Evolve: Eyes

The warm-up act for this program was a dinosaur program called “Jurassic Fight Club”, which was loaded with CGI and lots of gratuitous razzle-dazzle — but I thought it was a hoot. It also had enthusiasatic scientists talking about how they figured out what had happened (although it does bug me that they treated some speculative stuff in the narrative as if it were factual). Most of the show was taken up with glitzy animations, but it was balanced with at least some discussion of the process of science, so I’ll give it a thumbs up.

Now to settle in for the story of the evolution of eyes…

Oooh: “the sparks of evolution are tiny, random changes called mutations”. I’m pleased that it jumps right in without compromise. It also promptly pushes the timeline back to 600 million years, and describes work done on jellyfish eyes. They show some very cool behavioral studies of how jellies respond to different wavelengths of light, illustrating why even simple animals would find light-sensing organs beneficial.

Teaser before the first commercial: trilobites. It looks they’re trying for a chronological approach.

The commercials are really annoying: Kinoki foot pad quackery and bigfoot. Bleh.

Now we get a quick summary of the Cambrian explosion — I saw an anomalocaris swim by. The first fossil eyes are from the Cambrian; compound eyes on arthropods. Modern insects are shown, explained as not descendants of trilobites, but probably share the same genes Good acknowledgment of the successful utility of dragonfly eyes.

Dang. Too little time spent on invertebrates — they’re already switching gears to focus on vertebrates.

Pikaia! Cool. Kinda nice that they’re setting up the vertebrate eye as an icon of evolution, and a kind of machine — good dig at ID. There’s also a nice simple animation of how an eye patch could form an eye cup, then an eye with a lens.

Yeah, they already leap into those sexy, glitzy dinosaurs. A little more time should be spent on those unsexy hagfish and lampreys, more interesting as transitional forms, but OK, most people wouldn’t find them as interesting as I would. They show Kent Stevens (UO! Yay!) work on identifying visual fields from dinosaur fossils, and discuss binocularity.

T. rex makes for good visuals, but is it really the best animal for discussing the evolution of vertebrate eyes? The innovations were all in place before the dinosaurs came on the scene!

Next lead-in: we’re about to learn about mammals and night vision.

Primitive mammals were largely nocturnal. So what are the special adaptations in the mammalian eye for night vision? Lots of isolated eyes in jars; the answer from comparative anatomy is that the size of the cornea is important. Cool: tarsiers have eyes that are bigger than their brains.

Another strategy: the tapetum, a reflective layer at the back of the eye. Nifty dissection of a big cat’s eye to show the structure.

Looks like the last 15 minutes of the program will be about human vision…

We lucky humans have color vision. Mammals radiated into numerous niches after the great extinction at the K/T boundary, and primates moved into the trees. Why did natural selection favor improved color vision in primates? Monkeys are shown to favor the youngest, tenderest leaves…which have color differences from old leaves.

Primates also have binocularity for better depth perception, an adaptation for living in trees. This gives them a narrower field of view, unfortunately. Birds of prey targeted these animals with limited vision, which made group living more advantageous for primates. They suggest that this would promote more social behavior and intelligence.

Summary: Not bad. The title is a bit of a misnomer, though, since only a little bit of it was about the evolution of eyes. A program more true to its title would have spent much more time on invertebrates, would have said more about the molecular underpinnings of vision, and would have concentrated on hagfish, lampreys, and teleosts among the vertebrates.

I know…dinosaurs and people are much more popular creatures, so the show compromised on the science for the sake of visual appeal. That’s an unfortunate reality of the conventions of TV programming, but it would have been nice to see them break out of that straitjacket, especially since the early part of the show on jellyfish was arresting and cool, showing that it can be done.

It was unabashedly pro-evolution, too, not giving a second to the silly stories we get from creationists. That’s a real plus, too.

Snake segmentation

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Life has two contradictory properties that any theory explaining its origin must encompass: similarities everywhere, and differences separating species. So far, the only theory that covers both beautifully and explains how one is the consequence of the other is evolution. Common descent unites all life on earth, while evolution itself is about constant change; similarities are rooted in our shared ancestry, while differences arise as lineages diverge.

