Neil Shubin
Subject: How Change in Function Drives Evolution
Bio: Professor of Biology and Anatomy at the University of Chicago and the Provost of the Field Museum of Natural History
Reading: Some Assembly Required: Decoding Four Billion Years of Life from Ancient Fossils to DNA is here
Transcript:
Larry Bernstein:
Welcome to What Happens Next. My name is Larry Bernstein. What Happens Next is a podcast which covers economics, politics, and education.
The topic today is How Change in Function Drives Evolution.
Our speaker is Neil Shubin who is a Professor of Biology and Anatomy at the University of Chicago and the Provost of the Field Museum of Natural History. He is the author of a new book entitled Some Assembly Required: Decoding Four Billion Years of Life from Ancient Fossils to DNA.
I want to learn from Neil about how he discovered an ancient fish that millions of years ago walked out of the water, and who we are all distantly related to. I want to find out why that fish had developed lungs and nascent limbs to breathe, walk, and survive on land. What explains the transition in animals from life in water to life on land.
Buckle up.
Neil Shubin:
I'm a biologist paleontologist who for the past four decades has been studying the problem of invention, innovation, novelty and evolution. Look at life, it's been on the planet for about 4 billion years. For billions of years, life existed as single cells. Then a little over a billion years ago, multicellularity came about.
How do these changes happen? Scientists have studied this problem for over 150 years. The message is: nothing ever begins when you think it does. A phrase I love to tell my students here at Chicago, if you think that lungs arose to help creatures live on land, or feathers arose when creatures evolved to fly, you would be in wonderful company, but you'd also be entirely wrong. And we've known that for over a century. The game-changing innovations in the history of life always come about prior to the revolution that they're associated with. Lungs came about eons before creatures took their first steps on land, they arose in fish living in aquatic ecosystems adapting in new ways.
The same thing with feathers and dinosaurs before birds ever took flight. So game-changing inventions are around for a long period of time, oftentimes prior to the revolution they're associated with. And once you start seeing the world in that way, it changes how you do research and think. A new structure comes about using an old structure in new ways. And once they're used in new ways, then they take off. Their evolutionary trajectory changes entirely. Think about repurposing, modifying, tinkering, existing structures in new ways. And what's really changed our perception has been the revolution in molecular biology and studying DNA.
Three and a half decades ago, I trained as a paleontologist. I realized that I had to learn molecular biology because many of the problems are explained both by understanding DNA as well as fossils. Understanding the DNA that's active during the development of the organism when the body is built. The biological recipe that builds bodies from embryo to adult is active in each of us during our development, but it's changes to that that lead to major evolution.
To understand innovation, novelty, invention and evolution, we must understand the fossil record and the sequence of changes. We can now begin to ask these questions at a whole different level. And it's integrating those approaches that has been behind my own research and where the field is going.
Larry Bernstein:
A 4 billion old rock is the oldest fossil record we have. What did they find? Asteroids hit the earth all the time. There's no cell on any of those rocks.
Neil Shubin:
Some asteroids have the components of proteins, they have amino acids, they have certain molecules that were essential for living creatures, but they don't have any evidence of living creatures themselves.
Larry Bernstein:
Why would they have amino acids?
Neil Shubin:
When you think about the formation of rocks in the early solar system, which is what we're talking about when we talk about asteroids, geochemical reactions are happening in rocks, in dust, and in celestial bodies. And one natural outcome of those reactions can be molecules like ammonia and building blocks of life that aren't necessarily involved in living creatures, but they're just outcomes of the natural processes that happen in the planetary geology of these asteroids. So, it's not like they're being assembled to make living creatures on these asteroids.
They're just an outcome of the natural geological processes that are at work in these celestial bodies.
Larry Bernstein:
In your book, you highlight that these organisms affect the atmosphere, the soil, everything, and then it allows evolution to take a different path. There is time dependency. Tell us about how organisms change the dynamics of evolution.
