…and this is a 
Shubin had a tough act to follow, coming after Kingsley's great talk. I'm sure it will be good, though — last night I got a tour of his lab, saw the original Tiktaalik specimens and some new ones, and some of his work in progress (which I won't tell you about until it's published), so I'm confident I'm going to have a happy hour.
Darwin pulled together diverse lines of evidence to document his ideas. The different lines all reinforce each other making the argument even stronger, and what we're seeing now is new syntheses, which is the theme of this talk: how do we use different lines of evidence to make a case that is more the sum of its parts.
The questions is the origin of limbs, fins to legs. Fins and legs look very different, with fins having rays and many bones, while legs have few bones in a fixed pattern. Intermediate taxa show us the changes, with transitions with bony core of the limb pattern and fish-like rays. He uses geology and extant fossils to make predictions about where to find intermediates, and paleontology also informs his understanding of developmental processes that build the limb.
Began his work in Pennsylvania, which was like the Amazon delta 360 million years ago. They followed the PA dept. of transportation around looking at road cuts that exposed the rocks of that age. They found many fossils, but one that changed his thinking was a fin of sauripterus, with fin rays and a core of tetrapod-like limbs. Definitely fishy, but contained precursors to the pattern.
They searched in Ellesmere Island for Devonian age rocks and fossils that would reveal the history of the limb. The logistics were very difficult, since the area is inaccessible. First started working in 1999, in rocks that were from marine sources and didn't yield much. Moved east to freshwater sources. Found a layer of rock that was rich in bone, and found a snout of a flat-headed fish poking out. Eventually exposed about 20 specimens of this animal. Took months to fully expose the details of the specimen.
He showed off a cast of Tiktaalik — physical objects are really good at capturing people's imagination.
It took a year and a half to prepare out the fins; the bones show articular surfaces, so you can actually see how the structure bent in life. What does this tell us about extant fins?
A tetrapod limb has 3 components: 1 bone, then 2 bones, then multiple bones in wrist and fingers. The limb forms in phases, with an early phase of hox expression that sets up the proximal bone, then phase II in which hox genes switch on in a patterned way to form digits. Are there elements of phase 2 in fish fins?
Looked in Polyodon, and embryos do have a distal phase of hox expression, not identical to tetrapod pattern, but definitely a phase 2.
What is a limb and how did it develop? The AER sets up the proximo-distal axis, ZPA sets up anteriorposterior axis. Cutting off the AER at different stages produces progressive deletions of portions of the limb. ZPA is a source of Sonic Hedgehog and sets up a gradient of positional information.
Does the common ancestor of all fish have these same two-axis signals? Chondrichthyans do, with patterns that can be manipulated in the same way as we do in chickens. The appendage patterning system is general to all vertebrate appendages.
How do fins differ from other outgrowths? Branchial arches have the same patterning, with an AER and ZPA. Seems to be a universal way for vertebrates to set up the patterning of outgrowths. Gill, fin, and limb have similar toolkits of patterning genes.
The patterning mechanisms may have originated in a general outgrowth and been coopted for limbs and gills. Shubin proposes to do targeted collecting of Ordovician vertebrates, expecting to find novel non-limb outgrowths that may be precursors to the patterning mechanism. Paleontology guided by developmental biology!
Life Science
Comments
Posted by: Dahan
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October 31, 2009 2:43 PM
You got to see the actual Tiktaalik specimens? I'm so jealous...
Posted by: Nerd of Redhead, OM
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October 31, 2009 2:56 PM
No spoilers on his upcoming work? You are EVIL.
Posted by: Glen Davidson
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October 31, 2009 3:03 PM
Yeah, but the IDiots can tell you that it was all designed by God!
Glen D
http://tinyurl.com/mxaa3p
Posted by: brasidas | October 31, 2009 6:25 PM
I'm wondering whether there is a pattern in limb bones: one main bone (humerus/femur); then paired bones (radius/ulna - fibula/tibia); then a bit of a mess (wrist and ankle bones); then toes. Some gene doubles the number of bones at each joint.
Is there a progression 1/2/4/8? In other words with the mess being the remnants of the four-bone stage, and the toes in modern tetrapods being the five remnants of the original eight? I seem to remember that at least one ancient tetrapod had eight toes. I would predict from this that no tetrapod would ever be found with more than eight toes - the primitive tetrapod foot.
Incoherent blather over.
Posted by: The Science Pundit
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October 31, 2009 6:29 PM
I saw Shubin talk here in PA about a year ago, and I saw Ted Daeschler talk almost two years ago. Both of them dropped hints about their upcoming work, and I will reveal to you, out of the kindness of my heart (actually, if you've watched all the Neil Shubin lectures available on YouTube, you've already see the hint), that it has something to do with Tiktaalik's hip socket (actually, Ted Daeschler disclosed quite a bit more, but since I'm also EVIL I'll leave it at that).
:-P
Posted by: David Marjanović, OM | October 31, 2009 8:59 PM
No. The digits + metapodials + distal mesopodials form completely independently of the rest of the limb (or Australian lungfish fin for that matter). This is why they don't line up with it.
