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.

Superclades of the Cambrian

Allow me to introduce you to a whole gigantic superclade with which many of you may not be familiar, and some other groups in the grand hierarchy of animal evolution that I’ve mentioned quite a few times before, but would like to clear the fog with some simple definitions. Consider this a brief primer in some major animal groupings. Here’s a greatly simplified cladogram; I’ve left off quite a few groups to make the story simple.

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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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Genetics of virgin birth in the Komodo dragon

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I’ve just read the article on the parthenogenetic Komodo dragons in Nature, and it’s very cool. They’ve analyzed the genetics of the eggs that have failed to develop (the remainder are expected to hatch in January) and determined that they were definitely produced without the aid of a male.

We analysed the parentage of the eggs and offspring by genetic fingerprinting. In the clutches of both females, we found that all offspring produced in the absence of males were parthenogens: the overall combined clutch genotype reconstructed that of their mother exactly. Although all offspring were homozygous at all loci, they were not identical clones. Parthenogenesis was therefore confirmed by exclusion (clutches had different alleles from potential fathers) and by the fact that the probability of obtaining a clutch of homozygous individuals after sexual reproduction was very low (P<<0.0001). Sungai’s resumption of sexual reproduction confirmed that parthenogenesis was not a fixed reproductive trait (that is, it is facultative) and that asexual reproduction is likely to occur only when necessary.

That line about “all offspring were homozygous at all loci, they were not identical clones” might need a little more explanation. Mama Dragon is heterozygous at some loci, but the meiotic mechanism that produces a diploid egg means that one cleavage (most likely the second meiotic cleavage) was suppressed, so both homologous chromosomes in the resultant ovum were derived from the same replicated DNA strand. They are not clones of the mother, because they are all homozygous while she was heterozygous; they are not identical, because which of each of the paired homologous chromosomes was passed on to an individual is random.

(I’m a little confused by the statement that they offspring are homozygous at all loci, though; that would imply that there was no crossing over at all in meiosis I, which doesn’t sound right. There ought to be reduced heterozygosity but not complete homozygosity, unless reptiles are weirder than I thought.)

The other useful snippet of information is that sex determination in these reptiles is of the WW/WZ type, where the females are the heterogametic sex. Since all of the progeny of parthenogenesis are homozygous, they are all of the homogametic genotype, and therefore male.

Parthenogenesis can also bias the sex ratio: in Varanus species, females have dissimilar chromosomes (Z and W), whereas the combination ZZ produces males10, so the parthenogenetic mechanism can produce only homozygous (ZZ or WW) individuals and therefore no females.

This has theological implications, obviously. We can now understand how a female could give rise to a male by parthenogenesis: Mary Mother of God must have been a heterogametic reptoid. David Icke will be so pleased.

Watts PC, Buley KR, Sanderson S, Boardman W, Ciofi C, Gibson R (2006) Parthenogenesis in Komodo dragons. Nature 444:1021-1022.

Spongeworthy genes

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What are the key ingredients for making a multicellular animal, or metazoan? A couple of the fundamental elements are:

  • A mechanism to allow informative interactions between cells. You don’t want all the cells to be the same, you want them to communicate with one another and set up different fates. This is a process called cell signaling and the underlying process of turning a signal into a different pattern of gene or metabolic activity is called signal transduction.

  • Patterns of differing cell adhesion. But of course! The cells of your multicellular animal better stick together, or the whole creature will fall apart. This can also be an important component of morphogenesis: switching on a particular adhesion molecule (by way of cell signaling, naturally) can cause one subset of cells to stick to one another more strongly than to their neighbors, and mechanical forces will then sort them out into different tissues.

These are extremely basic functions, sort of a minimal set of cellular activities that we need to have in place in order to even begin to consider evolving a metazoan. Fortunately for our evolutionary history, these are also useful functions for a single celled organism, and while the metazoa may have elaborated upon them to a high degree, there’s nothing novel about the general processes in our make-up. The principles of signaling and transduction were first worked out in bacteria, and anyone who has a passing acquaintance with immunology will know about the adhesive properties of bacteria, and their propensity for modulating that adhesion to build complexes called biofilms.

So let’s take a look at the distribution of signaling and adhesion molecules in single-celled organisms, multicellular animals, and most interestingly, a group that is close to the division between the two (although more on the side of multicellularity), the sponges.

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We need a thousand Sagans

I’m joining in on the Carl Sagan Memorial blog-a-thon, but I can’t offer unstinting praise. Sagan wrote about biology now and then, and every time he irritated me; I always felt like arguing with him about some detail that bugged me, and I think that was actually among his virtues—he was a scientist you cared enough about to want to criticize, and he also addressed questions wide and deep enough that we all felt like this curious astronomer was touching on our part of the universe.

Here’s one example, a short excerpt from my favorite Sagan book, The Demon-Haunted World: Science as a Candle in the Dark(amzn/b&n/abe/pwll).

The blueprints, detailed instructions, and job orders for building you from scratch would fill about 1,000 encyclopedia volumes if written out in English. Yet every cell in your body has a set of these encyclopedias. A quasar is so far away that the light we see from it began its intergalactic voyage before the Earth was formed. Every person on Earth is descended from the same not-quite-human ancestors in East Africa a few million years ago, making us all cousins.

Whenever I think about any of these discoveries, I feel a tingle of exhilaration. My heart races. I can’t help it. Science is an astonishment and a delight. Every time a spacecraft flies by a new world, I find myself amazed. Planetary scientists ask themselves: “Oh, is that the way it is? Why didn’t we think of that?” But nature is always more subtle, more intricate, more elegant than what we are able to imagine. Given our manifest limitations, what is surprising is that we have been able to penetrate so far into the secrets of Nature.

At the same time that I want to tear apart his annoying analogy of the genome to a set of encyclopedias, while I deplore the incessant focus on human evolution rather than, say, the beauty of a sponge or a beetle, there’s one thing he did well: he represented the joy we can find in the natural world. That’s something we don’t communicate enough, I think, that science is this wonderful, powerful, far-reaching enterprise that reaches farther into the glories of the universe than any other idea that has ever occurred to humanity. That’s something he made explicit in the title of his book, too — the way we will beat back the darkness is to illuminate it with science.

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.