How I spent my morning at SICB

Here’s what I heard this morning. Wonderful stuff, all of it, and I’m having a grand time. This is a quick summary, and now I have to rush back to the meeting for more.

  • S. Kuratani: Craniofacial evolution from a developmental perspective. This was a lamprey and hagfish talk, comparing them to vertebrates. Hox gene expression patterns in lamprey, which assign anterior-posterior positional information, are very similar to those in vertebrates, but there is no temporal colinearity—timing is all over the place. There is no apparent dorsal-ventral patterning of Dlx gene expresion. They’ve collected a small number of hagfish eggs and embryos and gotten good histology (unlike much of the older work). The neural crest forms by delamination and migrates into the intersegmental spaces; it also looks very much like the vertebrate pattern.

  • A. Abzhanov: Pecking at the origin of avian morphological variation. This was the story recently published in Nature on the molecular basis of beak shapes in the Galapagos finches. In short, Bmp4 expression is important in regulating the width and depth of the beak, and Calmodulin expression affects the length; there is modularity in controlling the different beak dimensions. He promises to look in the future at a couple of different phenomena: a finch with a deep but narrow beak might help sort out the factors involved in those two dimensions, he’s examining Galapagos mockingbirds, and he’s looking at muscle-bone coupling, since muscles have to follow changes in bone structure.

  • J. Helms: Unraveling the basis for species specific facial form. More birds! Here the question is the role of differences in neural crest potential that affect beak/face morphology. In some cool transplant experiments, she put neural crest from a duck embryo (long, flat bill) into a quail (short, pointy beak), and found that the quail embryos from flatter, broader bills. The converse experiment, quail neural crest into a duck embryo, produced duck embryos with short, pointed beaks. Microarray analysis of the genes with differential patterns of expression in these two species revealed that the gene differences were turned on at the phylotypic stage, when the facial prominences were indistinguishable, and the gene expression patterns at the phenotypic stage were simply maintained or held over — there is a hidden variation at the phylotypic stage that precedes the morphological differentiation. She also showed some promising work for the future, looking at the molecular basis for beak variation in different breeds of pigeons.

  • Y. Yamamoto: Why cavefish lost their eyes? Natural selection or neutral theory. Hey, get the latest issue of Seed — I summarized this story already! Even shorter summary: it’s indirect selection for a pleiotropic tradeoff.

  • G. Schlosser: How old genes make a new head: recent insights into development and evolution of neural crest and placodes in vertebrates. This is a neat little story about structural innovations in the evolution of the head. In addition to brain and ectoderm in the head, you’ve got two other in-between populations of plastic and critical cells: the neural crest, migratory cells that contribute to a host of tissues, and placodes, or ectodermal thickenings, that form structures like ears, lenses, lateral lines (if you had a lateral line), etc. Both populations arise at the neural plate boundary. One evolutionary scenario is that the boundary population appeared first, and then later subsets specialized to form neural crest and placodes; this model emphasizes a common origin for both. Schlosser presented his evidence and argument that they were unique from the beginning: placods are derived from the ectodermal side of the boundary, while neural crest are from the neural side.

  • L.Z. Holland: Heads or tails? Amphioxus and the evolution of axial patterning in chordates. This was a very thorough summary of comparative patterns of early gene expression in Amphioxus and frogs, fish, and all those other excessively complicated derived forms. She made the case that in many ways Amphioxius is a basal chordate. and that it has great advantages for studying axis formation and gastrulation: cell movements are minimal and simple, and you can see gene expression domains untangled from all the smearing of the extensive cell movements we see in, for instance, a frog. Among the interesting conclusions are the idea that differential Wnt gene expression is instrumental in specifying the anterior and posterior ends of the animal, and that gradients of retinoic acid (which directly target Hox gene expression) sets up positional information along the A/P axis in between.