Now here’s a new example of both phenomena: the development of segmentation in snakes. We humans have 33 vertebrae, zebrafish have 30-33, chickens have 55, mice have 65, and snakes have up to 300 — there’s about a ten-fold range right there. There are big obvious morphological and functional differences, too: snakes are sinuous slitherers notable for their flexibility, fish use their spines as springs for side-to-side motion, chickens fuse the skeleton into a bony box, and humans are upright bipeds with backaches. Yet underlying all that diversity is a common thread, that segmented vertebral column.

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(Click for larger image)
Vertebral formula and somitogenesis in the corn snake.
a, Alizarin staining of a corn snake showing 296 vertebrae, including 3
cervical, 219 thoracic, 4 cloacal (distinguishable by their forked
lymphapophyses) and 70 caudal. b, Time course of corn snake development
after egg laying (118-somite embryo on the far left) until the end of
somitogenesis (~315 somites).

The similarities are a result of common descent. The differences, it turns out, arise from subtle changes in developmental timing.

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Altenberg 2008 is over

Massimo Pigliucci has posted the notes, parts 1, 2, and 3, from the Altenberg meeting that was unfortunately over-hyped by the creationist crowd (no blame for that attaches to the organizers of this meeting). It sounds like it was a phenomenally interesting meeting that was full of interesting ideas, but from these notes, it was also clearly a rather speculative meeting — not one that was trying to consolidate a body of solid observations into a coherent explanation, but one that was instead trying to define promising directions for an expansion of evolutionary theory. That’s also the message of the concluding statement of the meeting.

A group of 16 evolutionary biologists and philosophers of science convened at the Konrad Lorenz Institute for Evolution and Cognition Research in Altenberg (Austria) on July 11-13 to discuss the current status of evolutionary theory, and in particular a series of exciting empirical and conceptual advances that have marked the field in recent times.

The new information includes findings from the continuing molecular biology revolution, as well as a large body of empirical knowledge on genetic variation in natural populations, phenotypic plasticity, phylogenetics, species-level stasis and punctuational evolution, and developmental biology, among others.

The new concepts include (but are not limited to): evolvability, developmental plasticity, phenotypic and genetic accommodation, punctuated evolution, phenotypic innovation, facilitated variation, epigenetic inheritance, and multi-level selection.

By incorporating these new results and insights into our understanding of evolution, we believe that the explanatory power of evolutionary theory is greatly expanded within biology and beyond. As is the nature of science, some of the new ideas will stand the test of time, while others will be significantly modified. Nonetheless, there is much justified excitement in evolutionary biology these days. This is a propitious time to engage the scientific community in a vast interdisciplinary effort to further our understanding of how life evolves.

That’s a little soft — there are no grand reformulations of the neo-Darwinian synthesis in there, nor is anyone proposing to overturn our understanding of evolution — but that’s what I expected. It’s saying that there are a lot of exciting ideas and new observations that increase our understanding of the power of evolution, and promise to lead research in interesting new directions.

Unfortunately, one reporter has produced an abominably muddled, utterly worthless and uninformed account of the Altenberg meeting that has been picked up by many crackpots to suggest that evolution is in trouble. This not only ignores a fundamental property of science — that it is always pushing off in new directions — but embarrassingly overinflates the importance of this one meeting. This was a gathering of established scientists with some new proposals. It was not a meeting of the central directorate of the Darwinist cabal to formulate new dogma.

Where one ignorant kook dares to assert her inanity, you know the Discovery Institute will stampede after her. Both Paul Nelson and now Casey Luskin have cited her lunatic distortions favorably. Luskin’s account is egregiously incompetent, as we’ve come to expect — he even thinks Stuart Pivar was an attendee. Pivar is an eccentric New York art collector, heir to a septic tank fortune, who has no training in science and whose “theory” is a nonsensical bit of guesswork that is contradicted by observations anyone can make in a basic developmental biology lab. He was not at the meeting. No one in their right mind would even consider inviting him to such a serious event. Maybe if it was a birthday party and they needed someone to make balloon animals, he’d be a good man to have on hand.

