University of Chicago Professor Neil Shubin poses in the Chicago Field Museum's collection of ancient fish fossils © Ralf-Finn Hestoft/Corbis via Getty Images

Neil Shubin on evolution

Read the full transcript of our Science Focus Podcast interview with Neil Shubin about evolution - listen to the full episode at the bottom of the page.

Sara Rigby: So, first of all, can you please just tell us a bit about what your book is about?

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Neil Shubin: So, my book’s about evolution, the history of life. How did the great variety of creatures we see on earth today come about? And, you know, we’ve, you know, scientists have been thinking about this question for centuries.

But we’re at a really critical moment where new technologies from genome science to developmental biology, as well as the technologies that we analyse fossils with and discover fossils with, it’s really changed and it’s really given us a new window onto some of the classic questions of biology.

You know, how did some of the great evolutionary changes in the history of life happen? How did a fish evolve to walk on land? How did birds evolve to fly? How did those apparent impossible leaps happen? Well, I mean, new technologies are giving us new answers.

SR: So why do we need to still study evolution? Didn’t Darwin figure it all out with his survival of the fittest?

NS: You know, what’s remarkable is Darwin in 1859, in his first edition of The Origin, I mean, we went through about six of them, laid down the- laid the groundwork for some game-changing ideas, obviously, and how we, you know, we think about the diversity of life on Earth.

You know, there’s a before-Darwin time and after-Darwin time. Pre- and post-Darwinian. The reality is he came up with this notion before we had an any knowledge of genetics, you know, of heredity, let alone DNA. And so it’s interesting to take the Darwinian vision and think about it in a, sort of, in a DNA framework and a molecular biology framework. How does it comport with the, with the molecular evolution we’ve lived with in, with, for the last 30 years, and it’s really remarkable because, you know, some of his ideas apply very well. Others are fundamental. Still others not so much.

And so it’s very interesting to sort of see how the Darwinian view plays out, you know, in this new world of genetics, and the thing about it is it plays out extremely well. But there are tons of surprises.

SR: And so, one thing I found really interesting was the story in your book about St. George Jackson Mivart and how he influenced Darwin’s theory. And could you tell us a bit about that, please?

NS: Yeah, so sometimes, you know, great people are pushed by their greatest foes, you know. And so Darwin published the first edition of The Origin of Species in 1859. And it was he realised it was it was not entirely complete.

Well, you know, he had enormous detractors at the time, and supporters. But one of the people who was most influential in sort of pushing Darwin to greatness was Mivart. And he was just the ultimate contrarian in his personal life in a scientific life. I mean, he’d love to just disagree. You know, he changed his Anglican faith to Catholicism in his youth, really upset his parents and also upset his prospects for getting into Oxford and Cambridge at the time.

He was originally a Darwinian, but then turned on it and wrote a very influential critique of Darwin in a book he called On the Genesis of Species. You know, I mean, just that one word variant of the Darwinian title was pretty remarkable.

But he basically said, you know, look, you know, how do these, how did birds evolved to fly? You know, I mean, the number of changes that have to happen for birds to fly are just impossibly large, then they’d have to happen simultaneously, they have to have feathers, they have special lungs, special types of metabolism.

And the same is true for every great transition, whether it’s, you know, the origin of creatures to walk on land, you know, the lungs and, and legs and arms and necks and all this sort of stuff. And basically, he wrote a challenge to Darwin.

Darwin, then in the sixth edition of The Origin of Species five years later, really responded to Mivart in a very important way and came up with and solidified one of the foundational ideas that we use when we think about the great transitions in the history of life.

He said, you know, look, the biggest changes aren’t always the origin of new structures. It’s a change in function of structures that already exist. It’s repurposing and modifying things that already exist. And he, in that response really sort of set the stage for a new way and an important way, and a very modern way of thinking about these great transitions.

But it’s not always the origin of a new structure or a new gene. It’s taking what exists and finding new functions for them. And what that means is that organisms have at every stage, you know, a range of features genetics and development in their anatomy. And they vary a lot and considerably and they have a reservoir of this variability so that when the opportunity arises, they can evolve in new ways.

One of the one of the signature exemplars of this is the transition from life and water to life on land. You know, you think about something that I’ve been working on for a number of decades. You think about that. You could say, well, you know, well, how did fish have to walk online when they need like limbs and lungs and all this other stuff to arrive simultaneously?

