Scientists…in disagreement!

Yesterday, I reposted an article on homology within the neck and shoulder, which describes an interesting technique of using patterns of gene expression to identify homologous cellular pools; the idea is that we can discern homology more clearly by looking more closely at the molecular mechanisms, rather than focusing on final morphology and tissue derivation. Trust me, if you don’t want to read it all—it’s cool stuff, and one of the interesting points they make is that they’ve traced the fate of a particular bone not found in us mammals, but common in our pre-synapsid ancestors, the cleithrum. They argue from a common cellular origin that this bone has been reshaped into a ridge on our shoulder blade, the scapular spine.

As many readers might know, though, the word “homology,” especially when coupled with a novel technique for its determination, is always good for an argument. This one is no exception.

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Odontogriphus omalus

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(click for larger image)

A new report in this week’s Nature clears up a mystery about an enigmatic fossil from the Cambrian. This small creature has been pegged as everything from a chordate to a polychaete, but a detailed analysis has determined that it has a key feature, a radula, that places it firmly in the molluscan lineage. It was a kind of small Cambrian slug that crawled over matted sheets of algae and bacteria, scraping away a meal.

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Development, medicine, and evolution of the neck and shoulder

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Neck anatomy has long terrified me. Way back when I was a grad student, my lab studied the organization and development of the hindbrain, which was relatively tidy and segmental; my research was studying the organization and development of the spinal cord, which was also tidy and segmental. The cervical region, though, was complicated territory. It’s a kind of transitional zone between two simple patterns, and all kinds of elaborate nuclei and new cell types and structural organizations flowered there. I drew a line at the fifth spinal segment and said I’m not even going to look further anteriorly…good thing, too, or I’d probably still be trying to finish my degree.

Fortunately, Matsuoka et al. were braver than I was and they have applied some new molecular techniques to sort out some of the details of how the neck and shoulder are assembled. This is a developmental study of how the muscles and bones of the shoulder girdle and neck are derived, and what they’ve identified is 1) a fairly simple rule for part of the organization, 2) an explanation for some human pathologies, and 3) some interesting observations about evolution. It is very cool to find a paper that ties together molecular genetics, development, paleontology, and medicine together so inseparably.

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Bicoid evolution

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I’ve written about this fascinating Drosophila gene, bicoid, several times before. It’s a maternal effect gene, a gene that is produced by the mother and packaged into her eggs to drive important early events in development, in this case, establishing polarity, or which end of the egg is anterior (bicoid specifies which end of the egg will form the fly’s head). Bicoid is also a transcription factor, or gene that regulates the activity of other genes. We also see evidence that it is a relatively new gene, one that is taking over a morphogenetic function that may have been carried out by several other more primitive genes in the ancestral insect.

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Bicoid, nanos, and bricolage

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Intelligent Design creationists are extremely fond of diagrams like those on the left. Textbook illustrators like them because they simplify and make the general organization of the components clear—reducing proteins to smooth ovoids removes distractions from the main points—but creationists like them for the wrong reasons. “Look at that—it’s engineered! It’s as if God uses a CAD program to design complex biological systems!” They like the implication that everything is done with laser-guided precision, and most importantly, that every piece was designed with intent, to fill a specific role in an apparatus that looks like it came out of a high-tech machine shop at a Boeing aerospace lab.

This is, of course, misleading. Real organelles in biology don’t look glossy and slick and mechanical; they look, well, organic, with fuzziness and variability and, most importantly, mistakes and slop. What these biological machines look like is not the precisely engineered output of a modern machine shop, but like bricolage. Bricolage is a term François Jacob used to contrast real biology with the false impression of nature as an engineer. It’s an art term, referring to constructions made with whatever is at hand, a pastiche of whatever is just good enough or close enough to the desired result to make do. It covers everything from the sculptures of Alexander Calder to those ticky-tacky souvenirs made from odd bits of driftwood and shells glued together that you can find at seashore gift shops.

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Zygotic genes

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Last week, I wrote a bit about maternal genes, specifically bicoid, and described how this gene was expressed in a gradient in the egg. Bicoid is both a transcription factor and a morphogen. The gene product regulates the activity of other genes, controlling their pattern of expression in the embryo. Today I thought I’d get more specific about the downstream targets of bicoid, the gap genes.

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Transcription factors and morphogens

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In my previous comments about maternal effect genes, I was talking specifically about one Drosophila gene, bicoid, which we happen to understand fairly well. We know its sequence, we know how it is controlled, and we know what it does; we know where it falls in the upstream and downstream flow of developmental information in the cell. So today I’m going to babble a bit more about what bicoid is and does, and how it works.

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Upstream plasticity and downstream robustness in evolution of molecular networks

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In developmental biology, and increasingly in evolutionary biology, one of the most important fields of study is deciphering the nature of regulatory networks of genes. Most people are familiar with the idea of a gene as stretch of DNA that encodes a protein in a sequence of As, Ts, Gs, and Cs, and that’s still an important part of the story. Most people may also be comfortable with the idea that mutations are events that change the sequence of As, Ts, Gs, and Cs, which can lead to changes in the encoded protein, which then causes changes in the function of the protein. These are essential pieces in the story of evolution; we do accumulate variations in genes and gene products over time.

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Evolution of Hormone Signaling

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Last week, I received some delusional e-mail from Phil Skell, who claims that modern biology has no use for evolutionary theory.

This will raise hysterical screeches from its true-believers. But, instead they should take a deep breath and tell us how the theory is relevant to the modern biology. For examples let them tell the relevance of the theory to learning…the discovery and function of hormones…[long list of scientific disciplines truncated]

Dr Skell is a sad case. He apparently repeats his mantra that biology has no need of evolution everywhere he goes, and has never bothered to actually crack a biology journal open to see if biologists actually do use the theory. In my reply to him, I did briefly list how evolution is used in every single one of his numerous examples, but today I’m going to focus on just the one I quoted above: hormones.

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Octopus brains

Once upon a time, as a young undergraduate, I took a course in neurobiology (which turned out to be rather influential in my life, but that’s another story). The professor, Johnny Palka, took pains at the beginning to explain to his class full of pre-meds and other such riff-raff that the course was going to study how the brain works, and that we were going to be looking at invertebrates almost exclusively—and he had to carefully reassure them that flies and squid actually did have brains, very good brains, and that he almost took it as a personal offense when his students implied that they didn’t. The lesson was that if you wanted to learn how your brain worked, often the most fruitful approach was an indirect one, using comparative studies to work out the commonalities and differences in organization, and try to correlate those with differences and similarities in function.

At about that time, I also discovered the work of the great physiologist, JZ Young, who had done a great deal of influential work on the octopus as a preparation for studying brain and behavior. (Young, by the way, went by the informal name “Jay-Zed”, and there you have another clue to my affectation of using my first and middle initial as if it were a proper name.) It was around then that I was developing that peculiar coleoideal fascination a few of the readers here might have noticed—it was born out of an appreciation of comparative biology and the recognition that cephalopods represented a lineage that independently acquired a large brain and complex behavior from the vertebrates. To understand ourselves, we must embrace the alien.

Young’s attempts to understand mechanisms of learning in memory in the octopus were premature, unfortunately—they have very complex brains, and we made much faster progress using simple invertebrates, like Aplysia, to work out the basics first—but it’s still the subject of ongoing research. I was very pleased to run across a general overview of the octopus brain in The Biological Bulletin.

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