Neil Shubin:
For billions of years, blue-green algae undergo photosynthesis. They use light from the sun to produce metabolic energy. And one outcome of that is oxygen. These single cell microorganisms have produced oxygen for billions of years that made the atmosphere. If you were to take a time machine and travel to the earth 4 billion years ago, there would've been virtually no breathable oxygen. You'd need a spacesuit to survive on our own planet.
2 billion years ago, oxygen started to appear on our planet due to the action of these blue-green algae. That's a classic case where creatures doing their own things to survive produce compounds that change the planet. Once you have oxygen in the atmosphere, then that's a whole new game for the creatures that are there. Oxygen enables new forms of living.
Larry Bernstein:
Your book starts with a discussion of early critics of Darwin about how innovation should proceed. It was this criticism that resulted in a new way of looking at the problem. Take us through Darwin and his critics.
Neil Shubin:
The Origin of Species Darwin's great volume went through multiple editions. In 1859, the first edition, there were critics that brought real criticisms of Darwin's theory. One was Charles Mivart a famous curmudgeon who ended up pushing Darwin to modify his theory in very important ways because Mivart called him on a real problem. What he said in response to Darwin's first edition was, you're talking about these great changes in evolution, but how could they possibly ever happen? How could a wing come about from just an appendage? What good is 1/10th of a wing? Does that help the organism in any way?
Or when you think about the revolutions in the history of life that Darwin is talking about, so many changes would seem to have to happen at once that any great change would be impossible. So, for creatures to take their first steps on land, you must have the origin of lungs, limbs, new ways to eat, excrete, reproduce, and on and on. In the sixth edition, Darwin had his response to Mivart. What Darwin said was a piece of a wing is not useless. It can help an animal not fly, but it can help it do some version of staying in the air for short periods of time and maybe that's useful. So, these structures may have incipient functions that are beneficial for the organism over time.
That's one. But the other was, and this is what motivated me, is that in his answer to Mivart, it's not always the origin of a new structure that's important. It's using that structure in new ways. It's a change in function. That was critical. Changing the context of how an organ is functioning. That single insight explained so many things that seemed impossible before, but it also is a framework. It's very important for integrating not only understanding anatomy and how it changes, but understanding molecular biology and its role in development.
Larry Bernstein:
That concept of change in function is critical to your research. In your previous book Your Inner Fish, you asked yourself this question you saw in the fossil record that there were no mammals, and there were fish but no amphibians. And by that logical construct, you said, I guess a fish must have walked out of the water, but to walk out of the water would require something for you to do that. It must've been for a different reason originally using the same logic that Darwin suggested in that concept of change in function. Tell us about how this idea led your life work.
Neil Shubin:
The first thing is we're able to predict where to find fossils in the fossil record. We can use evolution to predict where to find key transitional fossils. That's what we did with the transition from life in water to life on land. We predicted that working in rocks of a certain age in the Canadian Arctic, we'd find a transitional creature between fish and amphibian. And we found it, took us six years and a lot of blood, sweat and tears. But we ended up finding a fish, which has fin rays and scales and many features that you would say that's very fish-like. But when you open the fin what you found was arm bones, upper arm, forearm, even parts of a wrist. Same thing is true with the leg bones and the hind fin.
This creature had both lungs and gills and other traits that were useful to live in water and maybe a little bit on land. But we see here in this creature and other creatures like it is that they're largely aquatic, but they're coming up with many of the features that animals later were to use to walk on land. For instance, lungs originally arose in creatures living in water, not creatures that were evolving to walk on land. These were creatures that were living in ancient swamps and streams. And they were true aquatic creatures.