And the answer was, I know, it’s the Darwinian vision that his lungs existed for eons before creatures took their first or distant ancestors took their first steps on land. Arms existed for millions of years, both legs existed for millions of years before the creatures took the first steps on land, fish living in aquatic ecosystems 380 million years ago or so, already had lungs, already had fins with arm and leg bones inside or and they were living using these features to live in water, such that when the opportunity to invade land happened they already had this stuff.

Basically they just change the function from walking in water bottoms, you know, on the bottom of the water column to walking your land from using lungs to breathe in water that might have low oxygen. They use them to live on land so it can change and function.

SR: Right. Yeah, that’s that’s a really weird thing to think about. Why would fish have evolved lungs in the first place?

NS: Yeah, so this was known for a long time before Darwin actually, originally is Jefferson. Tulare discovered this and others I didn’t heard it before. So when you think about this, so basically, if you look at fish, they have a got to write the mouth and the digestive tract, but lying adjacent to the digestive tract and the thoracic area and what’s equivalent of the chest area right.

In the fish equivalent of that are is typically an air sac that is related to the gut tube that develops from the gut tube, that sack In many fish serves as a swim bladder. It’s a typical bladder that serves for neutral buoyancy. And a lot of other fish that sac is vascularised. And when it’s filled with air can serve as a respiratory organ and that’s a lung. And it turns out many fish have this lung.

So how do they use the lungs? Well, the fish that have lungs and there are living exemplars of this today have lungs, but they also have gills and they use both to breathe. When there’s plenty of oxygen in the water, they’ll typically use the gills just like most fish, but when the oxygen level in the water decreases to a certain point, as it does in many, you know, freshwater systems throughout the year, they’ll rely more increasingly on the lungs and they’ll just go up to the surface, take a few gulps of air and then go back down.

So lungs are sort of an accessory organ for you know, for breathing when the oxygen level goes go down. It turns out they turned out to be a fabulous Oregon. This limit fish decided to make that commitment to life on land.

And then the same thing by the way applies to arms and legs. Fish had arms and legs inside their fins for millions of years before any critter took the first steps on land, and they were using them, we think, to walk on the bottom of the water like a lot of fish do today to, to station hold to grab the bottom and wait there as the current brings by prey for them to snap up, or sometimes even to live in the shallows, you know, in the mud flats and so forth.

So, you know, fish evolving in these aquatic ecosystems already had important inventions that when the shift land came, all they had to do is just change the function of stuff that already existed.

SR: So another example of this, I think you mentioned is the evolution of flight. And so in dinosaurs were evolving feathers, which was quite a controversial idea. Could you tell us a bit about that, please?

NS: Yeah, so you know, the traditional view of dinosaurs from about a century ago was these giant lumbering beasts and that view really changed dramatically starting about three decades or so when people started to realise the dinosaurs, particularly theropod dinosaurs, that you know, the carnivorous ones were fast running high metabolism rapid growth rates had hollow bones. And in fact, many of them had most derived ones. Had bird like structures had forms that look something like wings had a version of a wishbone all of a sudden, you know, they look really bird like.

And then starting in the mid late 1990s, coming out of China, where at first they were reports just like whispers, and then they became real, that the third dinosaurs with feathers discovered in the fossil record. And for what was originally just one or two, you know, species with feathers we now see almost all these carnivorous dinosaurs had some sort of feather like structure outside them. So just like lungs and the origin of limbed animals feathers, predate the origin of flight and we believe that feathers are used for courtship displays, like in birds today, and initially, perhaps in thermal regulation, you know, serving as insulation, but they weren’t used for flight.

You know, and so again, it’s a change in function. That Darwinian quote, you know, in his response to Mivart is just so perfect. You know, it’s, it just explains, you know, how you can get great changes without having to wait for mutations to occur independently throughout the body creatures already have these things.

SR: Right. So yeah, that’s quite quite an important distinction, isn’t it? So it’s not that dinosaurs evolved feathers to fly, but they evolved feathers, and that helps them to fly.

