How to make a tadpole

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I’ve been tinkering with a lovely software tool, the 3D Virtual Embryo, which you can down download from ANISEED (Ascidian Network of In Situ Expression and Embryological Data). Yes, you: it’s free, it runs under Java, and you can get the source and versions compiled for Windows, Linux, and Mac OS X. It contains a set of data on ascidian development—cell shapes, gene expression, proteins, etc., all rendered in 3 dimensions and color, and with the user able to interact with the data, spinning it around and highlighting and annotating. It’s beautiful!

Unfortunately, as I was experimenting with it, it locked up on me several times, so be prepared for some rough edges. I’m putting it on my list of optional labs for developmental biology—3-D visualization of morphological and molecular data is one of those tools that are going to be part of the future of embryology, after all—but it isn’t quite reliable enough for general student work. At least not in my hands, anyway. If one of my students were to work through the glitches and figure out how to avoid them, though, it could be a useful adjunct to instruction in chordate development.

If you want to play with it, I’ll give you a quick overview of what’s going on in the dataset. A paper by Munro et al. has used these kinds of data to summarize key events in the transformation of a spherical ball of cells into an elongate, swimming tadpole larva.

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Developmental Biology 4181: Week 1

I’m teaching a course in developmental biology this term, and as part of the coursework, I’m making students blog. The idea is to force them to ferret out instances of development in popular culture, in their personal experience, and/or in their reading—I’m not asking for treatises, but simply short articles that let me know their eyes are open. This year I’m also encouraging outsiders to take a look at and comment on what they’re saying, so every week I’ll be posting a round-up of links to the developmental biology blog…and here they are:

Feel free to comment on any of them if the mood strikes you, but I am going to be particularly protective of my students, so I insist on only constructive comments. I will ruthlessly delete anything abusive or irrelevant or otherwise distracting.

One other thing we’re doing in the class is working through Carroll’s Endless Forms Most Beautiful, and before each discussion I ask the students to write up short summaries of the reading. Tomorrow, we’re going over chapter 1 and 2, and there are six different summaries up on the site right now:

A,
B,
C,
D,
E, and
F (no, those are most definitely not the grades!). I’ll usually have these things linked up a little earlier before the class, but I gave the students extra slack this time since it was a holiday week. Comments and questions there are also appreciated—if there’s something you think the students ought to bring up in the discussion, let ’em know!

Generating right-left asymmetries

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We’re only sorta bilaterally symmetric: superficially, our left and right halves are very similar, but dig down a little deeper, and all kinds of interesting differences appear. Our hearts are larger on the left than the right, our appendix is on the right side, even our brains have significant differences, with the speech centers typically on the left side. That there is asymmetry isn’t entirely surprising—if you’ve got this long coil of guts with a little appendix near one end, it’s got to flop to one side or the other—but what has puzzled scientists for a long time is how things so consistently flop over in the same direction in individual after individual. There has to be some deep-seated mechanism that biases developmental events to favor one direction over the other. We know many of the genes involved in asymmetry, but what is the first step that skews development to make consistent asymmetrical choices?

In mammals, we’re getting close to the answer. And it looks to be beautifully elegant—it’s a simple trick to convert an anterior-posterior difference into a left-right one.

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Symmetry breaking and genetic assimilation

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How do evolutionary novelties arise? The conventional explanation is that the first step is the chance formation of a genetic mutation, which results in a new phenotype, which, if it is favored by selection, may be fixed in a population. No one sensible can seriously argue with this idea—it happens. I’m not going to argue with it at all.

However, there are also additional mechanisms for generating novelties, mechanisms that extend the power of evolutionary biology without contradicting our conventional understanding of it. A paper by A. Richard Palmer in Science describes the evidence for an alternative mode of evolution, genetic assimilation, that can be easily read as a radical, non-Darwinian, and even Lamarckian pattern of evolution (Sennoma at Malice Aforethought has expressed concern about this), but it is nothing of the kind; there is no hocus-pocus, no violation of the Weissmann barrier, no sudden, unexplained leaps of cause-and-effect. Comprehending it only requires a proper appreciation of the importance of environmental influences on development and an understanding that the genome does not constitute a descriptive program of the organism.

