Pathological cephalopod

Teratology is so interesting — it gives us hints about the mechanisms driving developmental processes. In some cases, when you just have a few isolated instances, it can be frustrating, because there isn’t enough information to go much beyond speculation. Here’s one of those tantalizing cases: an octopus with branching tentacles.

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Now that is fascinating. Look at limb formation as an abstract developmental problem in which you first have to initiate a protrusion from a specific place on the body wall; the protrusion has to elongate to a specific length; and it has to be patterned along its length. Cephalopod limb patterning doesn’t involve any branching elements, unlike vertebrate limbs which show a limited radiation of bony elements as you go distally. Vertebrates can exhibit phenomena like polydactyly which are basically counting errors or expansions of a field; the mechanisms for that don’t seem likely to be the case in cephalopods. What I’d guess is that this is an example of errors in initiation. Whatever the signal is that triggers limb extension from the body was triggered again and again as the arm grew, creating sub-arms and sub-sub-arms. This could be a consequence of a mutation that lifted normal constraints that pattern limb initiation (this animal lived for some time, and produced offspring with normal limbs, all of which died shortly after hatching, unfortunately, a result that is ambiguous in determining whether the problem is genetic), or it could be an environmental signal that mimics the normal developmental signal. You can’t tell from one dead octopus!

It’s still cool, though, and says we need more research on cephalopod development.

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.

Amphioxus and the evolution of the chordate genome

Blogging on Peer-Reviewed Research

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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IEDG2008: Model systems are dead, long live model systems

I’ve discovered a couple of important things at this meeting.

One, late night sessions at west coast meetings are deadly for any of us coming from more eastern time zones. At least the morning sessions are low stress.

Two, I haven’t heard one Drosophila talk yet, and the message is clear: we’re now in the stage of evo-devo in which everyone is diversifying and chasing down a wide array of species. There was a bit of model-system bashing, but at the same time, everyone is acknowledging the crucial role of those traditional, but weird and derived, lab critters in providing a point of comparison and being the source of many of the tools being used to explore phylogeny now. I thought, though, that the smartest comment of the evening was that now everything is a model system.

I’ve got some dense piles of notes on the evening session, but I’m going to give you the short version of everything, with an emphasis on the novel twists.

Michael Akam talked about segmentation genes, which every developmental zoologist now knows inside and out — trust me, this is a familiar topic with over 25 years of detailed research … in Drosophila. Akam made the point that now it’s looking clear that three of the major segmented phyla, the arthropods, annelids, and chordates, may be using related genes to accomplish segmentation, but they seem to be using different mechanisms — so he considers the question of whether segmentation in these three is homologous is still an open question. He also discussed recent work on the centipede Strigamia (definitely not a lab animal: they can’t breed them in the lab yet, so all the work is done by collecting embryos in the field, in Scotland). They have a dynamic pattern of segment addition that is very different from what you find in flies, and more similar in some ways to chodate segmentation.

Chelsea Specht talked about floral evolution in the Zingiberales. I’m an animal guy, so even the most basic stuff in this talk was entirely new to me. I know the general rules of the spatial development of in the fruit fly of the plant world, Arabidopsis, and she gave us a bit of context there, reminding us of the concentric development of sepals, petals, stamens, and carpels. The Zingiberales are a large and diverse group of plants that includes bananas and ginger, and one characteristic is an extravagant modification of the canonical pattern, with extra stamens, a loss of select stamens, and a fusion of stamens to form a novel structure, the labellum, which in these plants functionally replaces the petals. So of course they’re looking into the genes involved in the patterns, which turn out to be the familiar Arabidopsis genes redeployed in new patterns.

Paul Sereno had a talk that took a very different tack, and was unfortunately giving it at the equivalent of 11:00pm Minnesota time, so I’m sorry to say I didn’t follow it carefully. He was discussing the analysis of morphology, and was advocating the development of tools and techniques to compare data sets in addition to the usual output, phylogenetic trees. He was making the case that a lot of morphological studies are actually very poor (a creationist in the audience would have loved it, largely because he wouldn’t have understood the context) because the input data sets of different studies are not comparable.

And now I have to get back to work and listen to the next set of talks.

Bat wings and mouse feet

You may recall that a while back I mentioned how Jerry Coyne praised some work on bat evo-devo. I also said that I was going to have to write that paper up sometime. The bad news: I haven’t written it up for the blog. The good news: I did write it up for a future Seed column. The better news: Stephen Matheson has a summary right now, so you don’t have to wait for my column to come out.

