Evolution & Animal Development: How Nature Builds & Changes Bodies | Sean B. Carroll

About the Guests: Sean B. Carroll, PhD is an evolutionary developmental biologist at the University of Maryland, who recently stepped down as VP of Education at the Howard Hughes Medical Institute. He is the author of many popular science books, such as "Endless Forms Most Beautiful."

Episode Summary: Nick and Dr. Carroll discuss developmental biology & genetics; evolutionary biology; genetics, genome size & genetic mutation; animal diversity; snake venom; human brain evolution; and more.

* More M&M content about evolution.

* Support M&M if you find value in this content.

* Full audio only version: [Apple Podcasts] [Spotify]

* Full video version: [YouTube] [Odysee]

* Episode transcript below.

Full AI-generated transcript below. Beware of typos & mistranslations!

Sean B. Carroll 4:31

double duty there is both VP of science education and head of the studio 13 years as VP six years has had a studio that was incredibly busy and you cannot sustain that for infinity. Yeah. I thought it was time to step back and I had my lab here I was going every Friday to the lab but I thought this is I kind of feel like I'm refilling you know the well now back in science for A few months enjoying reading and joining daily conversations about research in the lab. Now still still have a hand in the film storytelling, but I'm not responsible for the production. So I am i I'm in a good place. Okay, great.

Nick Jikomes 5:20

What's How big is the lab now?

Unknown Speaker 5:23

Eight people?

Nick Jikomes 5:24

Oh, that's that's like, that's a good size, I think. Yeah. Yeah.

Sean B. Carroll 5:28

So enough for things to be happening and not so many that I'm overwhelmed and, you know, stretched stretched too thin. So yeah,

Nick Jikomes 5:36

what? Well, just for background, for people who don't know you, what do you study generally? And then can you just give give us a snapshot of some of the projects you're working on right now?

Sean B. Carroll 5:46

Yeah, the central question that's guided thinks for a long time is the origin of novelty, where new things come from, in the course of evolution. And that's really things that are sort of qualitatively novel that either it's body parts that do something new, or molecules that do something new, or give some sort of capability to an organism didn't have before. And I've decided to focus a lot of energy on the origin of steak Venom's and their toxins. Because the fundamental reason why that's interesting venom is had been invented multiple times in the animal kingdom, you know, spiders and scorpions and octopi, and snakes and all that kind of stuff. We've come up with Venom's independently many times. And the question is, where did those things come from are those sort of normal body proteins that you've sort of hijacked to do something new, or you really have this evolutionary stage something together that didn't exist before. And in snakes in particular, there's lots of just the history of snakes, which is under appreciated, how they've sort of invaded continents, brother relatively recently, in evolutionary terms, and flourished, radiated and all sorts of species. They're, they're really under appreciated as models of evolution.

Nick Jikomes 7:07

And, you know, one of the things I want to talk about first with you is, you study evolution, obviously, we're going to talk about a lot of evolution stuff, I can remember being, you know, 17, high school student, and I knew what evolution was in the abstract, you know, at the level that you learn about in high school biology, I know that I knew at the time, you know, millions and millions of years go by the DNA mutates, known things emerge. But it was all kind of abstract. And it wasn't until I read your book, endless forms most beautiful, that things kind of collected became much more concrete and just easy to intuit. And I think the reason for that is just, if you are trying to understand evolution, it makes it a lot easier if you first understand something about how bodies are built in development. And then you realize, oh, if I just sort of tweak this process, you know, it just makes everything a lot more blockable, I think to the mind. Yeah, so

Sean B. Carroll 8:05

we can all appreciate we all develop from an egg, right to single celled egg made all these body parts. So, you know, changes in anatomy, or due to changes in development, and you can appreciate with all these different processes going on, you know, a little tweak, here, a little tweak there can can make a pretty big difference. And, you know, we had no access to understanding those tweaks, you know, really until the 1980s. So that this interested biologists for a really long time, but we couldn't make it concrete until the 80s and 90s. And, and really get into to the the actual mechanism of how bodies are built and how they change. And that, that I think that changed a lot of things for the way we could talk about evolution. Evolution has, you know, evolutionary science has a big theoretical history, there was a concrete history that Darwin gave us, but there was a big theoretical period of, okay, you know, how to small changes add up to be big things, but we just couldn't get to the concrete. And I think a lot of people including me, need the concrete, I want to look at creatures, I want to look at parts of those creatures. I want to know why those parts matter. And they're, you know, and the world they live in. And I want to know how those parts change. And then I've got that it's like, I got a full description, you know, of the owner's manual, of

Nick Jikomes 9:24

how things work. Yeah. And I think part of what you're referring to there is, you know, there's literally, you know, between Darwin and you are Darwin and you know, the 1980s developmental biology. You know, there are decades and decades of research happening, but a lot of that was basically applied statistics, and it was the math to figure out in the number crunching to literally calculate like, Okay, if you've got this much time and this much DNA, yes, you could, you can account for things, but it was literally like math, and it wasn't like mechanistic biology. Yeah, it was.

