Wings, Legs, and Fins: How Do New Organs Arise in Evolution? with Neil Shubin


– This program is a presentation of UCTV for educational and
non-commercial use only. (funky music) – Good afternoon. We’re very pleased to have you here today. Thank you for joining us. My name is Ellen Gobler. I manage the graduate counsel lectures, and it is my pleasure at this moment to introduce Professor David Wake. (audience applause) – It’s my privilege to introduce the Hitchcock Lecturer today. As you see from your program,
the Hitchcock Lecturer is one of the highest honors that the Berkeley campus can bestow. And we’ve had a very
distinguished set of speakers. Our speaker today fits
very well in that company. I first met Neil Shubin when he was a graduate student at Harvard, preparing for what would be his major work on the transition from water
to land in vertebrates. He was studying at that
time with Farish Jenkins and with Pere Alberch and
was preparing a large, essentially monograph-length review of limb development in amphibians. This paper, which was
published with Pere Alberch, became a very influential piece of work and brought Neil to
the attention of people in a number of fields beyond paleontology. So, for example, comparative anatomists, developmental biologists,
people interested in the then very new field of evo-devo, took note of this work. And Neil has continued on this pathway of integration since that time. He’s well-trained in fields
such as geology and paleontology where he’s probably best known. But he also has done a lot
of, and continues to do, a lot of work in developmental biology, in particular in that
subfield known as evo-devo. In addition, he is a
comparative anatomist, a naturalist. He’s been in the field with me, collecting salamanders,
more than one occasion. And is a person who’s at home, both in laboratory and field work. So I really think that, as an
integrative biologist myself, that Neil Shubin exemplifies what we mean by integrative biology. Neil came to Berkeley as a
Miller post-doctoral fellow, and that’s where our interaction began. And I must say, the most pleasant
15-period of collaboration started at that point, and
we became good friends, and I became a great admirer
of him and his work ethic and the way he goes about
thinking about problems, the way he sees problems, and the way he’s able
to convey his enthusiasm for his work to others. Following his successful Miller period, he went to the University of Pennsylvania where he started his
career on a very fast track because he gained rapid attention by his outstanding discoveries
in the fossil field, and also, by his continued
work in evo-devo. In 2000, he worked, he moved
to the University of Chicago, where he is now the
Robert Bensley Professor of Organismic Biology and Anatomy. And it’s of great pleasure
to introduce you today, introduce you today to Neil Shubin, who will speak on Wings, Legs, and Fins: How Do New Organs Arise in Evolution. Welcome. (audience applause) – Thank you. Thanks again to the
Hitchcock Lecture Committee for making this possible,
my return visit to Berkeley. It’s a decided pleasure to be introduced by my mentor and friend of
over 18 years, David Wake. The underlying theme of my two lectures is really that most of
the major questions, important questions in biology, are solved by an integrative approach that unites fields from
diverse disciplines. That what defines us are our questions. And that the tools we use
can span multiple fields. And this is nowhere more
true in evolutionary biology. In particular in those parts
of evolutionary biology where we’re trying to
reconstruct and understand evolutionary history Now, in stepping back a bit, really, when we think about
this being the Darwin year, two great concepts really stem
from The Origin of Species by Charles Darwin. I mean, the first is
obviously natural selection, that there’s a struggle for existence that brings about a change
in populations over time. The other, and the one that really has captured my imagination, is the notion of descent
with modification. That it is just like we
are modified descendants of our parents, and understanding that
descent with modification in our own family enables
us to see our family trees, that our family tree
extends to other species, and our own species is
a modified descendant of other species that had
existed in the distant past. And that through this process
of descent with modification, the very simple beginnings can produce an extraordinary evolutionary tree. And it’s really that’s what
I’m gonna focus on today. Yesterday, the take-home message was, those of you who were
awake for the last slide, saw that evolutionary
trees are very important, that we can make very strong predictions about where to find fossils that answer major gaps in
our knowledge of evolution. And at the way we can best interpret them is not as a linear series of
events, a ladder-like process, but really is understanding
them as a branching tree of diversity and adaptive
diversification and radiation. And so, to understand that, we really kind of looked at the level of whole animals yesterday. Today, we’re gonna take
a sort of bore in a bit, and look at organs, how
do new organs arise, through change, through time. When you look at organs with a principle of
descent with modification, really becomes very clear that to understand “the new” in evolution, you have to understand the old. Because often what we
have to do is trace organs through time to understand
what the same organ is in different species over time, To understand the sequence of changes that happen in an organ from
one species to the next, we have to find a way of
defining what the same is. What’s sameness? What’s the same organ in
two different creatures? So, to understand novelty
or new organs over time, we really have to understand the old, and that means understanding
what is the same structure in different kinds of creatures. Now, at first glance,
you could not imagine a subject more boring or esoteric than trying to come to grips with what’s the same in evolution. But I’m gonna tell you that it’s actually, arguably, one of the
most important concepts in all of biology. And so much of what we do as comparative biologists,
evolutionary biologists, and even people interested
in biomedical discovery, stems from that. And where to begin? We begin with noses. So, here is a famous nose. This is Basil Rathbone
from Sherlock Holmes. And the question really is, what is a nose in different species? Is it the same as a nose in
some other kind of creature, like this creature here, with this object perched at
the end of it? (chuckles) Is it the same as this proboscis at the end of this creature? Is it the same organ in
these different species? Is it the same as a bill of a bird, of the giant proboscis of a paddlefish, or the many different kinds of probosci we find in arthropods and other creatures? Are these the same structures? How do we know it? What does it mean in