Now we can move beyond the garbled hype of the creationists. Pigliucci lists several concepts up there that have promise for further research, and that may help us understand evolution better. That’s the productive result of the meeting, and the only part that counts. Those concepts are also going to be discussed by many other scientists at many other meetings — even I talked about some of them recently — but don’t let the liars on the creationist side confuse you into thinking that the fact that scientists are talking about new ideas is a sign that evolution is in crisis. Talking about new ideas is normal science.

Atlanta GECCO 2008

I’m on my way home, and am actually using a fast internet connection at the airport — I’d forgotten what it was like! I quickly uploaded a few essential files, and my mail software is downloading my email. Unfortunately, I’d need a really fast connection to handle all that — the number of messages pouring in might actually hit 5 digits. If you’re hoping for a reply to anything, you might well be out of luck here.

Atlanta has been very pleasant, with friendly people and good company. I’ll have to come back sometime. The meeting itself was challenging for a mere biologist, but I might have absorbed a few glimmerings. At least it’ll help me dig into the literature a little more.

As for my talk, and since I haven’t had time to put much science here lately, I’m making my GECCO 2008 talk available as a pdf. These presentations are always a little cryptic when handed out without my explanatory overview, but at least in this one I’ve included my presenter notes, which might help a little bit. The first half is an overview of some concepts in evo devo, which includes those little reminders of what I was supposed to say; the last half is a description of two experiments, and I’m afraid my notes are a little thin there — the data in the research always seems self-explanatory to me. Sorry about that, you should have registered for the conference!

Email download complete: it didn’t quite hit 5 digits, only 9865 messages in the last few days. Maybe if I included the spam that gmail filters out for me…

Ack! I couldn’t add this note from the airport because “Your computer was automatically blacklisted (blocked) by the network due to an abnormal amount of activity originating from your connection.” Curse you, Boingo! What good are you if I can’t even download email without you suspecting I’m up to no good?

Altenberg meeting next week: expect evolution to simply evolve slightly

Remember Suzan Mazur, the credulous reporter hyping a revolution in evolution? She’s at it again, publishing an e-book chapter by chapter on the “Altenberg 16”, this meeting that she thinks is all about radically revising evolutionary biology.

I can tell that Massimo Pigliucci — one of the 16 — is feeling a little exasperation at this nonsense, especially since some of the IDists have seized on it as vindication of their delusions about the “weakness” of evolutionary theory. He’s got an excellent post summarizing some of the motivation behind this meeting, which is actually part of a fairly routine process of occasional get-togethers by scientists with similar ideas to hash out the concepts. Here’s the actual subject of discussion at the Altenberg meeting.

The basic idea is that there have been some interesting empirical discoveries, as well as the articulation of some new concepts, subsequently to the Modern Synthesis, that one needs to explicitly integrate with the standard ideas about natural selection, common descent, population genetics and statistical genetics (nowadays known as evolutionary quantitative genetics). Some of these empirical discoveries include (but are not limited to) the existence of molecular buffering systems (like the so-called “heat shock response”) that may act as “capacitors” (i.e., facilitators) of bursts of phenotypic evolution, and the increasing evidence of the role of epigenetic (i.e., non-genetic) inheritance systems (this has nothing to do with Lamarckism, by the way). Some of the new concepts that have arisen since the MS include (but again are not limited to) the idea of “evolvability” (that different lineages have different propensities to evolve novel structures or functions), complexity theory (which opens the possibility of natural sources of organic complexity other than natural selection), and “accommodation” (a developmental process that may facilitate the coordinated appearance of complex traits in short evolutionary periods).

Now, did you see anything in the above that suggests that evolution is “a theory in crisis”? Did I say anything about intelligent designers, or the rejection of Darwinism, or any of the other nonsense that has filled the various uninformed and sometimes downright ridiculous commentaries that have appeared on the web about the Altenberg meeting? Didn’t think so. If next week’s workshop succeeds, what we will achieve is taking one more step in an ongoing discussion among scientists about how our theories account for biological phenomena, and how the discovery of new phenomena is to be matched by the elaboration of new theoretical constructs. This is how science works, folks, not a sign of “crisis.”