Sean B. Carroll 9:54

It was math man. It is heavily mathematical models, brilliant people. I mean, you know, especially in it The 20s and 30s. But realize that, you know, a lot of that math came before we had the double helix of DNA. It's not till 1953 that really the world sort of understands that, you know, what the genetic material is, there was scientific evidence that it was DNA from some years earlier. But that was not kind of widely understood. And it was really the structural model of DNA that we said, Okay, here's the molecule that transmit the infant information generation to generation. And it was instantly obvious to Watson and Crick, how mutation happened, it was a change in the sequence of bases. And that would change the characteristics of organisms. Now we have concrete for the genetic material. And we know that evolutionary change must be due to changes in genetic material. So we really just couldn't put, you know, that kind of foundation underneath Darwin until we were able to look at the stuff that's changing and evolution.

Nick Jikomes 10:56

And, you know, one of the things I want to ask you about here, when I first started learning some of these key facts, I remember being blown away. And the question I'm going to ask you is, how many genes does a human being have? And I want, I want you to put them in historical context for us by telling us, how many genes do we do we know we have today? And what was the thinking? Before we actually did the Human Genome Project and actually could look and see. Yeah, so

Sean B. Carroll 11:25

the question of how many genes any creature has that was, that was a question I got sort of a front row seat to because the technology for sequencing DNA sort of sprang up just as I was hitting graduate school, that was then starting to be applied on a larger and larger scale. But there was still a good decade and a half, before between sort of being able to sequence a gene and being able to sequence a genome, the entire genetic complement of an organism. And I would say, for most of that time, well, there are several, I'm going to start with this as sort of like several biases that I can, I can recall, because I was exposed to all of them, biases in human medicine, biases in biology, but a huge human bias about human biology, that somehow we must be the most complicated, right? Now, you would be better situated than I am to comment on that from a neurobiological point of view. But from a genetic point of view. There was an anticipation that, you know, we would be, you know, genetically more complex than any creature on the planet. Well, it took a while to get to that answer. But, you know, the first picture we got was probably a VP of bacteria. And those are sort of on the scale of four or 5000 genes essentially, you know, run the metabolism and physiology and in bacterial cells. And then it took a while to get to animals, like the fruit fly Drosophila, or the nematode worm center epididymis. And in those cases, were probably getting into the ballpark 13 14,000 genes, something like that. And, and then the question would be, what would humans have? And there were, well, one of my, one of my heroes, Jacque Munno, I think I have them on tape somewhere, you know, there's a video recording them somewhere, this is in the 60s, just extrapolating because we knew that of the size of the amount of DNA in a human cell, that humans might have 2 million genes. And for a while there, I think the number that I heard circulating might be like 100,000 genes, so still, you know, far more than other animals or whatever. And I remember having this discussion with a really prominent fruit fruit fly researcher who had who had a good grip on things. And he said, Well, Shawn, you know, what do you think? And I said, it's not going to be much more than a flyer where, you know, 15 20,000, bingo, yeah, maybe it's 20,000. But it's not any more than a mouse or something like that. So, you know, first of all, that kind of, you know, vanquishes, our genetic, you know, specialty in our specialness genetically. But it really underscores something that is, you know, is fundamentally interesting to me about evolution, which is how you build diversity with essentially the same toolkit of genes. So you don't need more genes to make more different kinds of creatures. So you can use the same genes you got just in myriad different ways. So many ways, sort of the, you know, the leveling of the playing field for humans to Dabbagh similar genetic complement as mice, and now chickens and even fruit flies, was to also tell us that we shouldn't be thinking that the number of genes dictates the complexity of a creature, but it's, it's how genes get used that are the real source of diversity. And that is a major meshes that then emerged in research that was directly comparing Different animals were built and, and what the what the genetic machinery involved was. Yeah,

Nick Jikomes 15:05

so just just the simple observation that we don't have that many more total genes than a fly. And we've got comparable numbers too. And sometimes even less than, you know, creatures that we would basically universally agree are simpler than us, that tells you that, yes, it's about how you use this stuff much more than it is the amount that you have. Right? And, you know, obviously, you're going to tell us a lot about the how you use it part of it. I want to build up a little bit of vocabulary for people. So when we talk about genes, what exactly are we talking about in the DNA in terms of like protein coding sequences versus other stuff?