biology to be the same? This is the starting
point for understanding how new features arise over time. Now, you can say, “Wow, that’s
really kind of esoteric. Thanks for getting into that.” But I will tell you that it’s arguably one of
the most important concepts in biology, as I’ve said before. And so much of what, that
exists of why it’s important, we take for granted, as
biomedical researchers. Look at the title of this paper. Animal models of human disease:
zebrafish swim into view. Zebrafish and their
development are a model for human blood formation,
formation of the pancreas, and diabetes models, and so forth. It’s a model for biomedical discovery. Why stop at fish? A Drosophila model for
Parkinson’s disease. The only way to understanding that is really understanding that
what the events we’re seeing in Drosophila are the same, in this flying insect, in humans. Indeed, if you ever need an example of why evolutionary connections to
the rest of life on this planet are important, I encourage
you to a website. And that website is the
Nobel Prize in Medicine. And what you see here is a list of the Nobel Prizes in Medicine
over the last few years. Who’ve they gone to? They’ve gone to people looking
at Drosophila, fruit fly, to understand the genes that, many of the genes that
control development. Two Nobel Prizes in the last several years have gone to people working
on a little tiny worm the size of a comma on a piece of paper. Yet, that little worm,
Caenorhabditis elegans, is telling us how cells die,
kinds of programed cell death, or how our genes are silenced. And indeed, it’s discoveries such as that which have important ramifications to drug design and human health. Understanding the cell cycle has depended on studies of creatures as bizarre as sea urchins and yeast. And why stop there? Memory and sea slugs, although
not this particular one. And of course, since
we have this individual on the here, we also learn
about ourselves through corn. So, the important thing here is by applying, understanding
basic biological discovery and applying it to humans, we really have to have an understanding of what the same is in
different creatures. Now, like all important concepts, this concept has deep,
deep historical roots. Natural philosophers, indeed,
philosophers for centuries have been thinking very
hard about this question. And one of the more prominent
players in this regard is Sir Richard Owen, shown here. This is Richard Owen. He’s on your left. And Owen was a (audience laughs) Owen was an anatomist in the mid-1800’s. And it was a wonderful
time to be an anatomist because you could truly be
a comparative anatomist. He was fortunate to be an anatomist at a time new creatures
were being discovered, whole new kinds. He named Dinosauria. He originally described
the skeleton of a gorilla, and so forth. He was uncovering great natural diversity. And in uncovering that
great natural diversity of different kinds of
creatures and their skeletons and so forth, he saw common plans, common designs. And this, when I was a graduate student, this book, On the Nature of Limbs, a discourse by Sir Richard Owen, really caught my imagination
in a very big way. Because it’s in this
book where he lays out, in a series of figures,
his notion of sameness. And he had a couple
different notions here, and it’s worth spending
a little time on them ’cause we’re gonna touch back to them as we get into some experimental work that’s been happening in my lab lately. This figure. It’s a beautiful figure. It’s actually you fold it out. It’s like ye big in the bind. And he shows a human skeleton here. And he defines several
different kinds of sameness, and right off the bat, he’s
laid off the human skeleton with birds and other creatures, and you could see he’s colored it in to make specific comparisons
of the same feature in different creatures. You know, the vertebrae, the
appendages, and so forth. And this whole treatise
was really about limbs. And he sort of argued, like
many natural philosophers at the time, for two
different kinds of sameness. One is similar features
in different creatures. And the other is similar
features in the same creature, like arms and legs; they
have a similar sort of plan. And you know, the basic
take-home message is if you look at the arm of a
human, the wing of a bird, or the limb of any limbed animal, and you look at the skeleton inside of it, there is a common structural
sort of theme or design, which we have one bone going to two bones going to series of small
bones of wrist or ankle bones and then the digits. You see that both in the leg and the arm, and you see it in different species. This frog arm here,
actually has two bones, but they’ve been fused up. So, the changes we see are
due to changes in the size and shape and sometimes
loss of individual bones. Now that sameness that
Richard Owen talked about here is, between these
appendages, is very different from that we see, say, a fly wing. That this is somehow
a different structure. It’s not the same, even
though it’s a wing, just like a bird wing, but it’s
composed of different bones. It’s essentially a different design. Now, Owen was not an
evolutionary biologist. And so, just like I’m dancing
around the word history and evolution and so forth, Owen spent this whole book
on the nature of limbs dancing around the concept as well. Now, this whole notion
was actually a hot topic for a long time. This pattern of similarity was identified by people beginning in
the 1600’s (mumbles). One of the key players
here preceded Darwin by several centuries. And this is Saint-Hilaire. Saint-Hilaire was a natural
philosopher from France. And he looked at the
same pattern, actually, several decades before Owen. And he came up with a
really wonderful law, a natural law, called
the Law of Connections. And he was big into laws, as a lot of his contemporaries were, to try to understand
what are the regularities behind the designs of bodies. And his Law of Connections was, basically, that the way bones, the
pattern that bones articulate with one another is highly conserved among different creatures. That’s the way you can define sameness. And so, he identified this one
bone, two bone, little bone, fingers design as a pattern of connections that’s essentially in variance, okay? And that that is the design principle. And he extended this throughout the body, from the ears and the ear ossicles and ribs and the vertebrae and so forth. Everything changed Saint-Hilaire, Owen’s ideas. Everything changed with
Charles Darwin, obviously. And Charles Darwin saw
this pattern as well, and you know, he has this famous quote from The Origin of Species, “What can be more curious
than the hand of a man, formed for grasping, that
of a mole for digging, the leg of a horse, the
paddle of the porpoise, and the wing of the bat, should all be constructed