NS: That’s right, they evolved feathers to live as better dinosaurs. Not to fly. And likewise, lungs, you know, fish evolved lungs to, you know, be better fish. And it just so happens that later on, that was really great when fish started walking on land or when dinosaurs needed to fly, you know, and so, that’s the I think that’s the same point and what’s neat about that point, and what’s so foundational about it, you know, when you think about it, pression Darwin was was that it applies equally well.

So when we think about genes and how they come about like the that it’s not always the evolution of new genes that matters in some cases. But in a lot of cases, it’s not the evolution of new genes that really matters. It’s finding new uses for genes that already existed, redeploying them in new ways, and in new contexts to make new stuff.

SR: Can you give us an example of that, please?

NS: Oh, yeah, one of the great examples of this is the one of the change in my life, right. So the starting in like the, in the molecular biology tools became ever more powerful. It was discovered that certain genes play a very fundamental role in building bodies. And I think the interest in these genes started before we knew anything about DNA.

It started when people were really looking at flies as a model for genetics replies, and they were cataloguing different kinds of mutants, and these folks working in the fly lab and Caltech Columbia University and elsewhere found just mutants that were just head scratchers, they would find, say, fly wear with a leg where an antenna should be.

Okay, so legs sticking out the head, okay? Or they found a fly free fly that had two body segments that held wings instead of two wings it had for me they call it by thorax, the other was called antenna pedia you know, so legs were temporary. So these, these were like flies that had like, the right body parts, but the body parts, they somewhat cut and pasted them, you know, they they were in the wrong place.

So these mutants captured a lot of people’s interests such that when the DNA technology became ever more powerful, and this started in the early mid 1980s, folks discovered the actual bits of DNA that encode for those genes. And they discovered that there is a whole catalogue of these kinds of bodybuilding genes that control when and where organs develop in the body. And not only did they find these genes in flies, but they found that versions of these same genes are making the bodies of everything from chickens to mice to people.

So here was a fundamental toolkit that builds the bodies as different as flies and people. And I remember that set of discoveries came out in the mid late 1980s. I was training to be a paeleontologist, and I saw these discoveries are published in in nature and PNAS and elsewhere. And I looked at them and I said, Okay, I need to learn a little molecular biology here. So I am.

And so when we think about, like, get back to Darwin’s quote, as your core to your question, taking the long way to get to your question, we’re getting to it. So basically, you have these genes. The trick here is that these genes are involved in patterning the body, but they’re also involved in patterning parts of the limb. They’re involved in patterning parts of the brain.

So what you’re seeing is these genes arose for one purpose to pattern the body acts as the general body plan, but then they were co opted or redeployed to make a plan. appendages to make parts of the head and so forth. So it’s like once you have one tool, right one recipe, you can redeploy that recipe to make other things. So again, it comes down to sometimes the biggest shift is not in evolution, you know, new making new jeans, but is using old genes and new ways.

Another way we see that happening is in how some how oftentimes new genes actually come about when new genes come about oftentimes, although not exclusively, but often, they come about as duplicates their gene copying gone wild. So what we see is, whole families have genes in our genome that are related to one another, and they evolved by copying duplication in our genetic material.

So of these body building genes, you know, flies have like so one cluster of these things we have for, you know, so much more complexity. So we think fine gene duplication is a very common event and the origin of new genetic material. as well. So again, using the old to make the new, repurpose it, change its function or copy it and modify it.

SR: So I always assumed that if you were trying to piece together the evolutionary history of life, that would basically just be fossil hunting, you go and you find fossils, and then you’d have a look at it and see where it fit in, like putting a puzzle piece in the puzzle. But actually, it sounds like there are there’s a lot that we can learn from animals that are alive today. And so what what can we learn from from living animals about their ancestors?

NS: There’s an enormous amount so what we are so fortunate now that not only do we have fossils, but pretty much the the bodies and the genes and the DNA of every creature alive today is a library of its evolutionary history. That is every creature alive today, in inside its genomes inside itself inside its tissues, contains artifacts of billions of years. In the history of life, the trick is how do we know how to unlock that.

And we see that vividly. You know, with each new genome that we, that we discover, or that we read about, you know, we have the Human Genome Project, the rice genome project, the Lilly genome project, the corn Genome Project, genome projects for thousands upon thousands of different kinds of species, you know, we get them with ever increasing frequency. And what we’ve learned is now to compare the genome in many important ways, not just the sequence of DNA, but the structure of DNA, as well.