Sean B. Carroll 15:42

Yeah, so let's, um, let's do a little, little accounting. So basically, we've got 23 pairs of chromosomes, okay? A chromosome is a long molecule of DNA. A gene is a segment of that molecule of DNA that has some information that gets used in in cells. So you know, if we might say maybe, on average, there might be 1000 genes per human chromosome. I'm averaging things out a little bit. So an individual gene is going to take up a certain amount of linear space on a molecule of DNA, that gene, a segment of DNA, in order for it to then contribute to the physiology or development of an organism, it's going to have to be used to it as instructions to make proteins. And there's an intermediate in that, which is it's first transcribed into RNA, all this language, all this cryptographic language, by the way came from, you know, the discoverers, who are all had kind of a post world had a world war two background, right. So the, the gene is transcribed, right? So you make this intermediate transcript, and that transcript is translated decoded into making protein using genetic code, sort of, like, you know, a code book or, you know, think of things like the Rosetta Stone.

Nick Jikomes 16:59

I never actually thought about that, that. The discoverers here, were sort of operating in the the Oppenheimer era.

Sean B. Carroll 17:06

Yeah, yeah, they're coming out well, and you know, Crick, who is probably the is definitely the most brilliant theoretician in biology, Crick worked for the Admiralty in World War Two, you know, so all these folks, a lot of these folks had, if not a direct World War Two background, they were of the era just coming right out of World War Two. So they had this, you know, code books and transcripts and translations and decoding and deciphering all that language was, was there. But anyway, the point is, is that when we think about a gene, we're really talking about a stretch of DNA, a linear sequence of DNA, four letters, might take up 1000s, and 1000s of letters, maybe even 100,000 letters for a gene. But still, it's a discrete segment of DNA. And that information is in a stepwise process transcribed, and translated into the making of proteins. And proteins are linear chains of molecules called amino acids, but those proteins do essentially all the work in our bodies. They're the things that carry oxygen, they're the things that fight off invaders, they're the things that digest our food, et cetera. And really, to operate a cell just to do the work of any old cell looks like you probably need five or 6000 genes working. So some of the genes we have are specialized to various cells, we have genes that, as I said, to carry oxygen, they're in our red blood cells, genes, they're active in our red blood cells, genes that fight off invaders are active in our white blood cells, genes that transmit electrical signals, those are in our neurons. So genes that build bone, proteins that build bones, those are, of course, going to be in cartilage and bone. So you know, we've got a lot of things that are specialized, but we also have a cord that we share with almost everything on the planet, to just do basic metabolism up.

Nick Jikomes 18:45

And so yeah, so things like, you know, literally making ATP making energy or how the basics, the fundamentals of how cell divides things that every single cellular creature has to do.

Sean B. Carroll 18:56

Absolutely. And this stuff is deep. So we can see that that stuff is shared way back that's shared throughout. And there's many things we share with bacteria. There's lots of things we share with simple unicellular creatures. And so we know that stuff goes back. In fact, the genetic code we use is exactly the same genetic code that a fly uses that a bacterium uses, etc. So the genetic code is universal, or universal with respect to planet earth. But that tells you that stuff is old. But that machinery for doing all that stuff has been around a very long time, and every cell needs it.

Nick Jikomes 19:30

And when we say, you know, we often we often talk about genes with respect to proteins, like a gene encodes a protein. If you look at all, if you look at the whole genome, roughly speaking, what percentage of the letters are the code to make proteins versus other?

Sean B. Carroll 19:50

I think in the human eye, I'm not going to give you a precise figure because it's kind of left my aging brain. It's probably on the order of like 2%

Nick Jikomes 19:59

Okay, so But quite quite a small amount, it's

Sean B. Carroll 20:01

not a small amount. So there's tons of stuff, tons of other DNA in our cells not devoted to encoding proteins.

Nick Jikomes 20:10

And you know, the term, I used to hear that term a lot more, I don't hear it as much today. I've also probably tuned it out, because I do know what still gets used is junk DNA, you know, and I think the idea historically, you can correct me if I'm wrong on the details is, you know, the Human Genome Project came out, we started looking at the actual code more, we realized, okay, we only have x number of genes, we only have, you know, 2%, give or take of the genome devoted to encoding proteins. And so there's all this other junk DNA, what is junk DNA, and this is that term even makes sense today. Now,