They had both gills and lungs, but they'd used these lungs to take gulps of air when the oxygen content of the water was low. These lungs originally arose as an accessory organ to supplement gills, not as an organ that was necessarily used in walking on land. They were used to living in different kinds of water, such that when the animals were to take their first steps on land, they already had lungs, they already had arm bones, they already had leg bones. So, many of the inventions that were necessary for creatures to walk on land already arose in fish living in aquatic ecosystems. Now, they didn't come about in fully formed state. They were in the incipient state, but the initial steps originally happened in aquatic fish. And this is true with every great transition in the history of life.
Larry Bernstein:
In your book, you mentioned that lungs had multiple purposes. It might've been used to make sounds for mating. It might've been supplemental for oxygen when either the water level declined or whether if you were stuck in an area where oxygen in the water was poor. There may have been a variety of reasons beyond this supplemental oxygen issue.
Neil Shubin:
Yeah, exactly. The features arise in one context, but then they're useful in other contexts. That's exactly what we see repeatedly in evolution. Fish living in water came about with those arms and legs were initially useful in these fins because animals were walking on the bottom of the water. They were moving through weeds, streams, and ponds. They weren't necessarily walking on land for extensive periods. They were mostly living in water. And that's where these inventions were useful. Likewise, the lungs are also useful in providing buoyancy. Creature takes a gulp of air, it can float a little bit, doesn't have to use the muscles to support itself. It is a very efficient way to control buoyancy in water is to have lungs and take a gulp of air or exhale. You can go up and down that way in the water column. Some of these features can lead to new opportunities when the environment changes, when it's necessary for them to take those steps on land.
Larry Bernstein:
New topic. Figuring out common ancestors between different species. In your book you mention the work of Alan Wilson and his hypotheses that chimps and man had a common ancestor 5 million years ago. And he did that with an assumption about the rate of mutations in DNA. We can use statistics because we have such a huge amount of DNA and then we can look at the number of mutations per generation. Do you think the rate of mutation is constant among all creatures?
Neil Shubin:
If you have that constant rate and you have those differences, then it becomes a clock. The criticisms of the molecular clock hypothesis are how do you know that there's a constancy of rate? And the proponents of this notion, the late Alan Wilson, would say that over long periods of time, that mutation rates are constant. In any given generation, there may be changes, but over long periods of time, there's a constancy in their rate because they're determined by physical chemical properties.
Larry Bernstein:
In your book you highlight the importance of jumping genes. These are bundles of genes that jump around in their position on the chromosome and that have consequences. Tell us about how bundles of genes can jump as a collective mutation in a living individual and the natural process between parent and child.
Neil Shubin:
Our genome is not static. It's roiling with change.
Larry Bernstein:
While we're living?
Neil Shubin:
While we're living genes can make a copy of itself and insert elsewhere in the genome. And this can happen repeatedly. These are the famous jumping genes, transposable elements that is gene copy can be made and then it can land elsewhere in the genome, insert itself in the genome, and boom. And you can have these things happen repeatedly to the point where most of the genome can be made up of these jumping genes. Only 2% of our genome is our genes. 98% is other stuff. And 70% of that other stuff are these jumping genes that just make copies of themselves and land elsewhere in the genome. So, they can be like parasites, they just make copies of themselves and just go all over the genome.
Larry Bernstein:
If we had collected DNA from me immediately after my birth and then compared it with my genome today, is it different?
Neil Shubin:
Yeah, definitely.
Larry Bernstein:
And my genes are different because of these jumping genes?
Neil Shubin:
Well, not only. There are some viruses that entered the genome. There are epigenetic changes, different chemical changes that happen to the genome itself. So, your DNA, my DNA, your listener's DNA is very different from when we were born. Definitely, there is a core that's similar, but there's enough differences that they can be meaningful.
Larry Bernstein:
We hear about the importance of epigenetics, that actions that we take in life like smoking, stopping smoking
Neil Shubin:
Stress and exercise.
Larry Bernstein:
And that affects the genome. Tell us about how these genetic changes pass on to the next generation.
