Hox cluster disintegration

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Hox genes are metazoan pattern forming genes—genes that are universally associated with defining the identities of regions of the body. There are multiple Hox genes present, and one of their unusual properties is that they are clustered and expressed colinearly. That is, they are found in ordered groups on the chromosome, and that the gene on one end is typically turned on first and expressed at the head end of the embryo, the next gene in order is turned on slightly later and expressed further back, and so on in sequence. That the tidy sequential order on the chromosome is associated with an equally tidy spatial and temporal pattern of expression in the body has always been one of the more fascinating aspects of these genes, and they are one of the few cases where we see an echo of phenotypic form comprehensibly laid out in the DNA.

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Patterning the nervous system with Bmp

I’m a little surprised at the convergence of interest in this news report of a conserved mechanism of organizing the nervous system—I’ve gotten a half-dozen requests to explain what it all means. Is there a rising consciousness about evo-devo issues? What’s caused the sudden focus on this one paper?

It doesn’t really matter, I suppose. It’s an interesting observation about how both arthropods and vertebrates seem to partition regions along the dorso-ventral axis of the nervous system using exactly the same set of molecules, a remarkable degree of similarity that supports the idea of a common origin. Gradients of a molecule called Bmp may be the primitive mechanism for establishing dorso-ventral polarity in animals.

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What? No cephalopod genome project?

I was reading a review paper that was frustrating because I wanted to know more—it’s on the evolution of complex brains, and briefly summarizes some of the current confusion about what, exactly, is involved in building a brain with complex problem solving ability. It’s not as simple as “size matters”—we have to jigger the formulae a fair bit to take into account brain:body size ratios, for instance, to get humans to come out on top, and maybe bulk is an inaccurate proxy for more significant matters, such as the number of synapses and nerve conduction velocities.

There’s also a growing amount of literature that takes genomic approaches, searching for sequences that show the signatures of selection, and plucking those out for analysis. There have been some provocative results from that kind of work, finding some candidate genes like ASPM, but another of the lessons of that kind of work seems to be that evolution has been working harder on our testis-specific genes than on our brains.

The encouraging part of the paper is that the authors advocate expanding our search for the correlates of intelligence with another group of organisms with a reputation for big brains, but brains that have evolved independently of vertebrates’. You know what I’m talking about: cephalopods!

The Cephalopoda are an ancient group of mollusks originating in the late Cambrian. Ancestors of modern coleoid cephalopods (octopus and squid) diverged from the externally-shelled nautiloids in the Ordovician, with approximately 600 million years of separate evolution between the cephalopod and the vertebrate lineages. The evolution of modern coleoids has been strongly influenced by competition and predatory pressures from fish, to a degree that the behavior of squid and octopus are more akin to that of fast-moving aquatic vertebrates than to other mollusks. Squid and octopuses are agile and active animals with sophisticated sensory and motor capabilities. Their central nervous systems are much larger than those of other mollusks, with the main ganglia fused into a brain that surrounds the esophagus with additional lateral optic lobes. The number of neurons in an adult cephalopod brain can reach 200 million, approximately four orders of magnitude higher than the 20-30,000 neurons found in model mollusks such as Aplysia or Lymnaea. Cephalopods exhibit sophisticated behaviors a number of studies have presented evidence for diverse modes of learning and memory in Octopus and cuttlefish models. This learning capacity is reflected in a sophisticated circuitry of neural networks in the cephalopod nervous system. Moreover, electrophysiological studies have revealed vertebrate-like properties in the cephalopod brain, such as compound field potentials and long-term potentiation. Thus cephalopods exhibit all the attributes of complex nervous systems on the anatomical, cellular, functional and behavioral levels.

Unfortunately, the purpose of the paper is to highlight an unfortunate deficiency in our modern research program: there is no cephalopod genome project. The closest thing to it is an effort to sequence the genome of another mollusc, Aplysia, which is a very good thing—Aplysia is a famous and indispensable subject of much research in learning and memory—but it’s no squid. The authors are advocating additional work on another animal, one with a more elaborate brain.

A parallel effort on a well-studied octopus or squid should provide insights on the evolutionary processes that allowed development of the sophisticated cephalopod nervous system. For example, have cephalopods undergone accelerated evolution in specific nervous system genes, as has been suggested for primates? Have specific gene families undergone expansion in the cephalopod lineage and are these expressed in the nervous system? Are there clear parallels in accelerated evolution, gene family expansion, and other evolutionary processes between cephalopods and vertebrates? Answers to these and related questions will provide useful perspectives for evaluation of the processes thought to be involved in the evolution of the vertebrate brain.