Sean B. Carroll 20:45

that's a bad term because it lumps and we don't want to lump we don't want to lump it was appreciated. And this is, you know, it's kind of an inconvenience to biologists. And it's kind of aesthetically not pleasing. But there's reasons why genomes can accumulate pretty large amount of like repetitive DNA. So there's, we get exposed to agents, like some viruses and insert DNA and our Insert DNA into our genomes, there's processes going on where DNA can get amplified. And that doesn't mean that DNA necessarily contributes to how our cells perform, or anything that we do. So we know, humans, I'll just use humans as an example. There's not a say a lot of pressure to kind of prune out DNA. So you can sort of think of it as like, you know, kind of like the garage or some storage shed, you've got, you know, stuff can pile up there, whether you're using it or not, over evolutionary time, it can pile up. But in that garage, or that storage, shed, there are some useful tools, and there's still a small percentage. So if we, it's better to sort of talk about the coding fraction, which is small, there's a non coding fraction, which is very large. But some small part of that coding fraction is, is also crucial machinery that governs how genes are used. And I think the best category to sort of describe these are things like genetic switches, these are sequences in the DNA that the way they operate in the process of turning genes on and off. And so it's not all junk, right? Not the non coding DNA is not all junk, there's a part of that non coding DNA, that it's crucial to the whole choreography, of which genes get turned on and off in your cells and in which cells and which what times in the development of an individual. That stuff was really hard to find. Okay, so that I can give you sort of a historical reason why junk has, you know, kind of held on first people found, and then some other species, like some amphibians, there's a massive amount of DNA that doesn't encode anything. And people are like, you know, John, yeah. But because there's a universal genetic code, it's very easy for our computer programs, to identify stretches of DNA that encode proteins. Easy as can be. It's not easy to identify among that other DNA, which stuff operates in some important function in which stuff is just going along for the ride. Which stuff is just that, you know, that stuff in the car in the garage or the storage? Shed?

Nick Jikomes 23:24

It is some combination of both. Is that Is that true?

Sean B. Carroll 23:27

Yeah. Oh, for sure. Yeah. So so that had to be that has to be figured out experimentally, there's no kind of computer program that will tell you, this segment of DNA exactly operates this way. So it was longer to realize that probably about in the human, I'm gonna say about 3% of the DNA is devoted to orchestrating how that 2% of the DNA gets used. And all that stuff is really important. That's what orchestrates you know, that's how you put ahead in the right place and make the right number of red blood cells and, you know, a lots of other choreography of of how genes get used.

Nick Jikomes 24:05

One, I want to give people a sense that there's different there's different types of genes and coding different types of proteins. And so one distinction that I think is useful is, you know, there's a lot of genes that encode proteins that do like the every day, housekeeping physiology stuff of the cell, so enzymes chop up certain, you know, nutrients, or, you know, carry oxygen around or whatever. They're, they're, they're doing the the daily operations of the cell, right? And then there's other proteins and one example of a class would be transcription factors. So, what are transcription factors and how do they differ from say, like enzymes?

Sean B. Carroll 24:44

Alright, so transcription factors are proteins that govern the activity of other genes, and some transcription factors, while some of them may govern the activity of, you know, 500 or 1000 genes or more. So, if you want to think sort of hierarchical terms, you sort of any medical metaphor you want, you know, these are sort of the generals and the other genes are sort of the soldiers. But a smaller number of genes probably in the human, you know, might be on the order of 1000 or so. So it still might be 5% of our genes encode transcription factors. But these transcription factors, turn other genes on and off. Often they work in combination. So some of the some of the biological specificity and fine tuning comes from these transcription factors working in combinations. But if a transcription factor affects the activity of say, four or 500 other genes, so let's say for example, the body is building a muscle, there's a whole lot of stuff that you got to turn on. To give that muscle its property of muscles, the fibers that are in the muscle, the way energy gets used by the muscle, the way the muscle recovers after exertion, the anatomy of the muscle, there's all sorts of stuff that has to go on. And so there's a muscle specific genetic program, and there's a few transcription factors sort of in charge of that program. So those are really hierarchically speaking, sort of, you know, top of the hierarchy, genes, and their genes way, way, way will say, you know, at the bottom of the hierarchy that essentially just carry out some job in the in the differentiated cell, the final muscle cell, you know, some enzyme reaction or something like that, that cycle something in the, in the muscle cell. And you know, that's not, that doesn't influence other genes, it's carry out an important job, but it's essentially at the terminal end of the circuit is the terminal end of the hierarchy. So however you like to think about, I think hierarchies are probably a good way to think about it, you can imagine these genes or these transcription factors are so important, because they do so many things. And then we realize they're so important, the easiest way to demonstrate that is to knock them out. So biologists have all sorts of tools for knocking genes out whether that's, for example, in experimental animals, like fruit flies, or worms or mice, we can also do it in cells and culture and stuff. And we can show drastic, dramatic, sometimes catastrophic effects, when these transcription factors are altered, because whole batteries of things don't happen when those transcription factors are altered.