  • G.P. Wagner: Linking the evolution of genes with the evolution of morphological characters. This was the first of two talks that set a different tone. Wagner pointed out that the developmental approach favored so far is excellent for sorting out what genes affect what other genes and are associated with the morphological differences that arise during development, but that they don’t tell you what the molecular correlates of those differences are: what specifically are the sequence changes in the sonic hedgehog gene or its regulators that cause expansion of its domain in blind cavefish? He argued that evolutionary genetics can identify candidate molecular differences as part of a program of working out the precise details of evolutionary/developmental change. Readers of Carroll’s work and its emphasis on the importance of cis regulatory elements will be interested that Wagner goes the other way, and is much more interested in the evolution of transcription factors. He gave a couple of reasons: 1) the specificity of gene regulation arises from protein-protein interactions in regulatory complexes. While there is much emphasis on the conserved sites that bind DNA in an individual protein, that is a small part of the whole, and these proteins are often poorly conserved out in the 80% that doesn’t stick to DNA, but contacts other proteins. 2) Changes in these proteins change functionality in the organims in evolution. 3) There is evidence of directional selectivity in transcription factors. 4) It’s much easier to work with sequences that are actually expressed (ah, pragmatism!). In detail, he discussed the Hoxa13 gene in zebrafish, which has been duplicated again in teleosts into Hoxa13a and Hoxa13b forms. The Hoxa13a gene is associated with a quirky morphological feature of the cypriniform fish that we zebrafish people are familiar with, the caudal extension of the yolk sac. It’s an easily assayed feature, and Wagner showed that morpholino knockdowns of Hoxa13a cleanly suppressed yolk sac extension.

  • Lark G: Links between the genetic architecture and functional morphology of the canid skeleton. This talk was a radical break from the previous ones, and was almost purely genetics. I confess, I was starving and worn out and had to make a break for lunch, so I didn’t give this talk the attention it deserved or needed, but I’ll be looking into it later. Lark is looking at quantitative trait loci in Portuguese Water Dogs and the Red Fox, and arguing that there are conserved patterns of variability that have survived 10 million years of diverging evolution.

Oh, yeah, I think we’re doing a panel discussion about science media sometime today. I have heard that it’s at 4:00, but I think that’s wrong: the short outline of events lists a Media Workshop (I think that’s us!) from 7 to 9pm in the Curtis Room at the Hyatt. I’ll start panicking right after the science sessions end this afternoon and run around and find out what’s what, when, and where. They can’t start without me, can they? GrrlScientist wouldn’t abandon me, but I don’t know about that sneaky Lynch fellow.

Doushantuo embryos dethroned?

Almost ten years ago, there was a spectacular fossil discovery in China: microfossils, tiny organisms preserved by phosphatization, that revealed amazing levels of fine detail. These specimens were identified as early animal embryos on the basis of a number of properties.

  • The cells were dimpled and shaped by adjoining cells, suggesting a flexible membrane—not a cell wall. This rules out algae, fungi, and plants.
  • The number of cells within each specimen was usually a power of 2. This is something we typically see in cleaving embryos, the sequence from 1 to 2 to 4 to 8 to 16 cells.
  • They were big. Typical somatic cells in animals are 5-10 µm in diameter, but ova can be a millimeter or more in diameter, and individual blastomeres (the cells in the cleavage stage embryo) can be several hundred µm across. These cells and the whole assemblage were in that size range.
  • The individual cells were uniform in size, as seen in many cleavage stage embryos, and contained organelles arranged in a consistent pattern.
  • They were often found encapsulated in a thin membrane, similar to the protective membrane around embryos.

There are some concerns about the interpretation, though. One troubling aspect of their distribution is that they are all only in the cleavage stage: we don’t see any gastrulas, the stage at which embryonic cells undergo shape changes and begin to move in a specific, directed manner. Studies of taphonomy (analyses of the processes that lead to fossilization) have shown that these later stages are particularly difficult to preserve, which potentially explains why we’re seeing a biased sample. Another unusual bias in the sample is that all of the embryos exhibit that regularity of division that produces equal-sized blastomeres—yet many invertebrate embryos have early asymmetric cleavages that produce recognizable, stereotyped distributions of cells. That asymmetry could be a feature that evolved late, but at the same time, some of the fossils were described as resembling molluscan trefoil embryos. Why aren’t the examples of early asymmetry translated into a later asymmetry?