And when we do that, we can start to ask some really important questions. So we have a knowledge of the chimpanzee genome, we have a knowledge of the human genome, we have a knowledge of all kinds of fish genomes, and on and on and on, we can begin to ask the question at the level of DNA, what makes a human different from chimps? What genes are important, what genes aren’t, you know, what are the processes that are important and making distinctively human features? We could take the question back even further, we can come pair the genome, the human genome to that of a fish.

And we can ask what’s the same and what’s different? What’s different about the genetic recipe that builds the body of a fish, like live today from the genetic recipe that builds the body of a human or a chimpanzee alive today. And so these are questions that were formally the domain of fossils or comparative anatomy. Now we can unlock them with the knowledge of the genome.

SR: In your book, you have this diagram that compares the embryos of lots of different species of animals quite wide ranging species and a different periods through the development. And early on, they all look really strangely similar. And could you tell us a bit about that, that diagram and the implications of that, please?

NS: Yeah, so that diagram is a version of one that was done by Karl Ernst von Baer who was a embryologist who lived decades before Darwin and he was interested In asking the question, you know, how does the development from egg to adult of critters is different as turtles and fish and people in my mice? How do they differ?

And so he was collecting lots of embryos, and storing them in vials. So he’d have these different embryonic stages of different embryos, and he put them in vials with with alcohol or formalin and to preserve their, you know, preserve them. So because he looked at them under the microscope, but he forgot to label or the I believe the labels fell off a few of his vials, fell off a vial that contained, you know, so he had like turtle and mouse and fish embryos in these vials, but he knew that they were that but he didn’t know which was which.

And you couldn’t tell them apart, because they’re all early embryos. And so this is sort of led him to think about, you know, his theory and his ideas when I observe differentiation, that is, early embryonic and early embryonic stages of critters of different species tend to look much more Similar then do later embryonic stages. And that’s what you see in that, in that diagram you I mean, I put a version of his which is, you know, turtles and, and mice and fish and birds and so forth.

And early embryonic early embryonic stages, you know they, you might find some differences but they tend to look extremely like and then they acquire those differences later in in development. And that was really important. And then a version of the same sort of theory was altered a bit came out after Darwin published the origin of species. And it turned out to be wrong, but and not a good generalist and not a very good generalisation, but it’s stimulated an enormous amount of work.

And that was the notion that by Ernst Haeckel, which was the famous one: ontogeny recapitulates phylogeny, and by that what he meant is development from egg to adult ontogeny recapitulates phylogeny, which is evolutionary history. So his theory was a lot. It’s very different from going bears. His was basically if you look at the development of any species We’ll track its evolutionary history.

So if you looked at the human embryo, you’d see it go through it would go through like a fish stage, then amphibian stage and a reptile stage and so forth and so forth. Well, you can imagine, oh, and also Haeckel was an amazingly good and talented artist as well. And so his book was just rich with illustrations, rich with ideas, rich with conjectures, and so forth, and it was enormously influential.

Turns out that’s probably not a good generalisation that ontogeny recapitulates phylogeny. We see it in some structures, though, like if you look at the development of our kidneys, there definitely is sort of a it does track its evolutionary history to some extent, as well as some other structures, but it’s not like a law of nature, like what he wanted to then what he wanted to propose.

But honestly, I think where Haeckel was most influential was really in stimulating a an interest in studying embryos, as vehicles to understand evolutionary history even though his in particular theory is wrong. It stimulated so many others To think about embryos in new ways, and then that in so he was important, just like before, I actually kind of think that in being wrong in how it stimulated, you know, the, you know, really foundational work by others.

SR: So why is it that all of these species look so similar so early in their development?

NS: Well remember, I mean, one thing we’ve learned in genetics is a lot of them have similar kinds of genes. You know, so when I said that flies, and fish and turtles and mice and birds, and people all have versions of the same genes, building their bodies, what we find is, it’s not only even just the same genes, and sometimes it’s whole networks have genes that interact with each other during development.