Nick Jikomes 27:18

So in startup speak, it would be like you've got some genes that are individual contributors, like they're doing day to day tasks, they know how to do that one thing, and that's kind of all they do wherever you find them. And then there's managers that are telling them where to go and when to do what they

Sean B. Carroll 27:33

do, right. And some of these genes are kind of like executive vice presidents actually control a lot of the managers. Yeah, there's a, there's a hierarchy to this logic. And when things get changed way up in the hierarchy, the biological impacts are dramatic.

Nick Jikomes 27:53

I want to start talking a little bit about, you know, keeping some of this stuff in mind, and we'll connect the dots for people, but I want to give people a sense for some of the basic principles by which animal bodies are put together. And, you know, one of the things that that you're gonna teach us is, you know, even when you talk about something like a fly compared to a human, you know, remarkably, there are a lot of shared principles there. But you know, let's think about flies and bugs and insects first, because when you look at them, their bodies are. There's, there's literally segmented, right, like you can think of a millipede, it's got a bunch of these, almost like Lego blocks, pieces put together. Where does this sort of segmentation and modularity that we see in something like an insect come from in terms of this genetic toolkit?

Sean B. Carroll 28:42

Well, it gets set up very, very early in the development of the insect embryo, I mean, the best studied embryo being the fruit fly embryo. But I think to start to paint a picture for listeners about this, I like to think so a lot of a lot of embryos started out there, they're spherical, they're close to spherical and shape, sort of think about a globe. And I like to think about longitude and latitude. And, and poles, right, so you know, so think of something spherical, it's got a north and a south pole. Right? It's got that equator. But along that there's, there's all sorts of longitude. And of course, there's all sorts of latitudes marked out north to south. As a body is built, essentially, there has to be information as to what to build it and all these positions. So at a certain degree, longitude and latitude, that might be where the eyes are gonna go. A certain degree longitude and latitude, that may be where some appendages are going to go. And if you make this fully three dimensional on the inside, that's where you're going to put muscles and guts and all this other kind of stuff. So this three dimensional spatial information is really important in development. And you also have the aspect of time you're going to do some things before other things, right? It's almost like building a house. You realize you're gonna lay the foundation before you you No, paint the drywall in the kid's room, right? Same thing and building an animal body, you're going to lay out some of the basic foundation, sort of this grid work. And then you're going to start filling in with specific body parts specific organs in particular places. So segments are this very repeated pattern that lots of animals have. So insects belong to this group called arthropods. And if you think about, you know, crabs and lobsters and other favorite things like that, or or butterflies and millipedes, they have these segmented bodies, we do to the obvious part of our segmentation, if you look along our backbone, right, so we have cervical vertebrae, we have thoracic vertebrae, we have sacral, lumbar, vertebrae, etc. We are segmentally organized as well. So this and so both animals, both insects, and humans, have an organization of head to tail, right, we know the head goes in front, that's where the brains and the eyes go, right. And at the back end goes the, you know, where the waist comes out, right. So there's a lot of polarity, there's a lot of spatial information in a creature and all that has to be set up. And so segmentation, this major feature that you can see, so obviously, in insects, but it's also there in us, that's going to get set up early, because at different positions along that main segmented axis, that front to back axis to the animal, other things are going to form, you know, ribs along your backbone, for example. All that all that information has to be set up in an insect, the insect is laying out there's three main sick parts of an insect, we all know it from either from biology class, or from just looking under a magnifying glass, it's got a head, right, and that's got the mouthparts and the antennae and stuff like that on it, it's got a thorax, that's where the walking legs and the wings are. It's a winged insect, and it's got an abdomen, and often that abdomen is segmented it may or may not have anything sort of coming off of it. So in building an insect, you sort of laying out head, thorax, abdomen, and then within that a segmented pattern because the thorax has multiple segments, the abdomen has multiple segments, etc. So that sort of modularity is is a really common feature in the animal kingdom is that bodies are made of repeated bits. And then those repeated bits get specialized. So what gets built on the thorax of a insect, you know, our wings go their antennae go on the head. So there's a whole process for putting for laying out the basic body plan, and then for putting the various specific features in the right place on the developing body.

Nick Jikomes 32:45

And I would imagine, like, you know, when we think about the the managers, and the individual contributors in genetic terms, early on, right, there's gotta be, there's gotta be proteins in every cell, from the beginning that do like the most essential basic stuff. But then I imagine, right, there's, there's some period of time as development is proceeding where you're eventually going to start specializing, you're going to make things like neurons and skin cells. And they're going to have special proteins that most of the other cells don't have. But it's going to take time to get those on. And in between, you've got some kind of cascading temporal logic by which these other transcription factor things are orchestrating those changes,

Sean B. Carroll 33:32

right? So you've got transcription factors, setting up these main body axes, the front of the front to back and the top to bottom. So we know for example, that, you know, what's biologists will use the terms dorsal and ventral but dorsal is our back, ventral is our stomach side, right? So different things happen on that, that part of our body from the other side of our body, you know, think about a deer, right? It's colored differently on its back than it is on its ventral surface, front to back. So these transcription factors are setting up these regions of the body. And certain transcription factors are responsible for what goes on in a particular region. Those those managers are saying, Okay, I'm part of the head program here, or I'm part of the thorax program here. I'm part of the lumbar program here. And, again, those things have to happen earlier, and they have to go right, because when they go wrong early, you can imagine it's a cascade of disaster. So, you know, essentially think about birth defects, that sort of birth defects, we would probably never even see because they Strophic its enviable, right, you just you build, you don't build a viable animal when these things go wrong early.