Now there’s another reason to question the identity of the Doushantuo microfossils: they may be bacterial.

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Evolution of vascular systems

Once upon a time, in Paris in 1830, Etienne Geoffroy St. Hilaire debated Georges Léopole Chrétien Frédéric Dagobert,
Baron Cuvier on the subject of the unity of organismal form. Geoffroy favored the idea of a deep homology, that all animals shared a common archetype: invertebrates with their ventral nerve cord and dorsal hearts were inverted vertebrates, which have a dorsal nerve cord and ventral hearts, and that both were built around or within an idealized vertebra. While a thought-provoking idea, Geoffroy lacked the substantial evidence to make a persuasive case—he had to rely on fairly superficial similarities to argue for something that, to those familiar with the details, appeared contrary to reason and was therefore unconvincing. Evolutionary biology has changed that — the identification of relationships and the theory of common descent has made it unreasonable to argue against origins in a common ancestor — but that difficult problem of homology remains. How does one argue that particular structures in organisms divided by 600 million years of change are, in some way, based on the same ancient organ?

One way is sheer brute force. Characterize every single element of the structures, right down to the molecules of which they are made, and make a quantitative argument that the weight of the evidence makes the conclusion that they are not related highly improbable. I’ll summarize here a recent paper that strongly supports the idea of homology of the vertebrate and arthropod heart and vascular systems.

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Last gasp of my development course

Today, I gave my final lecture in developmental biology this term. We have one more class session which will be a final discussion, but I’m done yapping at them. Since I can’t possibly teach them everything, I offered some suggestions on what to read next, if they’re really interested in developmental biology. They’ve gotten the fundamentals of the dominant way of looking at development now, that good ol’ molecular genetics centered modern field of evo-devo, but I specifically wanted to suggest a few titles to shake them up a little bit and start thinking differently.

  • For the student who is interested in the field, but doesn’t feel that development is necessarily their discipline, I recommended Richard Lewontin’s The Triple Helix: Gene, Organism, and Environment(amzn/b&n/abe/pwll). It’s short, it’s easy, and it’s a good counterweight to the usual gene-happy approach we see in developmental biology.

  • Since we are a liberal arts university, and we value a philosophical approach in addition to the usual bluntly pragmatic tactics we follow in the sciences, I also recommended one work of philosophy: The Ontogeny of Information: Developmental Systems and Evolution(amzn/b&n/abe/pwll), by Susan Oyama. That one is not an easy read, except maybe to the more academically minded. I mentioned that Developmental Systems Theory does not have the powerful research program that is making evo-devo so successful, but it’s still a usefully different way of thinking about the world.

  • If any of my students wanted to go on to grad school in developmental biology, and hoped to make it a profession, I had to tell them that they are required to read D’Arcy Wentworth Thompson’s On Growth and Form(amzn/b&n/abe/pwll). It’s old, it’s a little bit weird, but it’s still a major touchstone in the discipline.

  • Lastly, I told them that there was one more book they had to read if they wanted to consider a career in development: Developmental Plasticity and Evolution(amzn/b&n/abe/pwll), by Mary Jane West-Eberhard. If I were a young graduate student in the field right now, I think I could just open that book to a random page and find an interesting and challenging research problem right there. I might have to flip through a few dozen pages before I found one that wasn’t impossibly hard, but hey, it’s one of those books that fills you in on the array of issues that people are worrying over at the edge of the science.

I don’t think any of these would be a good foundation for an undergraduate course (either Thompson or West-Eberhard or Oyama would probably have a lethal effect on the brain of any unprepared student trying to plow through them), but they’d be great mind-stretchers for any student planning to move on.

So all my lecturing is done for the term, and all that’s left are monstrous piles of grading that will grow ominously in the next week and a half even as I struggle to keep up, and then I can try to polish it all off by Cephalopodmas.

