It’s not just the genes, it’s the links between them


Once upon a time, I was one of those nerds who hung around Radio Shack and played about with LEDs and resistors and capacitors; I know how to solder and I took my first old 8-bit computer apart and put it back together again with “improvements.” In grad school I was in a neuroscience department, so I know about electrodes and ground wires and FETs and amplifiers and stimulators. Here’s something else I know: those generic components in this picture don’t do much on their own. You can work out the electrical properties of each piece, but a radio or computer or stereo is much, much more than a catalog of components or a parts list.


Electronics geeks know the really fun stuff starts to happen when you assemble those components into circuits. That’s where the significant work lies and where the actual function of the device is generated—take apart your computer, your PDA, your cell phone, your digital camera and you’ll see similar elements everywhere, and the same familiar components you can find in your Mouser catalog. As miniaturization progresses, of course, more and more of that functionality is hidden away in tiny integrated circuits…but peel away the black plastic of those chips, and you again find resistors and transistors and capacitors all strung together in specific arrangements to generate specific functions.

We’re discovering the same thing about genomes.

The various genome projects have basically produced for us a complete parts list—a catalog of bits in our toolbox. That list is incredibly useful, of course, and represents an essential starting point, but how a genome produces an organism is actually a product of the interactions between genes and gene products and the cytoplasm and environment, and what we need next is an understanding of the circuitry: how Gene X expression is connected to Gene Y expression and what the two together do to Gene Z. Some scientists are suggesting that an understanding of the circuitry of the genome is going to explain some significant evolutionary phenomena, such as the Cambrian explosion and the conservation of core genetic processes.

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Hemichordate evo-devo

Every biology student gets introduced to the chordates with a list of their distinctive characteristics: they have a notochord, a dorsal hollow nerve cord, gill slits, and a post-anal tail. The embryonic stage in which we express all of these features is called the pharyngula stage—it’s often also the only stage at which we have them. We terrestrial vertebrates seal off those pharyngeal openings as we develop, while sea squirts throw away their brains as an adult.


The chordate phylum has all four of those traits, but there is another extremely interesting phylum that has some of them, the hemichordates. The hemichordates are marine worms that have gill slits and a stub of a tail. They also have a bundle of nerves in the right place to be a dorsal nerve cord, but the latest analyses suggest that it’s not discrete enough to count—they have more of a diffuse nerve net than an actual central nervous system. They don’t really have a notochord, but they do have a stiff array of cells in their proboscis that vaguely resembles one. They really are “half a chordate” in that they only partially express characters that are defining elements of the chordate body plan. Of course, they also have a unique body plan of their own, and are quite lovely animals in their own right. They are a sister phylum to the chordates, and the similarities and differences between us tell us something about our last common ancestor, the ur-deuterostome.

Analyzing morphology is one approach, but this is the age of molecular biology, so digging deeper and comparing genes gives us a sharper picture of relationships. This is also the early days of evo-devo, and an even more revealing way to examine related phyla is to look at patterns of gene regulation—how those genes are turned on and off in space and time during the development of the organism—and see how those relate. Gerhart, Lowe, and Kirschner have done just that in hemichordates, and have results that strengthen the affinities between chordates and hemichordates. (By the way, Gerhart and Kirschner also have a new book out, The Plausibility of Life (amzn/b&n/abe/pwll), which I’ll review as soon as I get the time to finish it.)

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