Nick Jikomes 34:42

So these, yeah, some of these key genes, these master regulators, that would mean that, you know, if they mutate, it's catastrophic. The other cut well, actually, let me back up a second. So, you know, we think about all of animal diversity Flies, worms, bugs, humans, birds, everything. They're all very different. But they've all got head and tail. So there's that polarity there that you mentioned, they've all got some kind of body symmetry left and right, top and bottom, all this stuff gets set up. Maybe, you know, cuz I don't want to go too, too into the weeds and like the molecular details, but why don't why don't I just ask you like, let's take polarity, we all have a head and tail all animals do. How does the embryo know which side the head is on?

Sean B. Carroll 35:29

Yeah. So it gets set up differently, it's, it's sort of funny, like there's not a universal rule for how it gets set up in some animals and say something like a fruit fly, there's information there in the egg, the egg is pretty big. And actually, so as the egg is developing in the mother, in the female, there's information being laid down, the way that cell is forming, there's information laying down, that are ready, essentially, is specifying polarity in the cell. And the polarity in the cells becomes the polarity of the embryo. In other species, for example, where the sperm fertilizes the egg, starts to set up that information. So the egg is kind of agnostic. And then where the the point of sperm injury happens, can set things in motion. So you need something to create an initial asymmetry, it may be built into the egg before it's fertilized that maybe once the egg is fertilized, but once you have that initial asymmetry, and cells start dividing, that means you have the st, you'd have different information across the egg, you have something that's localized, you have more some stuff in one place than you have in another place. And that chemical difference, can set in motion, a whole cascade of things that can really then distinguish those different regions of the body from each other. I think if you just hopefully, that's a decent enough verbal description, again, without getting into molecular details you need and it's some kind of initial asymmetry that then cues, a whole bunch of events that happen after that. And the molecules that are involved in these asymmetries. You know, we've gotten our hands on all these things, they, they do spectacular things, we can manipulate them. So if we put those molecules in a different place, you know, you can make some pretty freaky looking embryos. And that's a good way to test it, you understand how things work. But that spatial information in the embryo is really what that means is there are chemicals in the form of proteins that are distributed asymmetrically. Early on, and those asymmetries are elaborated upon in building bodies.

Nick Jikomes 37:34

So you know, maybe you can imagine a perfectly spherical egg, and it doesn't know which side has had which is tails to perfect sphere, but the sperm enters at some point on that sphere. And maybe there's a chemical on the sperm, and it's so it's highly concentrated where the sperm the egg, physically touch, and then there's a diffusion gradient that goes away from that point, and the head is like that point and the tails, then the other point.

Sean B. Carroll 38:01

And it could also be something inside the egg that reacts to that and says, Okay, this is a change is now taking place at this point in the egg, that's going to be sort of my North Star, that's going to orient the whole egg and things are going to happen from there. So it can be sort of a physical change, that then triggers a chemical change, a cascade of chemical changes. So different animals use different mechanisms, it turns out kind of a little bit, there's kind of a variety of logic out there. Yeah, a variety of mechanisms that's out there. But I guess

Nick Jikomes 38:30

the principle here is some initial asymmetry is set up, that polarity then starts to get built in and elaborate it on. And to put it in a very coarse way, you've got these cascades of different transcription factors and proteins to get turned on. And at different points along that embryo, they get turned on sort of in different combinations. And then ultimately, that's what's going to get you one segment being unarmed versus a leg versus or whatever.

Sean B. Carroll 38:56

And people may start thinking, Well, you know, how do you make How do you make those distinctions? Well, these transcription factors also talk to each other essentially. So some transcription factor, for example, may turn off other transcription factors. So you sort of get zones of exclusion. So you start setting up finer and finer, you start with very coarse, I guess the best way to describe it is course to find delineation so that you start with very coarse, okay, this is the front, this is the back, this is the top, this is the bottom. But that course, sort of map becomes much more finer scale as time unfolds. And it's all sorts of mechanisms, including sort of crosstalk between these transcription factors that are saying, Hey, I'm active over here, stay out of my zone. And then that next thing is active in another zone. And it's and it's talking they can set up these you know, very restricted pattern, very restricted zones within the animal were different things are going to happen both along the main axis, including into the body because we also need to know what to think there's a lot of songs about this from the fifth These are what have you got to know, you know what goes on the outside and what goes on the inside, right? You want you want a gut running through the middle, not on the outside of the animal you want, you know, skin on the outside, you want to put a skeleton in the right place. So it's three, it's, you know, three dimensional information.