Neil Shubin:
We have changes in our genome that happen for a lot of reasons. One is normal mutation. That is when DNA makes a copy of itself, sometimes it makes mistakes. That's a mutation. We have genes that can jump around what we're talking about. Those changes can happen over many generations. They can happen with an individual. You have these epigenetic changes where you have environmental changes. Environmental influences can affect the genome directly. The chemical structure of the genome and some of those changes can control when and where genes are active so they can have meaningful results in our lives. And think about it, we have 23 trillion cells in our body. It's a big number. And DNA in those cells is dividing as we speak. Right now, DNA is being made in each of us in 23 trillion cells.
In those cells, the DNA is having some errors that are happening, and some of those errors crop up. They can cause cancer. So, we do experience a problem from some mutation, and that is based on sometimes our environment as well. We're living with the consequences of the mutations that are happening as we make choices, by what we do, what we eat, what environment we live in, what chemicals we are exposed to. Viruses can come in and insert themselves in the DNA. That happens and in fact, if you look at our DNA, about 9% of our genome is composed of ancient viruses that invaded our ancestors long ago and then got knocked out. We have a graveyard of ancient viruses in our own DNA, and then we had the jumping genes everywhere.
Larry Bernstein:
Ancient man or maybe in the ancient fish got exposed to a virus, that virus genome embedded itself in our ancestors’ genes and then it passed on?
Neil Shubin:
It sounds nuts, but it happens to be supported by a lot of evidence. Not every virus invades DNA. There's lots of different flavors of viruses that invade the DNA and some of these inserted DNA carry information such that over time they can be what's called domesticated by the host creature to do new functions. So, they can be rewired. It's a very insidious little trick. Where you have a virus that lands in a certain place, they exist to make copies of themselves, but sometimes they can be jury-rigged by the host organism to make new proteins.
One protein known as ARC is produced in the brain and is heavily involved in transmitting information among different cells in the brain. And it's involved in making memories in mice and humans along with other proteins, of course, many others. But this one has a very close similarity to HIV, the virus that causes AIDs. And if you look at the evolutionary history of this protein, it's present in land living animals, but it's not present in fish. So the idea that has been proposed by many people and with other lines of evidence as well, I'm just giving you just a very simple overview of it, is that sometime in the distant past when in those creatures that were taking their first steps on land, a virus invaded that carried the information to make a particular protein, and that what happened is that virus got domesticated, which essentially became used in making memories. But we see this viral relationship to proteins in our own bodies, in the immune system, in the tissues involved in pregnancy, in the brain. We see it repeatedly. And indeed 9% of our genome reflects some of this.
Larry Bernstein:
Your book is a story of evolutionary biologists coming up with radical new hypotheses often viewed as ridiculous by their peer set. Some are ridiculous, but many of them were not and radically changed the field. How important are radical theories and is it a challenge getting into your major journals? What's wrong with our major journals that they can't be more open to some crazy ideas?
Neil Shubin:
Yeah, you bring up a good point. There are a lot of crazy ideas that there, most of them are crazy, but a small fraction is revolutionary. So, how do you identify the revolutionary crazy, to the crazy, crazy? And that's the thing, because what we tend to homogenize our thinking in many ways, we all have these cognitive biases where we know what's right, we know what's wrong. That's our lens, which we see the world. Science is a human enterprise and is most definitely not immune to that.
We suffer from that enormously. And we have this system for better or for worse of peer review, which tends to standardize certain thinking. So, if you do have a radical idea, it's hard sometimes to get it published, let alone funded because the funding mechanisms tend to be incredibly conservative.
I take my own case, we have this idea to look in the Arctic for this fossil fish at the cusp of the transition of life and water, life on land. You're not going to get money to do that. I was going on a fishing expedition in the Arctic and they're like, it's a needle in haystack.
It was essentially private funding that enabled us to do that. The more we have a textured landscape for funding and publication, the more we'll be able to identify those theories that are crazy to many but are likely to be game changing over a long period of time.