on the same pattern.” And what struck Darwin was that despite significant variation… despite significant variation
and function, right? So you have wings. You have flippers. You have, sort of generalized
forelimbs of different kinds, forelimbs for digging
and running and so forth. That this one bone, two bone
pattern is sort of the template for all this adaptation. And it became clear to him
that the functional argument for why you have have
this one bone, two bone, little bone ray pattern is useless. It really only makes sense if these creatures evolved
from a common ancestor that also had this one bone, two bone, little bone ray plan as well. So, he explained this
concept that Owen was, of sameness that Owen was
dancing around for years, and Saint-Hilaire was trying
to develop laws of form for, he explained it through
the principle of descent with modification. And that concept was really powerful because what it does is it
enables us to make predictions. That we could then say
that if this pattern, one bone, two bone, and so forth, has a history, we should see
that history in the rocks. We should see that history
in comparative anatomy. It should be written in the
bodies of other animals. And that’s exactly what Darwin did. And he said, you know,
well, I mean, he implied that essentially you would see that this pattern in other
creatures that don’t have limbs. What about the fins of fish? I’m just showing you a
forelimb of a coelacanth here. And indeed when you
layer it in, you see… You see the skeleton. And again, it has the one bone, but only doesn’t have the
rest of the pattern as well. You should see some, but
not all of that pattern as you go deeper in the
evolutionary tree, if you will. And it’s those predictions
I’ve spent my time as a paleontologist trying to look at, to see the assembly of this pattern, the one bone, two bone
pattern and so forth, by finding fossils, looking
at genes and development, and so forth. And indeed, when you look at
Devonian Age limbed animals, from about 365 million years ago. This one’s backwards, sorry about that. But you see the one bone, two bone, little bone, finger program already set up in the earliest limbed animals. And as we look their finned
relatives in the fossil record, things like Tiktaalik
and the other creatures in the evolutionary tree,
more distant and so forth, we begin to see the
assembly of this pattern. So, here’s a early limbed animal, and then you have the other
creatures on the tree, each one further away or
more distantly related to the limbed animals, Where you see an early limbed animal here, it has the one bone, two
bone, finger pattern. Tiktaalik has one bone, two bones, has other more distal bones, which we can actually compare
in some ways to this cohort. And as you go deeper and
deeper and deeper in the tree, what you still see is
this one bone, two bone, little bone ray pattern
already set up in fish fins doing a diversity of things
early in the radiation of these kinds of fish,
in fins, with fin webbing. And it turns out the
fossils are very useful for us to understand
and trace this pattern and its adaptive
diversity in the Devonian. Things get less sure as we begin to look at extant or recent fish. So, here you have a fin of a lungfish. Here you have fins of paddlefish
and sharks and so forth. And when you see what
appears to be a very big gap between extant limbs and extant fins, although, as you get into
lungfish, no surprise, you start to have one bone at the base, just like all these other creatures, as opposed to many bones at the base like other fish more deeply,
more distant in the tree. So, we can actually begin
as comparative anatomists and so forth, to begin
to really understand what happens to the same
appendage in different creatures, and for better and worse,
we can make some hypotheses about what is the same bone
in different creatures. This one bone is the same bone in all these different creatures. And then, it gets a little tenuous as we go further out in the fin, but we can still do this to
different degrees of accuracy using different kinds of fossils. Now, when we talk about sameness, I sort of want to introduce the concept, and I’m left with some no real analogies, and so I just sort of made one up. (chuckles) When I was
thinking about this… And when you think about,
you know, an organ, an organ has parts, and then an organ also has processes that make those parts. So, you can think about the same thing at many different sort
of hierarchical levels, so that you can think about the model, this sort of obnoxious
car here, a Hummer, right? And you can trace the history
of the car, the Hummer, over time from small sort of obnoxious car to big obnoxious car to sort of smaller
Recession-time obnoxious car. And then you can dissemble it
into its pieces, its parts, which also have a history. The tires have a history of
processes that are behind them. The windshield, the lights,
the windshield wipers, and so forth, all have histories. So, you can think of the sameness and the history of the
whole entity, the car, the Hummer in this case, and you can think of the sameness and the history of the parts
that make it up as well. But you can also think of
the history of the processes that make these parts, the vulcanization, the processes behind
the making of the rubber and the steel and so forth. So, you can think about this
at many different levels, and each level has explanatory power. Indeed, a Hummer and
a Prius appear to have very little in common, yet at the level of the processes that make the car, the tires and so forth, they share quite a bit. And so, essentially, I want
to look at organs in that way. I don’t want to push the analogy too far ’cause like all analogies, it’s limited. But when you think about a
limb with a skeleton inside, you can ask about the limb and
the history and the sameness inside this organ, the
pattern of bones here, Saint-Hilaire and Owen
and Darwin’s pattern, you can ask about its parts,
the bone and the cartilage, and then you can also, on top of that, ask about the sameness and
the history of the toolkit, of the biological recipe and processes that build these structures
in different creatures. And it’s really kind of
linking these different levels that we’re gonna spend our
time today on in the talk. So, I want to do is spend some
time on this toolkit issue. And to do that, we’re really
gonna focus a little bit on limb development, and how it arises. You know, you think about development. It’s one of the most wonderful
problems in all of biology. You begin as a single-celled egg. You end up as a two trillion cell adult. Well, a nine trillion cell adult, only two trillion of them are yours. The other seven trillion are
microbes that inhabit you. But over time, that one cell becomes a very precisely packed organism with the cells packed in the right way, differentiated cells doing