Nick Jikomes 40:15

And I would imagine, so like, as we start to think about like, okay, you know, we get some sense for how the body is put together. And we've got, you know, we can talk about transcription factors and the mechanisms that underlie that, immediately, you know, in as we're talking about this, you can start to intuit I think that, okay, if I'm now going to start think about evolution, and think about how mutations tweak this developmental process to create a new type of animal, it becomes pretty clear and pretty intuitive. I think that, okay, if I mess with the, the sequence of one of these master regulators, that's probably going to be catastrophic. So I'm gonna break everything because right from the beginning, things are gonna go wrong. And then that gets you thinking about constraints. In what type of genes and and where the gene, can you start to get mutations that that tweak what the animal looks like,

Sean B. Carroll 41:06

right? So let's give some concrete examples about that sort of catastrophic argument. So, you know, we know that whether you want to think about humans or mice, or fruit flies, or whatever, we know, what happens when these genes are rendered, non functional. And generally, it's a very obvious and terminal effect, you could be missing whole parts of the body, you can be missing whole organ systems, you can be missing entire appendages, things like this, okay? So that's, that's what we mean by the scale of what can what can be disrupted when these things are missing. But when you think about, let's just think about, you know, four legged animals. So you think about the bodies that you see out there, and you think about, oh, you know, giraffes with their longer necks, you know, or, you know, something with maybe shorter limbs or something with a longer body or a shorter body and things like this, you're like, they kind of all look like the same sort of animals been bent through a funhouse mirror, right? You know, kind of elongating this or shortening that or whatever, though, that kind of the basic outline is there, but what's changed is the portions of things. And you have to do that in a way that's viable. Right, these things, these evolution is a matter of, you have to tinker while the engines running, right? You don't do these things are not designed from the ground up, like they build cars. at Ford, right, you have to tinker while the engines running. And what we appreciate now is that subtle changes in where these genes are turned on how many cells are turned on in subtle changes in the subordinate subordinates that they regulate? These are the kinds of changes that are happening in the course of evolution. Not, you know, not in one step wholesale rearrangement. Those big, big changes generally aren't aren't very viable. But subtle changes in size, subtle changes in the relative position of something. That's what you see happening. How do you do that? Well, you don't, you don't have to tinker with the transcription factor as a protein itself, you tinker with the subtle aspects of space and time? Well, I turned it on in a few more cells, or I leave it on longer, and those are those cells divide longer, that's going to change the size and shape of something in a in a viable way. That's the sort of stuff that variation is is made of. So how are what kinds of mutations have those properties? Those are generally mutations in the switches. Those are mutations in the non coding parts of DNA, that influence this choreography of how these genes work in space and time. And they're not catastrophic. And furthermore, these mutations, these switches in individual gene, say one of these top regularity genes, it might itself have 10, or 20 switches associated with it. So no mutation in one switch has no effect on the other switches. So if you think about a gene, for example, that might be involved in building bone, it might have a switch that turns on very late, say, for example, in the elaboration of the fingers, okay. Well tinker with that, and you might be changing the width and length of fingers. But you're not changing the backbone, you're not changing leg length or things like this, right? So it gives fine tuning control over the proportions of body parts and the compositions of body parts. Yeah, the action, the evolutionary action in terms of the evolution of anatomy, the evolutionary action is in the switches that control this choreography. It's not actually in the proteins themselves. And that was that was we probably may need to get into that. Maybe not. But that was sort of a breakthrough and thinking for evolutionary science, because until then people were really thinking about how proteins change.

Nick Jikomes 45:07

Yeah. And I liked the I liked the funhouse mirror analogy that you brought up. It reminds me, you know, it's commonly like a textbook, you know, when you start talking about evolution and homology, and how the basic structures are often shared across distantly related organisms, you know, you might see the picture of the human arm and hand next to the whales fin and the bats wing. And even, you know, even as a, you know, even as a young student, you can appreciate, oh, yeah, like, it's the same basic set of pieces and the same geometric arrangement. But one, this piece is longer and this creature and shorter and this creature, and it sounds like what you're saying is, you can get there slowly. And little by little over time by just saying, Okay, turn on this protein a little bit more, or leave, leave it on a little bit earlier, whatever. And those are all coming from mutations in these non coding switches. Yes, yes. Yeah.