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The Politically Incorrect Guide to Darwinism and Intelligent Design: Chapter 3: Simply incorrect embryology

This article is part of a series of critiques of Jonathan Wells’ The Politically Incorrect Guide to Darwinism and Intelligent Design that will be appearing at the Panda’s Thumb over the course of the next week or so. Previously, I’d dissected the summary of chapter 3. This is a longer criticism of the whole of the chapter, which is purportedly a critique of evo-devo.

Jonathan Wells is a titular developmental biologist, so you’d expect he’d at least get something right in his chapter on development and evolution in The Politically Incorrect Guide to Darwinism and Intelligent Design, but no: he instead uses his nominal knowledge of a complex field to muddle up the issues and misuse the data to generate a spurious impression of a science that is unaware of basic issues. He ping-pongs back and forth in a remarkably incoherent fashion, but that incoherence is central to his argument: he wants to leave the reader so baffled about the facts of embryology that they’ll throw up their hands and decide development is all wrong.

Do not be misled. The state of Jonathan Wells’ brain is in no way the state of the modern fields of molecular genetics, developmental biology, and evo-devo.

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Morphological embryology of a sea spider

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Tanystylum bealensis male, ventral view, showing eggs and instar 1 (protonymphon) on
ovigerous legs. in. 1, instar 1 (protonymphon); pa, palp; pr, proboscis; 1, first walking leg; 2, second
walking leg; 3, third walking leg; 4, fourth walking leg.

Surely, you haven’t had enough information about pycnogonids yet, have you? Here’s another species, Tanystylum bealensis, collected off the British Columbian coast. That’s a ventral view of the male, and those bunches of grapes everywhere are eggs and babies—males do the childcare in this group. These animals also live in relatively shallow water, in the lower intertidal zone, so it was possible to collect thousands of them and develop a complete staging series. Below the fold I’ve put some illustrations of the larvae, which are even cuter.

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Regulatory evolution of the Hox1 gene

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I’ve been getting swamped with links to this hot article, “Evolution reversed in mice,” including one from my brother (hi, Mike!). It really is excellent and provocative and interesting work from Tvrdik and Capecchi, but the news slant is simply weird—they didn’t take “a mouse back in time,” nor did they “reverse evolution.” They restored the regulatory state of one of the Hox genes to a condition like that found half a billion years ago, and got a viable mouse; it gives us information about the specializations that occurred in these genes after their duplication early in chordate history. I am rather amused at the photos the news stories are all running of a mutant mouse, as if it has become a primeval creature. It’s two similar genes out of a few tens of thousands, operating in a modern mammal! The ancestral state the authors are studying would have been present in a fish in the Cambrian.

I can see where what they’ve actually accomplished is difficult to explain to a readership that doesn’t even know what the Hox genes are. I’ve written an overview of Hox genes previously, so if you want to bone up real quick, go ahead; otherwise, though, I’ll summarize the basics and tell you what the experiment really did.

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Evolution of median fins

Often, as I’ve looked at my embryonic zebrafish, I’ve noticed their prominent median fins. You can see them in this image, although it really doesn’t do them justice—they’re thin, membranous folds that make the tail paddle-shaped.

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These midline fins are everywhere in fish—lampreys have them, sharks have them, teleosts have them, and we’ve got traces of them in the fossil record. Midline fins are more common and more primitive, yet usually its the paired fins, the pelvic and pectoral fins, that get all the attention, because they are cousins to our paired limbs…and of course, we completely lack any midline fins. A story is beginning to emerge, though, that shows that midline fin development and evolution is a wonderful example of a general principle: modularity and the reuse of hierarchies of genes.

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Voices of science

If you’re at work, I hope you have headphones; if you don’t, check in once you get home. Here are a couple of audio recordings of good science.