One of the things I tried to do in the book is to show that a lot of these people who were considered crazy, Lynn Margulis had a game changing idea about the evolution of cells. Her paper was rejected by 17 journals, and eventually she got it published in some obscure journal, but it ended up changing the field years later.
Larry Bernstein:
When you were at Harvard, Stephen Jay Gould was teaching there. I read a couple of his books when I was in high school. He was interested in the jump in the fossil record often, and he questioned whether Darwin had it right. How should we think about Stephen Jay Gould's contribution to evolution? Was he right to focus on the dislocation in the fossil record? What do you think of his work?
Neil Shubin:
Remember what we're dealing with when we're looking at the fossil record. When I say something happened over 2 million years, that's a very different timescale from the evolution that's happening from generation to generation. Gould would be saying is, evolution can happen extremely fast when measured over the fossil records. So, you can get those jumps that the change may have happened in 500,000 years. But 500,000 years is still a lot of time.
When you add up the number of generations that were involved there, the real question becomes stasis. Why would creatures stay the same for long periods of time? That can happen for many reasons. One argument which people made, which I'm not sure is entirely right, but it's worth entertaining, is that maybe developmental systems don't like to change that much. That is if you perturb the process from embryo to adult developmental biology, you're more likely to make a change that kills the organism. So maybe it's only a small number, the space of beneficial mutations versus the space of lethal mutations. Maybe you have a small space of beneficial ones. Maybe it's a pretty rare event to have those. So that's one argument.
Another argument would be that maybe you have fluctuating selection, maybe over long periods of time. You have selection that happens in different directions. An organism has to deal with hot periods and then cold periods and hot periods and cold periods, and maybe then their physiology will not change all that much because they're going to be over long periods of time through that fluctuating changes. Maybe staying constant over time is actually a good strategy in some cases. So there are lots of different arguments like that that are out there. I don't know. There may be many different reasons for different groups.
Larry Bernstein:
I like to end each episode with a note of optimism. Could you use your optimistic statement to relate back to Darwin's insight that organisms use something developed in the past, for a different purpose and how that change in function is critical to evolution.
Neil Shubin:
Today is an incredibly exciting time to be scientists because the technologies, imaging, molecular biology and artificial intelligence and our capabilities as scientists are incredibly powerful.
We're repurposing questions that our forebearers came up with. The questions of Darwin only now can we address them in a way that we can have outcomes that affect human lives. That is the more we understand these bodies and how to manipulate them that can affect human wellbeing, cures to disease, enhancing performance. By understanding other organisms, we can understand ourselves in profound new ways.
Larry Bernstein:
Thanks to Neil for joining us today.
If you missed our previous podcast, check it out. The topic was Reducing the Number of Foreign Students. Our speaker was Jay Greene who is a Senior Research Fellow at The Heritage Foundation’s Center for Education Policy. He was previously the Department Chair at the University of Arkansas’s Department of Education Reform.
Foreign students can make wonderful contributions to every college campus but there are downsides as well. My alma mater the University of Pennsylvania is now 25% international and over 35% foreign if you include the optional practical training program. We discussed whether we should reserve more spots for American citizens and fewer spots for foreigners at our best universities and medical school residency programs.We also chatted about the importance of our universities and their critical function of inculcating American values in our next generation of American elites.
I would now like to make a plug for our next week’s podcast about the conviction of Alferd Dreyfus of treason by the French Military and why they intentionally sent an innocent Jewish military officer to prison. Our speaker will be Maurice Samuels who is a Professor of French at Yale and the director of their Program for the Study of Antisemitism. Maurice is the author of a new book entitled Alfred Dreyfus: The Man at the Center of the Affair.
You can find our previous episodes and transcripts on our website whathappensnextin6minutes.com. Please follow us on Apple Podcasts or Spotify. Thank you for joining us today, good-bye.
Check out our previous episode, Reducing the Number of Foreign Students, here.
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