Sean B. Carroll 46:02

And whereas if you actually mess with the transcription factor, you might be missing the limb altogether.

Nick Jikomes 46:08

Yeah. Yeah. And that would also, I guess, kind of make sense of why so much of the genome isn't protein coding sequences, so you actually have a large palette to play with to do this fine tuning.

Sean B. Carroll 46:19

Right. And that's what's evolved. I mean, I mean, I think, let me give you let me just give you another example of sort of how to think about this. We of course, we're thinking about our bodies, we're most familiar with our bodies added, right, we all change, etc. But one way to drive home that the role of these switches is think about a caterpillar and a butterfly. Okay? Same species, right. We've all seen a beautiful monarch, Caterpillar, pick your favorite butterfly, whatever, I'll just pick a monarch, most people have seen him, right? That caterpillar is living a certain lifestyle, as it crawls up that plant and it's feeding on that plant. And you know, what it's eating, what it's doing, et cetera, doesn't have wings, yet, anything like that. And then it goes through this incredible transformations metamorphosis, into a butterfly migrates to Mexico, right? Those that's essentially two animals from the same genome. This caterpillar with an obvious segment of body, it even has little little legs on the abdominal segments, and several the abdominal segments, no wings, and then the beautiful butterfly with wings, you know, that that flies away. So same genome, same genes in that animal. But a certain program takes it so far to be a caterpillar, another program kicks in, in making the butterfly that shows you the power of regulation, it's all the same DNA in that creature. And essentially, it's almost like getting two entirely, you're getting two entirely different lifestyles out of one genome. And that's all about the choreography. So we don't have such, you know, incredible transformations. But I think it's a very helpful way to think about how such different things can be built using the same set of genes. A caterpillar and a butterfly is probably the most dramatic thing I can think of probably the most visually appealing.

Nick Jikomes 48:17

And it's it's easy to think about mutations and some of these master regulator genes that set up and orchestrate this whole developmental process. It's easy, it's easy to imagine how mutating them can be catastrophic, because everything downstream is affected. But are there ways in which they can actually lead to functional mutations that are dramatic? And here I'm thinking about, you know, some of the stuff that you can tell us about in terms of the identity transformation of tissues? Or how do we think about the fact that okay, at some point, you know, the centipede and millipede actually got more segments? Well, what's the genetic basis for actually changing the identity of something or creating more units?

Sean B. Carroll 49:02

Well, people are working on this, this is still a, this is a pretty lively area of research, this is getting into some of those subtleties, but if you think for example, about you may not have appreciated just how different crustaceans are from each other. But if you like Adium, you can sort of appreciate you know, shrimp and lobsters and crabs are, are are different, but they all have a really sort of some similarities and body design. But what makes a lot of them different is the number of different kinds of segments what's devoted to what how many segments carry legs, how many segments carry swimming, appendages, etc. Clearly, evolution is playing with the number and kinds of for example, appendages and these creatures, right, the number of guides and segments and what they and what they bear. So somehow, there's while there's that commonality, you still a crab is a crab and it's not a lobster, right? So you gotta go way back in time to when they had a common ancestor and realize they've gone there. separate ways. So what we know is as the embryo is being set up, there is a battery of about nine genes, eight or nine genes that are that are specifying what's going to happen along that main body axis, the head, the thorax, the abdomen, and the territories they lay out, can be subtly modified. So if you sort of think I'm going to give Okay, here's another analogy. I hope everybody goes with it. I gave you the globe and longitude and latitude. Now, it's Super Bowl Sunday, think of a football field. All right, and you got the yard lines, the 100 yard lines, okay? Well, you can imagine that if I just say, let's divide those up into the 1010 yards, divisions, that if you say, well, the you know, the zero to 10 is different than 10 to 20 is different than 20 to 30, different than 30, to 40, etc. But now, if, as you're setting up this field, you know, there's an interaction that allows that 30 to 48 is to spread to 42. Now, 42 gets shortened to just, you know, 42 to 50, you've just changed the proportion between two segments, just a little little ticker, well, then what's going to happen in those segments is going to be different. And it's these, it's the territories that gets set up that are occupied by these master regulators that are being tinkered with, early in development. So by shifting the relative I'll just call them territories of these of these genes, you can dramatically modify and sort of sculpt the animal to be different, and you don't get it overnight. Okay, we can do things in the laboratory and make really big changes. But that's kind of evolution can't can't deal with it, like the one of the most famous mutations in fruit flies, is a mutation that transforms the antenna into legs. That's a, you know, it's a nice little trick in the laboratory, you will not find flies in the wild, with legs coming out of their head, because they need those antenna to find their way in the world. Okay. But it sho