So to some extent, I think it’s reflecting history. You know, I mean, it’s, it’s reflecting the fact that these creatures have similarities. Getting back to Darwin that the reason why they have these similarities is that all of them shared a common ancestor sometime in the distant past, you know, and some of them shared very distant common ancestors. Some of them share more recent common ancestors, but common ancestors they all share. And so we’re seeing that as a reflection of this common ancestry.

SR: So, there are some species, which have juvenile states, like, like frogs have a tadpole stage and things like that. And, and so could you tell us a bit about how these juvenile states can sort of influence evolution of species?

NS: Yeah, hugely. So. I mean, I’m one of those vivid examples of this was Auguste Duméril, who was the keeper of reptiles and amphibians at the Paris Natural History Museum in the 1800s. And tomorrow, one of the iconic stories is when Duméril who was famous at the time, and he was he became a Darwinian after the 1859.

The first edition of Darwin Duméril was enthusiastically a Darwinian so and he was famously so so people would send him specimens from all around the world. And one day he received a box from colleagues who are working in Mexico, and it was a box that contained a handful of salamanders fully grown And the reason why they sent them to do Mario was these fully grown adult salamanders were also aquatic. They had external gills. They had big like the fleshy fin limbs that looked a little bit like fins. They had a tail that had a big fold on it like fin like sort of thing. Lots of like, aquatic features in a, in a sexually mature adult salamander.

So I thought, well, I’ll just study these maybe I could tell us about give us insights into the transition from fish to land living creature, so do male but then he got busy with other things. So we store these things in his enclosure, would feed them and then came back at one point. And he found two different kinds of salamander in his box.

He found at one point he had full adult, the ones who were sent the ones with, with the external gills and all the aquatic traits, but then living right next to them were other salamanders fully grown aquatic, fully grown adults. But these had no external gills. These were fully terrestrial. They had terrestrial limbs, they had no fin like tail. Nothing flipper like tail, none of that stuff.

So it’s almost like some he put like chimpanzees in a cage one year came back eight months later and found chimpanzees and gorillas, you know, happily living together. He’s like, what is going on in my box? So that stimulated Duméril to think about larvae. And so Duméril and others started to think about, you know, let’s look at the life history of these things.

Let’s look what happens from egg to adult and you found as your question suggested, that the importance here is what happens to the larval stage. So as we know, in tadpoles, you know, tadpoles hatch from the egg, they swim around as larvae. And those larvae, the tadpoles are aquatic and they have aquatic mechanisms, they swim around, they feed in water with suction, feeding and so forth. then something happens and it’s called, you know, a surge in usually in the thyroid hormone.

And then they undergo metamorphosis and in metamorphosis, we all know they go From a tadpole to a frog, their legs change, their sculpt changes, their whole body changes and they become jumping frog. Well, the same thing is true with salamanders. They go through many species salamanders, although not all will undergo the aquatic larvae. They’ll swim around live in water, undergo metamorphosis and then become fully terrestrial adults.

What Duméril found is that metamorphosis is optional. And it can it can vary. And so that you know the species that are fully terrestrial undergo metamorphosis, the ones that were those, you know, fully aquatic adults, they did not undergo more metamorphosis there was a simple shift that happened in their endocrinology and their hormone levels. Very simple.

And that simple hormonal shift led to changes across the entire body which would have been, you know, just an enormous amount of genetic change, it wouldn’t happen otherwise. So we found that you can have through simple shifts have development, enormous changes to the bodies of critters. And so those two different kinds of salamanders just came back from just simple, you know, whether you metamorphosis metamorphose or not.

And it turns out that those kinds of properties are important for evolving systems more broadly from invertebrates to other kinds of creatures. That is one very fundamental way of evolving is by changing the timing of developmental events, stopping early or stopping later, you know, slowing things down or speeding them up. The more you do that, the more you can have changes that are coordinated across the entire body. And that was work that was stimulated largely by Duméril and the people that followed him.

SR: So, there’s an example of this sort of, you know, changing of the speed of development that really surprised me. And that was the example of the sea squirt. Can you tell us about how the sea squirt led to vertebrate life.

NS: Well, I mean, one of the, you know, when you think of vertebrates like us, right? So, you know, where did vertebrates with backbones and skulls and skeletons come from? Well, if you look at that, and you try to trace that in terms of comparative anatomy, there are three traits that are seen in early development that all vertebrates and their closest invertebrate relatives have. And that is they have a nerve cord that runs along the backside. So it’s called a dorsal nerve cord Hollen nerve cord.