You should still subscribe anyway. It’s pretty on shiny paper.

Optical Allusions

Jay Hosler has a new book out, Optical Allusions(amzn/b&n/abe/pwll). If you’re familiar with his other books, Clan Apis(amzn/b&n/abe/pwll) and The Sandwalk Adventures(amzn/b&n/abe/pwll), you know what to expect: a comic book that takes its science seriously. Hosler has a fabulous knack for building serious content into a light and humorous medium, just the kind of approach we need to get wider distribution of science into the culture.

This one has a strange premise. Wrinkles the Wonder Brain is an animated, naked brain working for the Graeae Sisters, and he loses the one eye they share between them — so he has to go on a quest to recover it. I know, it sounds like a stretch, but it works in a weird sort of way, and once you start rolling with it, you’ll find it works. Using that scenario to frame a series of encounters, Wrinkles meets Charles Darwin and learns how evolution could produce something as complex as an eye; talks about the sub-optimal design of retinal circuitry with a cow superhero; discovers sexual dimorphism with a crew of stalk-eyed pirates; learns about development of the eye from cavefish and a cyclops; chats with Mr Sun about the physics of radiation; there are even zombie G proteins and were-opsins in a lesson about shape changing. This stuff is seriously weird, and kids ought to eat it up.

It isn’t all comic art, either. Each chapter is interleaved with a text section discussing the details — you can read the whole thing through, skipping the text (like I did…), and then go back and get more depth and directions for future reading in the science. This is a truly seditious strategy. Suck ’em in with the entertainment value, and then hand ’em enough substance that they might just start thinking like scientists.

It’s all good stuff, too. A colleague and I have been considering offering an interdisciplinary honors course in physics and biology with the theme of the eye, specifically for non-science majors, and this book has me thinking it might make for a good text. It’ll grab the English and art majors, and provide a gateway for some serious discussions that will satisfy us science geeks. I recommend it for you, too — if you have kids, you should grab all of Hosler’s books. Even if you don’t have kids, you’ll learn a lot.

Jay Hosler also explains the intent of the project, and you can read an excerpt.

The Sunday morning session at the Oregon evo-devo symposium

[Since I had to fly away early this morning and missed all these talks, I had to rely on regular commenter DanioPhD to fill in the gaps … so here’s her summary:]

This morning’s final series of talks each focused on a different phylum, but the unifying theme was one of bridging the processes of microevolution and macroevolution. The first talk after breakfast (and a long night of Scotch-drinkin’ and story-swappin’ prior to that) was Bernie Degnan of the University of Queensland. He summarized his work on Amphimedon queenslandica, a sponge species developed as a model of a representative primitive metazoan. Sponges diverged from the metazoan lineage ca. 700 MYA and possess the most minimalist metazoan body plan–no nervous system, muscles, nor any discernible tissues in the adult body architecture. Their embryos, however, feature robust anterioposterior patterning, distinct cell types organized into tissues, and cell morphogenesis typical of more complex metazoans. These embryonic characteristics are achieved by a regulatory network of genes, which, while inactive in the adult sponge, strongly support the presence of similar molecules in the ancestral metazoan genome. A few million years after the divergence of porifera, metazoans were able to co-opt these molecular toolkits to build the diverse, molecularly and morphologically distinct tissues common to all bilaterians. PZ has previously written up one such sponge tale here describing the molecular precursors to a nervous system in the sponge genome. Precursors to pretty much every other developmental ‘big gun’, e.g, Hox genes, Pax genes, Wnts, Hedgehog, etc. are also present as a basic prototype, in the Amphimedon genome.

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The afternoon session at the Oregon evo-devo symposium

I’m going to get off a quick summary of this afternoon’s talks, then I have to run down to the poster session to find out what the grad students have been doing. Are we having fun yet? I’m going to collapse in bed tonight, and then unfortunately I have to catch an early flight back home, so I’m going to miss a lot of cool stuff tomorrow.

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The morning session at the Oregon evo-devo symposium

My brain is most wonderfully agitated, which is the good thing about going to these meetings. Scientists are perverse information junkies who love to get jarred by new ideas and strong arguments, and meetings like this are intense and challenging. I’ve only got a little time here before the next session, so let me rip through a short summary of my morning.

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