their jobs in different ways. And much of this development
is written inside the DNA that exists within the egg and its interaction with
the environment around it, as well as the internal
environment in the embryo. One of the outcomes of that is actually we can watch development
happen as things get bigger and more complicated and
differentiated over time. And the limb is no different. So, limbs begin as little
pouches out the side of the body. And over time, they grow out. And as they grow out and
extend out of the body, it’s called a limb bud at this stage, ’cause it’s a limb and it’s a bud, and it comes out of the body. And inside the limb bud cells go from kind of looking all
alike to differentiating. You start to see cartilage cells and, eventually, muscle cells, and the cartilage differentiating,
develops into bone, and this good stuff. And you could watch over time
the formation of the pattern as the limb bud grows out. Now, underneath this,
controlling this in many ways, are a series of events that are
sort of written in the genes if you will. And here I have a limb bud showing you some of the
main signaling centers that if you were to open a text book in developmental biology, or actually, introduction to biology that you see, and this is a limb bud with two patches of tissue that are known as signaling
centers, more or less. And what they do is, their
behavior actually promotes and patterns the limb in many ways. Now, there are factors
that exist in the body that actually set these
things up initially, early in development. But then once they’re set up, they’re really major properties of how the appendage grows and
forms in early development. And one thing that underlies
it, is a series of genes that are turned on, and
we can actually map those with a variety of techniques
to see their activity, and look to see the chain of events by which these two
patches, the AER up here, and the ZPA here, I’m just gonna use their
abbreviations to talk about them. And then there series
of genes that interact. So, in the ZPA, there’s a prominent gene that marks ZPA activity
called Sonic hedgehog, here shown as SHH . And in the AER, there
are genes known as FGF’s. FGF8 is a real prominent one. And let me just go into these, and just talk a little bit about them ’cause they’re gonna be our
road map to look at sameness in a variety of different
limbed and non-limbed animals. So, if you look at a embryo. Here’s a embryo early in development. It’s a chick embryo, and it’s stained with one of
these called dyes, if you will, and what it does, is
this is attached to FGF8. So it’s a marker for the AER, okay? And you could look at the AER here, and it’s where this
gene FGF8 is turned on. It’s turned on no where
else in the fin bud, that’s signature of that. And when you pop this
thing under a microscope, what you see is, it has a ridge there. It’s a ridge of tissue, and you see, if you ever cut this as a section, this is what that section would like. And it’s a thickened ridge of sort of epithelial-cut type cells separated from sort of more disorganized
cells in the center. And it has special properties, and those properties are really important for our stor because
when it has a property such that it seems to promote
the growth of the appendage, so that if you remove the
AER early in development, say at stage 18 here,
you’re left with a limb with only a humerus. If you remove the AER at
a slightly later stage, say at stage 20, you’re left with a limb that has a humerus and
part of a radius and ulna. And so, you’re left with
more at the later stage that you remove the AER. It clearly promotes the
growth of the appendage in a lot of ways. And so, that’s a stage-specific effect. So, the AER is very
important in that regard. There’s another one, and that’s the ZPA. Remember we talked about the ZPA? And it had that gene Sonic
hedgehog, the SHH gene. This is another chick embryo, and what you could see here is, here is a Sonic hedgehog
that’s been stained there. It’s also been stained with FGF8, so you see the AER here,
and there’s the ZPA. Now, the ZPA seems to be involved with a lot of events across the body. In the appendage, it
also has a lot of events that are associated with it. But one of the real prominent
effects with the ZPA and Sonic hedgehog lies
in the differentiation of the digits, the fingers. Because if you look, what you can do is you
can take the ZPA tissue, you can dissect it out, and you can pop it on the
other side of the appendage. When you do, you get a
very characteristic effect. And you could also get the same effect when you cause Sonic hedgehog, the gene that is turned on here, to be expressed on the
opposite side, ectopically, misexpressed on the other side. So, you could do all this surgically, or you can actually implant a bead of a compound known as retinoic
acid, form of vitamin A, which will induce another patch
of Sonic hedgehog activity. So, normal would only have
Sonic hedgehog in the ZPA, which is the normal ZPA here, but you can induce another
ZPA, an ectopic one, through this bead of retinoic acid. And voila, what you get? You get a mirror image
duplication of the fingers, okay, in a variety of different species. And if you knock down,
if you sort of inhibit Sonic hedgehog expression, or
take out the ZPA in some ways, you reduce the number of fingers. So it seems to be the
specification of the fingers as you go from the
pinky to the thumb side. It really depends on
the activity of the ZPA. So, we really have these two centers, the AER and the ZPA, this is a good part of the
toolkit that builds appendages. Now, why am I going into all this? Good question. Well, it’s a useful question to ask, given light of our Hummer
analogy I showed you earlier. And that is the notion that, what’s the sameness of the toolkit? We could trace the bones. What about the toolkit itself? So, the idea here, what
we have to do here is to look at the toolkit,
the AER and the ZPA, and ask the question, what
are they doing in fins? And if we choose our creatures right, we could begin to come to get, and these are the fins of these creatures, and we do it along a
phylogenetic evolutionary tree, mapping with Chondrichthyans
here, sharks, skates, and rays, Actinopterygns, which are ray-finned fish like paddlefish and teleost and so forth, and look at limbed animals. We could begin to ask the question is, how ancient is the toolkit? Is it the same thing in fins and limbs? Is it doing similar kinds of things? Are genes doing the
similar kinds of things? And this is another way of asking how these organs came about. So, what we’ve been doing in
my lab is looking at fish, and most lately, we’ve
been looking at sharks, not Great Whites, but we’ve
been looking at skates, ratfish, the three major groups:
skates, ratfish, and sharks. It’s a challenge working
with some of these creatures. It’s not like you can buy