They have gill slits in the pharyngeal area. And they have a supportive rod called a notochord. So those three traits when I teach intro bio I teach these are the three fundamental traits of the vertebrate body plan. And there are a number of, you know, invertebrate creatures that have them their closest relatives. And so we talked about this.

So people have always asked, you know, where did this come from, you know, and there’s some, there’s lots of really interesting living creatures alive today. There’s one called m PHY oxus, which has beautiful aspect of the vertebral body plan even though it’s not a vertebra image, but it shows the what they’re derived from.

But others, some Russian biologists as well as a Garstang, who was a great, great biologist in the UK came up with a different idea that is that the the closest relatives of vertebrates they proposed were the oddest looking ones. So Garston, Walter Garstang is his name came up with the idea that building on what Russian biologists did a few decades before, that the closest relatives of vertebrates looks something like a sea squirt.

That is sea squirt to paint a word picture. A sea squirt, is something that does not even look alive. It’s like, basically, they’re the sessile animals attached to rocks. It looks like a formless lump of clay. If you were to take a peek at it, it has like a hole at the top and they pump water, but there’s no obvious head, no obvious body, no obvious tail, there’s no option. Via nerve cord, no obvious cartilage rod that notochord I was telling you before, let alone Gill slits.

There’s nothing there, but yet Garstang believe that they held the secret. And because he knew something about development, he knew something about embryology. Because if you look at sea squirts, they don’t start their development like that. What they start like is they are hatched from an egg and the larval sea squirt, looks something like a tadpole. It has a head and a long, slender body. it swims around in the water. And when he looked at the tadpole, what do you see? It has that nerve cord it has that that cartilage rod called notochord.

And it has the gill slits and what happens is, these little larvae swim around and at some point, they decide okay, it’s time to settle down and they swim to a rock they attach to the rock, they proceed to lose the tail, lose the head, lose the notochord loose the nerve court, lose most of the gill slits and change their body to become this you know, this form. This lump of clay with a little hole on top.

So basically what Garstang said is, well, the shift to vertebrates was real simple. You begin as a larval, a larval, tuna, Kate, Animal, and then don’t metamorphose. You know, it’s basically stopped early, and then just grow from there. And so there’s a case where, you know, putting the stopping metamorphosis on not undergoing that metamorphosis, and just continuing development from there, it was a likely big part of our own distant evolutionary history.

SR: So that’s a really weird example of something that’s happened in our evolutionary past. What is your favourite thing that you’ve learned about from this book? evolutionary quirk like that? What’s your favourite one?

NS: My favourite. So one of my favourites, is I have so many so it’s hard to choose one. It’s like, you know, you’re asking me which my children like the most. But, ah, you know, it’s hard not to love salamander tongues, to be quite honest. So Not all salamander tongues but most so one you know there are two kinds of animals in this world there are animals that bring their head to the food, think lions, and cheetahs.

Then there are there are animals that bring the food to their head think salamanders living on land. So some salamanders living on land have evolved a really amazing biological machine. And that it’s a machine to project their tongue, they slip out to snap out their tongue, about almost the length of their body in like less than a millisecond. And they catch an insect and bring it all back.

I mean, it’s just an amazing biological machine that they shoot their tongue out. ballistically like a missile, attaches to an insect and just as fast brings it back into their mouth. And for that to happen, it takes lots of changes, it takes changes to the gill apparatus, it changes the muscles of the body. I mean, you’re inventing a whole new machine, but lots of different parts. It turns out that that machine with lots of different parts likely came about two to four times independently in the history of salamanders.

So this amazing biological machine was obtained multiple times independently, the more we study the DNA record, we see that and it just shows an example to me, which I think is very important in evolution. That is, oftentimes, in fact, more often than not, there is not just, you know, one pathway to something, there’s multiple pathways, evolutionary pathways to the same invention that we find is an evolution over and over again, the independent origin of the same invention in distantly related species.

You know, and I think that’s, the more we learn about genetics and development. The more we learn about how you know how animals function as machines, the more we see that these these limited number of solutions are hit upon again and again. And that’s telling us something very important about you know, the nature of evolution and biology and so forth. So salamander tongues, love them.


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