it in an important way. And it’s only when we had these technologies that we can see we’re not fully able to explain what they thought they could explain.
ALEXA LIM: I’m Alexa Lim, and this is Science Friday from WNYC Studios. What are the big questions in evolutionary biology that are still unanswered or that you are particularly interested in?
NEIL SHUBIN: Well, one question I really love and I think we still have to find answers, and I think we now have the tools to do it, is why do some lineages not evolve much over millions of years and others evolve dramatically? And by evolve, I mean, speciate and produce many descendants where are the others may not. Compare beetles to horseshoe crabs, for instance. Why do we have thousands upon thousands of species of beetle and relatively few species of horseshoe crab, and that kind of thing? And I think, understanding that dynamics of speciation, understanding diversity and why some things are more diverse than others, I think, we’ll– it’s something that those insights will come from linking studies of ecology to molecular biology to anatomy and so forth.
ALEXA LIM: You and your team found a fossil called, Tiktaalik which is something you called a fishapod and shows a transition between water and land. That was 14 years ago and you just recently took a CT scan to it? What more did that CT scan reveal?
NEIL SHUBIN: [INAUDIBLE] it just keeps giving us all kinds of new insights. So we can scan inside these things and we see how the bones fit with one another. What we discovered is the skull of Tiktaalik is highly mobile. It can open and close like a fish, but it can also bite.
We put new CT scans on the skin and we can see just how the fin is really built to walk and just support the animal. So surprising insights that follow what we did 14 years ago. Because we can do anatomy now with new technologies that didn’t exist 14 years ago.
And so, Paleontology itself has been changed by drone technology, by CT scanning technology. So it’s not just molecular biology that’s been compelled by technology, it’s working with fossils [INAUDIBLE].
ALEXA LIM: Thank you so much for joining us.
NEIL SHUBIN: Yeah. Whole lot of fun. Thanks.
ALEXA LIM: Neil Shubin is a professor of anatomy at the University of Chicago. His new book is, Some Assembly Required– Decoding Four Billion Years Of Life From Ancient Fossils To DNA. This is Science Friday. I’m Alexa Lim.