shark embryos at the store. What we get them from is the
Shedd Aquarium in Chicago. We also get them from the
Marine Biological Laboratories in Wood’s Hole, what provides us a supply of
about 20 or 30 eggs a month. Not a whole lot to do embryology on, but enough for our purposes. This all began, really, in my laboratory with a post-doc by the name of Randy Don. Randy worked on chicken eggs for his PhD, looking at limb development. And when he looked at shark eggs, he saw that they looked
a lot like chickens. So, we decided to all the
experiments he did on chickens, only on sharks and skates. So, this is a wonderful comparative test to see how they lie together. One of the things you’ll see is every time I show a molecular
biologist from my lab, in this talk, they’re in the
field collecting fossils. So, I want you to know
that molecular biologists make very good fossil finders. So, there’s hope for those
of you, you guys yet. (chuckles) Alright, sorry about that. Anyway so, you can ask questions. There’s AER in limbs, here it is. And you can see the section here, and here is the FGF8 expression. You look in shark fins,
and what you see is, in a skate in this case, Chondrichthyan, there’s the FGF8 expression,
and you also have an AER. And in fact, you have an AER, and it actually gets long and turns into another
structure called a AEF, which is related to fin formation. So, it has the AER and that seems, and it’s also in all fish fins, and so what you have is we can trace this as the same structure all the way through. Then what about the ZPA? ‘Cause you remember the ZPA has this Sonic hedgehog expression here. And when we misexpress
it with retinoic acid, we get these duplicated structures. So for this, we look at
the eggs of these things. And so, here you see the yolk of a skate, and there’s the embryo on top of the yolk. They develop inside an egg case. Here’s a shark, again with the embryo. And you can treat these things by injecting retinoic acid. And this took a while to figure out, of different concentrations, into the egg at different stages, and to see what it does. Because in this chick what it’ll do, is induce that ectopic AER
with the Sonic expression, and you’ll get duplicated digits. In sharks, here’s the normal, where you have the expression
of the Sonic hedgehog in the posteriorum margin of the fin. Just like in a limb. So, the expression, the activity
of the gene is the same. And when you treat it
with this retinoic acid, you turn it on, you turn
it on all the way distally, and then you also turn it on
on the anterior end as well. So, you induce expression in novel places, particularly in the anterior end. You can ask what the anatomical
readout of all this is. Here’s a dorsal fin, and
you can see a dorsal fin. This is the normal one, untreated. And you could see it has, the
cartilage is stained blue, and you could see it has,
like, little stubs here. That’s the axis of the fin, and
off of this come these rays. When we treat it with retinoic
acid, more often than not, we find, voila, a mirror
image duplication. That is, you end up with
an axis here, an axis here, and rays coming off of either side. And these axes can take, these
mirror-image duplications, can take different forms. But again, in chicks
and in Chondrichthyans, and in not showing you, but
also in other kinds of fish, what do we find? We find a great continuity of
big portions of the toolkit that make fins and limbs. AER, ZPA, and I’m not even
showing you all the other genes in that cascade, that are
involved in this formation. So, the beautiful thing here
is when we find it in a lot of these groups here,
we could begin to say that this genetic
toolkit is the same thing in all these creatures, and we can begin to say
that it was a property of the common ancestor of
all fish with appendages. Now, how do you begin
to approach the question of comparing this to creatures that don’t have appendages at all? So, appendages had to come into being at some point in evolutionary history. And for this, what we begin to use is one of Owen’s notions, that is, to look at the
repeated parts in the body. And this is Vesalius
showing the human skeleton, and what you see here is
a hindlimb and a forelimb. And you could see there’s lots of repeated parts in the body. There’s repeated vertebrae. There’s repeated ribs. There’s repeated appendages
between forelimb and hindlimb. Lots of repeated parts in the body. To Owen, this was really
significant because what he did, even though he wasn’t an
evolutionary biologist, what he did was he showed he had an idea that all this diversity that
we see here in these bodies with all these repeated parts can be traced with something
he called an archetype, which was a philosophical ideal. This little thing here that
does not exist in nature, okay? But to Owen, it was the sort of thing that all vertebrate animals
diversity is derived from. It basically consisted of
a series of repeated parts, of the vertebrae, and
the ribs, and so forth. And that the appendages
and the jaws and the heads all come about from the consolidation of these repeated parts in different ways to make different appendages. This is a very attractive idea
to comparative anatomists, and actually to developmental
biologists as well. Let’s just take a peak at a fossil shark. And I’ll just show you how
we’ve been approaching it. And here’s a shark known as Enneacanthus. It’s a fossil shark, and you
could see the appendages here, and ribs and so forth. And what really sort of
caught a lot of people’s eye, and I’ll show you one of the people who’s very important in a
second, is this area here. ‘Cause look at the repeated parts. Here is the gill skeleton. This is the upper and lower jaw. And then you have the gill structures, and you see they form these little hoops. And doesn’t it seem, and
this is the shoulder here, and the fin, doesn’t it
seem like the shoulder is a repeated part of the gill structure, the structures that
support the gill skeleton? The study of these gill arches has been very, very, very important in understanding anatomy. ‘Cause what you see is, let’s
just look at the front end in these repeated structures. I’m not including the shoulder here. What you have is several
different gill arches. There’s the first arch,
which is the jaw arch, which I’ve colored in here, which is the upper and lower jaws. There’s the second arch,
which is the hyoid arch, which consists of this
bone here and another bone. This bone is very important. It’s gonna appear later in the talk. So, remember, HM, hyoid mandibula. And then you have a series of
these arches, the gill arches, which support the gills. This really captured the imagination of comparative anatomists,
and most famous of these is Karl Gegenbaur, who is sort of the father of
comparative anatomy in Germany. And he came up with a notion that basically held, and this is the gill skeleton. This the mandibular arch.