You cannot imagine how pleased I was to see this — not because I was at all concerned about this meeting, but because I’ve been scribbling down notes for the last few weeks on the subjects I want to discuss in my keynote at GECCO 2008, and that’s practically an outline of my plans. I was going to go over some of these concepts and define them and give examples; I didn’t have molecular buffers on my list (maybe I’ll have to add it), and I was going to say a bit about conservation/canalization vs. plasticity, but at least I’m reassured that I’m on the right track.

Origin of life

Nick Matzke has a fine summary of progress in research into abiogenesis. He chastises those people who try to argue that abiogenesis is independent of evolution, or that you can get out of trying to answer the question of where life came from by simply saying that that isn’t evolution. It is! I’ve said it myself, and I really wish people would stop trying weasel out of that question by punting it off to some other discipline.

Evolving proteins in snakes

Blogging on Peer-Reviewed Research

We’ve heard the arguments about the relative importance of mutations in cis regulatory regions vs. coding sequences in evolution before — it’s the idea that major transitions in evolution were accomplished more by changes in the timing and pattern of gene expression than by significant changes in the genes themselves. We developmental biologists tend to side with the cis-sies, because timing and pattern are what we’re most interested in. But I have to admit that there are plenty of accounts of functional adaptation in populations that are well-founded in molecular evidence, and the cis regulatory element story is weaker in the practical sense that counts most in science (In large part, I think that’s an artifact of the tools — we have better techniques for examining expressed sequences, while regulatory elements are hidden away in unexpressed regions of the genome. Give it time, the cis proponents will catch up!)

This morning, I was sent a nice paper that describes a pattern of functional change in an important molecule — there is absolutely no development in it. It’s a classic example of an evolutionary arms race, though, so it’s good that I mention this important and dominant side of the discipline of evolutionary biology — I know I leave the impression that all the cool stuff is in evo-devo, but there’s even more exciting biology outside the scope of my tunnel vision. Also, this paper describes a situation and animals with which I am very familiar, and wondered about years ago.

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Ventastega

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The paleontologists are going too far. This is getting ridiculous. They keep digging up these collections of bones that illuminate tetrapod origins, and they keep making finer and finer distinctions. On one earlier side we have a bunch of tetrapod-like fish — Tiktaalik and Panderichthys, for instance — and on the later side we have fish-like tetrapods, such as Acanthostega and Ichthyostega. Now they’re talking about shades of fishiness or tetrapodiness within those groups! You’d almost think they were documenting a pattern of gradual evolutionary change.

The latest addition is a description of Ventastega curonica, a creature that falls within the domain of the fish-like tetrapods, but is a bit fishier than other forms, so it actually bridges the gap between something like Tiktaalik and Acanthostega. We look forward to the imminent discovery of yet more fossils that bridge the gap between Ventastega and Tiktaalik, and between Ventastega and Acanthostega, and all the intermediates between them.

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Amphioxus and the evolution of the chordate genome

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This is an amphioxus, a cephalochordate or lancelet. It’s been stained to increase contrast; in life, they are pale, almost transparent.

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It looks rather fish-like, or rather, much like a larval fish, with it’s repeated blocks of muscle arranged along a stream-lined form, and a notochord, or elastic rod that forms a central axis for efficient lateral motion of the tail…and it has a true tail that extends beyond the anus. Look closely at the front end, though: this is no vertebrate.

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It’s not much of a head. The notochord extends all the way to the front of the animal (in us vertebrates, it only reaches up as far as the base of the hindbrain); there’s no obvious brain, only the continuation of the spinal cord; there isn’t even a face, just an open hole fringed with tentacles. This animal collects small microorganisms in coastal waters, gulping them down and passing them back to the gill slits, which aren’t actually part of gills, but are components of a branchial net that allows water to filter through while trapping food particles. It’s a good living — they lounge about in large numbers on tropical beaches, sucking down liquids and any passing food, much like American tourists.

These animals have fascinated biologists for well over a century. They seem so primitive, with a mixture of features that are clearly similar to those of modern vertebrates, yet at the same time lacking significant elements. Could they be relics of the ancestral chordate condition? A new paper is out that discusses in detail the structure of the amphioxus genome, which reveals unifying elements that tell us much about the last common ancestor of all chordates.

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