I’m all for it—let’s see a Euprymna genome project!

Jaaro H, Fainzilber M (2006) Building complex brains—missing pieces in an evolutionary puzzle. Brain Behav Evol 68(3):191-195.

Molecular machines!

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If you’ve ever wondered what the heck Behe was smoking when he claims there are literal trucks trundling about on literal highways with literal traffic signals inside of cells, well, I don’t have an answer for you…but there is a wonderful Flash movie that will show you the Inner Life of a Cell so you can see what “molecular machines” look like, more or less. It’s a spectacular show. What you’ll see is the series of events that transpire when a lymphocyte encounters a cell surface signal that triggers emigration out of a capillary and into other tissues; it zooms rather abruptly from a cellular view to the molecules on the surface interacting with one another, then into the interior of the cell to see the response. All kinds of cool stuff fly by: actin and microtubule assembly and disassembly, kinesin-mediated vesicle transport, protein synthesis on ribosomes, ER processing, vesicle fusion, etc.

I do have a couple of gripes, though. One is an understandable shortcut: the cell is far too uncluttered, and events proceed in too directed a manner—there ought to be much more stochastic noise at the molecular level. We’re seeing chemistry in action, after all. Another is that there is no explanation at all for anything we’re seeing, it’s simply a weird and trippy voyage into a subcellular world. This clip was created under the auspices of Harvard scientists, so I hope there is a viewing guide somewhere, otherwise it’s only going to be appreciated by people who have already read Molecular Biology of the Cell(amzn/b&n/abe/pwll). I think it also needed a disclaimer somewhere that this video too is a visual metaphor for cellular activity.

But I’m being picky. Otherwise, it’s an excellent introduction to the profound weirdness of the processes going on inside a cell.

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.

Ancient rules for Bilaterian development

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Assuming that none of my readers are perfectly spherical, you all possess notable asymmetries—your top half is different from your bottom half, and your front or ventral half is different from you back or dorsal half. You left and right halves are probably superficially somewhat similar, but internally your organs are arranged in lopsided ways. Even so, the asymmetries are relatively specific: you aren’t quite like that Volvox to the right, a ball of cells with specializations scattered randomly within. People predictably have heads on top, eyes in front, arms and legs in useful locations. This is a key feature of development, one so familiar that we take it for granted.

I’d go so far as to suggest that one of the most important events in our evolutionary history was the basic one of taking a symmetrical ball of cells and imposing on it a coordinate system, creating positional information that allowed cells to have specific identities in particular places in the embryo. When the first multicellular colony of identical cells set aside a particular patch of cells to carry out a particular function, say putting one small subset in charge of reproduction, that asymmetry became an anchor point for establishing polarity. If cells could then determine how far away they were from that primitive gonad, evolution could start shaping function by position—maybe cells far away from the gonad could be dedicated to feeding, cells in between to transport, etc., and a specialized multicellular organism could emerge. Those patterns are determined by interactions between genes, and we can try to unravel the evolutionary history of asymmetry with comparative studies of regulatory molecules in early development.

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Flap those gills and fly!

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I am going mildly nuts right now—somehow, I managed to arrange things so multiple deadlines hit me on one day: tomorrow. I’ve got a new lecture to polish up for our introductory biology course, a small grant proposal due, and of course, tomorrow evening is our second Café Scientifique. Let’s not forget that I also have a neurobiology lecture to give this afternoon, and I owe them a stack of grading which is not finished yet. I’m really looking forward to Wednesday.

Anyway, so my new lecture for our introductory biology course is on…creationism, yuck. What I’m planning to do is to describe some of the most common creationist arguments and then give a biologist’s rebuttal. Creationism is really a waste of our class time, but using it to explain some general concepts that any informed biologist should understand (and that the creationists, including Mike Behe, are astonishingly clueless about) will make it a little more productive, I hope. We’ll find out tomorrow.

One of the common creationist claims I plan to shoot down is the whole idea of “irreducible complexity” as an obstacle to evolution. I was going to bring up two ideas that invalidate it: the principle of scaffolding (which I discussed here), and exaptation, in which features evolved for some other purpose than the one that they play in an organism we observe today. I was looking for a good example, and then John Wilkins fortuitously sent me a paper that filled the bill (we evilutionists, you know, are sneakily sending each other data behind the scenes to help in our assault on ignorance. We’re devious that way.)

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