This is that hyoid arch, and these are the gill arches here. He basically said is if you
compare these structures, the shoulder is the same
thing as these gill arches, and the appendage skeleton, the fin, is the same things as these rays in blue that extend from the gills. And he proposed this gill-arch hypothesis that everybody laughed at. And it was basically the notion, he took it one step further. He says not only are these the same thing, but that fins arose as
being modified gill arches. And it was a hypothesis that was almost, quickly ignored after it appeared. Andrew Gillis is a graduate
student in my laboratory. And this is Andrew, again, in the field. He happens to be a very good
fossil collector as well. And he decided to look at this question, to ask the question, Gegenbaur’s question, the idea is, well, do the
gill arches have the toolkit? Do they have the AER and the ZPA? If so, what does that mean,
and how do we interpret it? So, this is what it looks like. There’s the gill skeleton
shown in textbook view. This is the real world, (chuckles) so it’s a lot harder to see. But basically what you have
are the gill rays here. See these gill rays shown in red? These are the gill rays themselves. So, this is what Gegenbaur
would compare as being fin, similar to the fins. That’s the question is really when we look at the
structures that pattern this, do they have the AER and ZPA? Do they have the toolkit
that makes appendages, aspects of the toolkit
that make appendages? I mean, you dissect it out. It looks like something like this. You have the gill cartilages and the rays that extend from them. So, let’s look at the
AER. Here’s a chick limb. Again, there’s the FGF
at the tip at the AER, and there’s what it looks like in section. Here’s the skate fin that Randy, I showed you from Randy’s
work with the fold. And when you look at the arches, what you see is we’ve
removed the gill arches here, so this is all damaged. So, you have the stain in there. But here’s the strip, right there. And when you look at this
strip, it’s stage-specific, so you’ll see the arches in the front in this particular preparation are lighting up with the FGF8. The ones in the back haven’t lit up yet. But when you section them, what you find is a very similar histology
at the tip as to the limb. Indeed, when you remove this AER, it’s the same stage-specific
truncation of development. So, the AER seems to be
functioning in the same way with a similar set of genes,
which I’m not showing you, I’m just showing you one, in sharks, shark gills,
and shark appendages. Again, to ask the ZPA is a Sonic express. So here’s Sonic hedgehog as it turned on in the posterior portion of the appendage. Here it is in the chicken. Here it is in the skate. And when you look at the arches, what you see here is the fin, and there’s the Sonic, its activity turned on
in the posterior portion. And here it is in the arches. All limited to the posterior, or rear portion of each gill arch, right at the area where
the gill rays will form. And then we looked at other things like the receptor for it and so forth. So, there’s parts of this cascade I’m just sort of taking the
top level comparison here. The question then becomes, is
let’s treat it like a limb. If you treat it with RA, do you get this other patch
of Sonic hedgehog turned on. So you inject these
things with retinoic acid using the same treatments, and boom. What you see here is the normal, looking at side-on view of the arches. And here you see the Sonic hedgehog. And then you see a stage-specific effect. This is a gill ray that’s in face, but it’s induced on another patch of expression in this particular arch, on the other side . Okay, and it’s stage-specific. So, this one’s still showing it lightly. If I was to do it slightly
later in development, this thing would go off, and
you’d see it here in deeper, as deeper stain. The question then becomes what is the anatomical readout of this? And so you have, it’s
behaving in the same way. So, here’s a chick limb. Here’s one when you treat
it with retinoic acid. Again, you induce another ZPA,
a Sonic hedgehog expression. And what you see is here is the normal, and then in the treated ones, you find rays branching
out in the opposite side. For all intents and purposes,
being a mirror duplication. And we can dissect these things out, and characterize what these
duplicated rays look like. And for all the world, it looks like they’re coming
out in the opposite side of the gill cartilage. And this gets even more exquisite
as we look in more detail. There’s a relationship
between the AER and the ZPA, between the genes in them, the Sonic hedgehog and FGF8. There’s all sorts of intermediary genes and a feedback loop between them. And that feedback loop and all those genes are present doing similar
things in the gills, and in the gill rays,
and in the appendages. So, it really seems at
a developmental level, that the toolkit that’s used
to pattern an appendage, the fin, in this case, of a shark, is the same toolkit, is the same thing as this pattern in the gill rays. This is a developmental extension, a sort of level of the
mechanisms that make anatomy, of Gegenbaur’s theory. Question really comes
down to how would you know if gills actually were transformed into these things over time. And what we need here are fossils. And this is where fossils would tell us the sequence of stages in
the transformation, perhaps, of gills to rays. Right now, what we know is
if you look at jawless fish, which don’t have appendages,
but have these gill rays. Okay, they have a full set of rays that are sure very large
in the posterior end. They’re very well developed. Ideally, what we’d like to
find is intermediate stages in this process in the fossil record. And all someone has to do
is target Silurian age rocks to test their hypothesis. The other thing about
these gill cartilages is they are wonderful for anatomy. Here you see the arches again. It’s the upper jaw and lower jaw. It’s first arch. Here’s the hyoid arch with
the hyoid mandibular there, and the gill cartilages. They all develop within the swellings, the branchial arches that develop in the front end of the embryo. Here’s the pair of eyes. And you see there’s a pair of arches here that we colored in. If you follow the fates of
the cells that are in there, and these cells come
from a variety of places as well as develop in situ. These cells differentiate
into respective structures in the arch. You can look at any creature
that has a head, take a human, and you see these same branchial arches with this first pair, second
pair, third pair, and so forth. What happens in a human with these arches, they become portions of, the first arch becomes a
portion of the lower jaw and two bones of our middle ear. The second arch becomes a
bone that supports the throat and one bone in the middle ear. And the others become
portions of the voice box. The take-home message here
is that developmentally the bones that you’re using, many of the bones and muscles and nerves that your using to hear me with right now, and many of the bones
and muscles and nerves, or some of them, that I’m using
to talk to with right now, correspond to gill structures
developmentally in fish. Now, what’s interesting about this story, and this shows the importance
of integrative biology and understanding descent
with modification is, okay, you see this in development, but in paleontology and the fossil record, what I should see is a transformation of jaw bones into middle ear bones, and a transformation
of a second arch bone, namely this hyoid
mandibula into an ear bone. And guess what we see. When we look at the fossil
record in comparative anatomy, what we see is the hyoid
mandibula, the hyoid arch gill bone over time it gets smaller