Said rest of the limb consists of a tree structure consists of stuff that segments and bifurcates while it grows as long as there's space between it and the place where the distal metapodials have formed or (more commonly) will form later: using forelimb bone/cartilage names... Here is the minimum:
--humerus--+--ulna--+ | `--intermedium `--radiusThese are the bones found in Acanthostega (mind you, depending on how the hand is reconstructed, there could be space for more elements that stayed cartilage and didn't become bone) and in dolphins (where there's no such space).
Here's the maximum, found in some Carboniferous and Permian animals:
--humerus--+--ulna--+--ulnare | | ,--centrale 3 | `--intermedium--+--centrale 4--+--centrale 2 `--radius--radiale--centrale 1--distal precarpal--prepollexThe prepollex, when fully formed (which is very rare), looks like a digit (or "radial" in the Australian lungfish). However, it's not one.
I hope this helps!
Posted by: David Marjanović, OM | October 31, 2009 9:06 PM
The word that is cut off is "prepollex".
Also, the metapterygial axis (humerus-ulna-ulnare) has two more elements in Tiktaalik and shitloads more elements in lungfishes.
Also, the centrale 1 is called "element y" in salamanders, the centrale 3 is called "element m" at least by Shubin, and so on and so forth...
Posted by: George Emerson | October 31, 2009 11:18 PM
Evolution isn't a science its a theory, and a flawed one at that. The truth is that science is really going the other way....away from Darwinism. I may be an idiot (Glen Davidson), but I'm no fool. God did create the earth and everything in it and it won't be long before you will have the earth to yourself. I think the comment here says it all, "..He showed off a cast of Tiktaalik — physical objects are really good at capturing people's imagination".
Posted by: mythusmage
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October 31, 2009 11:42 PM
What did AER and ZPA work on originally, before gills?
Posted by: Nerd of Redhead, OM
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October 31, 2009 11:44 PM
Wrong, your deity is imaginary, no evidence for it. Imaginary things do nothing. Evolution occurred, until you can show physical evidence otherwise. And you have failed to do so. Your opinion is worthless without hard physical evidence.Posted by: Kel, OM | October 31, 2009 11:51 PM
psst, over here.You know, there comes a point where really one should be at least informed on the basics. If you're going to argue science, try to at least understand the terminology. Otherwise you're going to sound like a complete boob who doesn't know what he is talking about. It's only common courtesy...
Posted by: raven | November 1, 2009 1:40 AM
How would you know? You clearly don't know any science. Many of us are scientists and we've never seen anything but more and more proof of evolution. In science, the controversy was over a century ago. You are just lying.
may be an idiot (Glen Davidson), but I'm no fool
You are both and probably insane as well.
did create the earth and everything in it and it won't be long before you will have the earth to yourself The world would be a much better place without fundies. We would cheer wildly and wave good bye when the Rapture comes. It is 2,000 years late, and by now, everyone knows it was just a failed 1st century guess.
I think the comment here says it all, "..He showed off a cast of Tiktaalik — physical objects are really good at capturing people's imagination".
So let's see a picture of your god(s). Bring them around to Happy hour. There is no proof that they even exist and people have been looking for thousands of years.
George needs a better Halloween costume. His rational adult one is highly unconvincing.
Posted by: Scott Hatfield, OM
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November 1, 2009 2:29 AM
I just wanted to say that this sounds like a great talk, but in outline the same terrific presentation that Shubin gave on UCTV that aired just a few days ago. For those of you who can't wait to see the Chicago stuff put on the web, enjoy Shubin's act here:
http://www.uctv.tv/search-details.aspx?showID=16924
Oh, and for GEORGE EMERSON:
Evolution itself (genetic change in populations) is a fact. Darwin's proposed explanation for evolution, is also a fact. What is theoretical is the relationship between evolution and natural selection in all cases. To a scientist, theories are not 'hunches' or 'guesses', but well-tested models with a great deal of explanatory and predictive power that are widely (but provisionally) accepted for the purpose of doing further science. Darwin's basic model, see, is just so useful that some version of it is going to be essential to the business of doing biology. But it's not a belief system, as the brief 'Darwinism' often suggests.
And, speaking of beliefs, if you think that (in effect) saying 'neener neener neener I'll be raptured soon' is an argument that's going to carry weight in talking to scientists, well, you are a fool. The people on this blog are going to want evidence. They are also people who want to preserve the natural world. You, on the other hand, are offering a faith claim about an Apocalypse, and the end of the present order, an end that you almost certainly look forward to. You might as well insult their mothers.
(PS Don't waste your time excoriating me for my lack of faith, I'm a Methodist.)
Posted by: truthspeaker
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November 1, 2009 3:01 PM
Doesn't your religion have a commandment against lying?
Posted by: Sven DiMilo | November 1, 2009 3:08 PM
I'd guess that gills were the very first "outgrowths" needed by Cambrian protochordates, once they started getting big and active enough to benefit from them.
Posted by: Luke | November 2, 2009 2:26 PM
I really enjoyed Shubin's book - sorry to have missed his talk. Hopefully they'll be online soon enough.
Posted by: ChicagoPat | November 2, 2009 9:01 PM
Emergency Physician here, thought I was keeping up with the biology okay until I reached :"...ZPA is a source of Sonic Hedgehog..." Eh?
Posted by: Owlmirror | November 5, 2009 2:15 AM
I remembered that ZPA is Zone of Polarizing Activity, but I had to look up AER=Apical Ectodermal Ridge.
As in, that's where Shh is expressed?