Notch

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One of my favorite signal transduction pathways (what? You didn’t know that true nerds had favorite molecular pathways?) is the one mediated by the receptor Notch. Notch is one of those genes in the metazoan toolkit that keeps popping up in all kinds of different contexts—it’s the adjustable wrench of the toolbox, something that handles a general problem very well and therefore gets reused over and over again, and the list of places where it is expressed in Drosophila is impressive.

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Animations of urogenital development

I found these on youtube, a couple of nice cartoony animations of the development of the urogenital system. This is one of the weirder modules in organogenesis, I think; many strange things go on that are relics of ancestral states. We actually build three pairs of kidneys—pronephros, mesonephros, and metanephros—and throw each one away in succession, except the last. Both sexes form paramesonephric (or Müllerian) ducts, in blue in the animation, and these form the core of the female plumbing, but again, males basically throw it away and use a more primitive duct (the mesonephric or Wolffian ducts, in green). It’s a bizarre way to construct an organ, but what’s going on is that we have two systems, excretion and reproduction, tied together in ways that constrain the other’s development, and each is building on elements of the other.

It’s in French, but that shouldn’t slow anyone down. It’s easy to figure out what “paramesonephrique” must refer to, for instance.

Males:

Females:

Womb with a view

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The BBC is going to be showing a program with images of developing embryos (there are some galleries online) generated from ultrasound, cameras inserted into the uterus, and largely, computer-generated graphics. It’s all very pretty, and I hope it will also be shown in my country, but…these pictures violate all the rules of scientific imaging. The images are clearly generated by imposing artistic decisions derived from the conventions of computer animation work onto the data that was collected—I can’t tell what details in these embryos were actually imaged, and which were added by the CGI guy.

I can tell you that the way they’re rendered as free-floating individuals suspended in great airy spaces lit by a glow through distant membranes like stained glass windows is complete hokum, and the textures just look all wrong. They ought to be slimy, wrapped in membranes, and enveloped closely in maternal tissues. I hope the program includes some honest description of the process of making the images, with before and after photos, so viewers can see how much of the work is interpolated and artificially added.

MADS boxes, flower development, and evolution

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I’ve been writing a fair amount about early pattern formation in animals lately, so to do penance for my zoocentric bias, I thought I’d say a little bit about homeotic genes in plants. Homeotic genes are genes that, when mutated, can transform one body part into another—probably the best known example is antennapedia in Drosophila, which turns the fly’s antenna into a leg.

Plants also have homeotic genes, and here is a little review of flower anatomy to remind everyone of what ‘body parts’ we’re going to be talking about. The problem I’ll be pursuing is how four different, broadly defined regions of the flower develop, and what that tells us about their evolution.

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The sea urchin genome

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Oh happy day, the Sea Urchin Genome Project has reached fruition with the publication of the full sequence in last week’s issue of Science. This news has been all over the web, I know, so I’m late in getting my two cents in, but hey, I had a busy weekend, and and I had to spend a fair amount of time actually reading the papers. They didn’t just publish one mega-paper, but they had a whole section on Strongylocentrotus purpuratus, with a genomics mega-paper and articles on ecology and paleogenomics and the immune system and the transcriptome, and even a big poster of highlights of sea urchin research (but strangely, very little on echinoderm development). It was a good soaking in echinodermiana.

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Dissecting embryos from half a billion years ago

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There is a treasure trove in China: the well-preserved phosphatized embryos of the Doushantuo formation, a sampling of the developmental events in ancient metazoans between 551 and 635 million years ago. These are splendid specimens that give us a peek at some awesomely fragile organisms, and modern technology helps by giving us new tools, like x-ray computed tomography (CT), scanning electron microscopy (SEM), thin-section petrography, synchrotron X-ray tomographic microscopy (SRXTM), and computer-aided visualization, that allow us to dig into the fine detail inside these delicate specimens and display and manipulate the data. A new paper in Science describes a survey of a large collection of these embryos, probed with these new techniques, and rendered for our viewing pleasure…that is, we’ve got pretty pictures!

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