and smaller and smaller, such were in Tiktaalik,
which I’m not showing here. It’s intermediate in condition, and then it gradually
shrinks to go into the ear to become the stapes. Fossils and embryos
showing the same story. And what about those jaw bones
that go into the middle ear? Same thing. If you look at the jaw of
things we call reptiles, which have multiple bones in the jaws, you can trace two of
these ones in the back. They get smaller and smaller and smaller ’til they translate into the middle ear. So, development and fossils are showing us the same thing in the ear. And it’s also showing us
something very important about descent with modification because the same things
in different creatures, if descent with modification is acting, the same thing doesn’t have
to look like, look like it. That is, these middle ear
bones, this stapes here, looks nothing like the
hyoid mandibula of a shark. Yet it’s the same thing
in different creatures. These two bones here,
the malleus and incus, look nothing like the two bones in the back end of one of these jaws. Yet it’s the same thing
in an evolutionary sense. And that’s the power of
descent with modification because over time, with small changes, you can get great differences. And we can pick those differences up when we look at embryos
and we look at fossils. So, the take-home message to
much of what I’ve been saying is that similar biological
recipes make different organs, whether it’s gills, rays, and appendages. And I’ll show you some other cases. But the important thing,
in terms of thinking about descent with modification
at the level of recipes or toolkits or mechanisms
that make bodies, is that new organs can come about by the modification of ancient recipes. Just like we have
descent with modification and we can interpret it at the level of anatomical structures, we can have descent with modification at the level of the toolkit, the processes, and the genes that compose that toolkit that make organs. And so, this allows us to
return to Owen’s theme, really, in the sense that he
was saying, basically, that these appendages are the same thing, but they’re utterly different from something like this,
which is the wing of a fly. And indeed, when we look at Darwin and we follow descent with modification, that appears to be correct
in an evolutionary sense, is that fly wings have a
separate evolutionary origin than do the appendages
of vertebrate animals. But when we start to look at
the toolkit and the recipe, this convenient distinction begins to break down in an odd way. So, let’s look at a fly leg or wing, I have it on the left,
and a limb bud here. And what’s interesting,
if you can think about, and I’m just gonna do an overview of it, the biological processes
that determine the pattern of these appendages in three dimensions, that along this z-axis, the
y-axis, and the x-axis here, let’s look at the tools that pattern that. Well, we already talk about
some of these in the limb. And I’m just showing a drawing here, which shows if you look at the x-axis, it’s really the ZPA with Sonic hedgehog, and there’s another gene which
I didn’t talk about, BMP. If you look at a fly imaginal disc, which looks nothing
like a limb bud at all, or the imaginal disc of a wing or a leg, they have a hedgehog gene
that’s evolutionarily related to Sonic hedgehog, and it is turned on in the entire sort of posterior half of the developing fly imaginal disc. And there’s another gene, DPP, which is turned on just
along the margin here, and that, by the way,
is the same gene as BMP, if you could trace it in
evolutionary trees of genes. What happens when you misexpress
Sonic on the opposite side, you remember, we showed
that to you a million times, you get a duplicated
fin, or duplicated limb. What happens if you misexpress hedgehog, its equivalent in the fly, wing imaginal disc on the
opposite side, or even this DPP. What do you find? You find a duplicated wing. Okay, these are differently
derived structures, but you find duplicate,
same effect, same genes, evolutionarily doing similar
kinds of things, equivalent. And I can say the same thing for genes that are on the y-axis, which I’m not gonna get into. You have genes like wingless,
which I didn’t draw, apterous. And here you have genes that are wingless as here, too, in LMX1. And you also have in the x-axis,
the axis which grows out. You have other genes which control the… which are within the AER but actually are also controlling the
outgrowth of the thing. DLX here in distalis, in the
fly leg, but not in the wing. So really, if you look at it, and just the take-home message is here you have two organs,
which by all accounts, are different, okay, in
an evolutionary sense. Yet the toolkit, the underlying
toolkit that makes them is actually looks to be very similar, so similar in many ways
that it may be the same in an evolutionary sense, that it’s continuous in doing something. This leads me to sort of the final sort of sequence of the talk, which is to really think
about what this means with regard to the origin of organs. And there was a analogy, a flawed analogy, but an analogy that was very powerful, that was set up by Francois Jacob in 1977. It’s the notion of tinkering. He took a very teleological
view of evolution, so let’s just ignore that for a second. But he had an analogy that
has some intuitive power. And that is what he says
is evolution doesn’t act as an engineer who can build
structures from scratch. In his mind, evolution
acted as a tinkerer, modifying existed odds and ends, things that exist to make the new. Now, put in non-teleological terms, what it means is that
the fuel for evolution, the variation that natural
selection actually acts on is really the result of changes to the existing genetic
structure in an organism, genetic and developmental
structure in an organism. It acts on what exists at every stage. And what exists in every
stage are the genes and developmental processes,
indeed, much of the toolkit that’s making the organs
of ancestral forms. So, this leads me to sort of think about when I look at cladograms,
I think of something as, how when we deploy this
notion of the Hummer analogy, being able to trace the
structure of organs in one way, but also the toolkits that pattern them and aspects of those toolkits. It makes one think of almost
a biological cut and paste, and not as much as the Wall Drug Jackalope or the Wisconsin Narrows Basscat, but it leads to several different notions. The first is versions of the same toolkit pattern different organs. Obviously, we’ve seen
that with the fly wings and the limbs of vertebrates. We’ve seen that in fins and gill arches. That ancient tools can be redeployed during the origins of new organs. That may have been the case in the origin of appendages themselves from, perhaps, the gill arches of unfinned ancestors. And finally, and this is something that my introducer, David Wake, has talked about for a long time, that is having a common
toolkit, having common processes that build bodies makes
the independent evolution of similar structures more
likely rather than less likely. Nobody’s really read Stephen
J. Gould’s final tome, ’cause it’s about 1,700
pages, but I actually did. I was one of the students
who worked with him. He devoted 200 pages, more than
200 pages of his final book to looking at the consequences
of conserved genes on parallel evolution. And I really think he put his finger on something that’s very important. That the independent evolution
of similar structures is something that’s
gonna be made more common rather than less common by
the unity of the toolkit that we see in diverse kinds of creatures. And this sort of allows us to
return to our opening nose. And that basically answering the question that we can look at the
nose, and we can say, quite confidently, looking at phylogeny, evolutionary history, we can say that the sort of the
nasal organ of mammals is the same thing at the level of organs. Scientists are still undecided
about this particular one. But yet it’s not the
same thing as an organ in an evolutionary sense. This is the beak of a bird, and the proboscis of a paddlefish, and the proboscis of a beetle. Yet despite that, as these things grow, as these things develop, they
use the same general tools to form their structures inside. So, I wanna close with the same series, the same sequence of
things I talked yesterday, and that’s the power
of thinking with trees. We tend, I tend even, when I’m presenting to think evolution and present evolution as a linear series of
events, a gradual series that happens within one species, with one set of organs
changes into another species with another set of organs, and so forth. But we really need to return
to Darwin’s original vision, of which his actual original
vision is right here, which is his notebook with his first tree, which is, I think here, to the notion of a tree. Because the notion of a cut and paste becomes quite powerful. Because the diversification of creatures and their evolutionary development of their evolutionary
diversity from one another, from their common ancestors. As changes happen genetically
within different populations, it will be more likely
rather than less likely to see similar kinds of
anatomical structures arise in different creatures. Often times, what we’ll
see is whole modules, whole assemblages of the
toolkit that makes bodies redeployed and turned on in ways to make all kinds of new structures. And I’d like to close just with a thought in integration and in integrative biology, and I think in this context, we really have a power
to integrative biology. Because to understand
the origin of new organs, we have new tools, and it’s
really how we use those tools to answer our questions that
it’s so vitally important. And we have fossils to
tell us about the sequence of anatomical changes that
exist in ancestral states. We have embryology to tell
us about how cells interact to build organs. And now, we have at our disposal, understanding of genomes and genomics to understand the regulatory elements, the elements, the little pieces of DNA, and the pieces that bid
to those pieces of DNA that actually control developmental events in different creatures. Because it’s not trivial at all if we can link genomics,
fossils, and embryos to understand how whole new toolkits can be redeployed to make whole new ways of living in an ecosystem. I’d like to thank, and to close again, by thanking my host here at
Berkeley for a marvelous week. I’d like to thank you for
being such a great audience. Thank you very much. (audience applause) – [Woman] Can you comment a little bit on how far back, in terms of, for example, going back into microbes some of those developmental genes go? – Oh, sure. If you look
at the way cells interact with their environment, and
the way that information from outside a cell is
translated to inside a cell, which is such an important
part of building bodies, such an important part of
interacting with the environment, virtually all that apparatus
in some way, shape, or form can be originally traced to microbes. So to really understand, like Nicole King, who’s here at Berkeley, to understand the origin
of bodies themselves, you really have to understand microbes, ’cause that’s where many
of these mechanisms first arise as microbes are doing
their jobs being microbes, interacting with the world. – [Man With Accent] Over the journey of your fossil discovery or finding, have you find any… vertebrate animals that have more than four sets of limbs, like six limbs? – No, I haven’t, but they exist. And so, if you look at, it
depends what you call a limb, if you look at some sort
of, many of these things called spiny sharks, what you find is they can have multiple
sets of paired appendages. Whether they’re the same thing
as the true-paired appendages that we have, I don’t know. But these are very sort of basal fish, and they have multiple sets and eggs. – [Man With Accent] You think
if there is any explanation of why we don’t see any creature
with more than four limbs? – We’ll you see it. So, like, the whole,
remember, multi-legged frogs? Where frogs would develop with… – [Man With Accent] Or
something like grackons? – Right, so you actually see mutations or you see perturbations in development that can produce a
creature with lots of legs. The problem is, they can’t get around. They can’t walk. Those are
not typically innervated, and they’re not coordinated within the central nervous system. So, you can have a limb,
but you may not have a limb that can be functional
because it’s not part of, wired into the central nervous
system in any effective way. Often times, they’re just
dragging these things along, and it’s a liability, as
the outcome of predation. But that’s in vertebrates. I don’t know what
happening in invertebrates. I just know the frog world. (chuckles) – [Man In Plaid Shirt] Professor,
so you showed the pictures of the gills structures and the jaw bone and the ear bone in humans. So, with what degree of certainty, can you make these sort of connections when you do this kind of study? – Yeah, I mean, one of the
the things I gotta tell you that absolutely blew me
away when I was a student was seeing the transformation of jaw bones to ear bones in the fossil record, in the mammal-like reptiles. And that’s actually what
initially almost attracted me to work on Triassic age rocks, which is at the origin of mammals where much of that transition happened. It really can be traced very powerfully, and there’s several lines
of evidence that do it. Number one is the embryology. Number two is the genetics, that is there is a genetic
signature to each of these arches that’s present in the arches of fish, but also in the ear bones of mammals. It’s also in the
innervation of these things, the first arch structure in both cases, which is mandibular, has a
certain type of innervation that’s different from the
second arch structure, which is the facial nerve and so forth. So, it’s written deeply in
the comparative anatomy, in the muscles, the nerves,
the arteries, the bones, in the developmental
processes that produce them, in the genes that specify
that developmental process. I mean, it’s really… I’m frothing at the
mouth, it’s so beautiful. (audience laughs) – [Man In Orange Shirt]
In your first lecture, you mentioned that the
transition from water to land happened only once. What are the evidences that it
did really happen only once? – Yeah, that’s an awesome question because if parallel evolution is the rule, maybe it happened multiple times. The thing about it is that
the reason why we think it had only happened once, is ’cause the number of characteristics we can use on the
evolutionary tree as evidence to support that view, that
evolve across the body. So, if there was parallel
evolution in that way, it would have to be body-wide and multiple systems from
the vertebrae to the head to the limbs, to the
shoulder, and so forth. So, at our evidence for
that is the characteristics, the multiple large number
of them that support the evolutionary tree
that’s just only once. I should say that
embryologists in the ’30s thought it happened at least twice. Once in salamanders,
and once in the lineage that led to frogs and amniotes, creatures that develop in eggs. But no, the evidence
is the characteristics that we use to make trees, and there’s a lot of them in that case. – [David] Please join me in
thanking Professor Shubin for these two outstanding lectures. (audience applause) – Thank you. (audience applause) (funky music)

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