Granpappy was a Neandertal

Fascinating stuff…read this paper in PNAS, Evidence that the adaptive allele of the brain size gene microcephalin introgressed into Homo sapiens from an archaic Homo lineage, or this short summary, or John Hawks’ excellent explanation of the concepts, it’s all good. It’s strong evidence for selection in human ancestry for a gene, and just to make it especially provocative, it’s all about a gene known to be involved in brain growth, and it’s also showing evidence for interbreeding between Homo sapiens and Neandertal man.

The short short explanation: a population genetics study of a gene called microcephalin shows that a) it arose and spread through human populations starting about 37,000 years ago, b) this particular form of the gene (well, a small cluster of genes in a particular neighborhood) arose approximately 1.1 million years ago in a lineage distinct from that of modern humans, and c) the likeliest explanation for this difference is that that distinct lineage interbred with modern humans 37,000 years ago, passing on this particular gene variant that was then specifically selected for, a process called introgression.

The work looks sound to me, and I’m convinced. The one thing to watch for, though, is that there will be attempts to overreach and couple possession of this gene to some kind of intellectual superiority. We don’t know what this particular variant of the gene does yet! All we can say at this point is that some abstract data shows that a particular allele spread through the human population at a rate greater than chance would predict, that the gene itself has as one of its functions the regulation of brain growth, but that it is highly unlikely that that particular function is affected by the variant. Whatever it does, I expect the role is more along the lines of subtle fine-tuning rather than simply making people smart.

Hands off those genes

Here’s an annoying case of political correctness run amuck.

…the Human Genome Organisation (HUGO) Gene Nomenclature Committee…is renaming a number of genes that have potentially offensive or embarrassing names.

The shortlist of 10 genes - including radical fringe, lunatic fringe and, bizarrely, Indian hedgehog – was compiled in response to physicians’ worries about “inappropriate, demeaning and pejorative” names.

The problem arose because most of the genes were initially discovered in fruitflies, and their names were then transferred to the human versions of the genes, which were discovered later…when applied to the human versions of the genes, many of these names become uncomfortable.

While no one wants to curtail the creativity of fruitfly geneticists, it will be important to ensure that, in the future, no joky names are adopted for human genes where they might cause offence. Other quirky names in the fruitfly genome include headcase and mothers against decapentaplegia (MAD).

Darn prissy physicians. They’ve got no sense of humor. Will they try to rename one-eyed pinhead next? How about half baked? The zebrafish geneticists are just as amusing, you know.

I’d like to know what the physicians are concerned about, anyway. It’s not as if they’re going to be informing patients that their illness is caused by a broken frizzled gene, nor is it going to be somehow better or easier if they rename it “Wnt Receptor X-17” or something similarly dry and empty. I hope whoever started this knows a good proctologist who can do a stick-ectomy.

And seriously, there ought to be something like the priority rules of taxonomy to prevent random gomers from running around changing names just because they don’t like them.

Strange worm, Xenoturbella

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This odd marine worm, Xenoturbella bocki, is in the news right now, and I had to look it up in Pechenik’s Biology of the Invertebrates(amzn/b&n/abe/pwll) to remind myself of what it was. Here’s the complete entry:

Xenoturbella bocki

This marine worm, first described in 1949 as an acoel flatworm and later claimed as either an early metazoan offshoot or a primitive deuterostome, has recently been affiliated with primitive bivalve molluscs, based upon a study of gamete development (oogenesis) and an analysis of sequence data from both 18S rRNA and mitochondrial genes. Little is known about its reproductive mode, and developmental studies that might help to resolve the phylogenetic issues are just starting to be reported. A second species was described in 1999.

The animals are up to 4 cm long, vermiform (worm-shaped), and covered by locomotory cilia. They have no digestive tract, and indeed no organs at all. Their only conspicuous morphological feature, other than their cilia, is a statocyst for determining orientation. To date, they have been collected only off the coasts of Sweden and Scotland, in sediments at depths of 20 m to 100 m.

That’s it. Part of that is now known to be wrong: the data showing an affinity to the molluscs is an artifact, caused by the fact that it somehow eats bivalves, and partly digested clam material contaminated the samples. Otherwise, not much is known; I’ve found papers describing the presence of oocytes inside the animal, but no one as far as I know has actually observed its development. It’s a strange, mysterious blob of a worm.

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Feminism is undermining human evolution!

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Human X (left) and Y (right) chromosomes

Did the internet get stupider while I was away this past week? I mean, it’s gratifying to my ego to imagine the average IQ of the virtual collective plummeting when I take some time off, but I really can’t believe I personally have this much influence. Maybe the kooks crept out in my absence, or maybe it was just the accumulation of a week’s worth of insanity that I saw in one painful blort when I was catching up.

What triggers such cynicism is the combination of Deepak Chopra, Oliver Curry, and now,
William Tucker. Tucker wrote a remarkably silly piece in the American Spectator in which he drew deeply faulty conclusions from human genetics to support a thesis rife with misogyny and foolish chauvinism on human evolution. It was like a piece on evolutionary psychology written by someone who didn’t know any genetics at all.

Hang on to your hats—we’re going to see a factoid from one magazine article balloon up into a declaration of the superiority of the male species (I use “species” here both ironically and mockingly).

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Evolution of sensory signaling

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How we sense the world has, ultimately, a cellular and molecular basis. We have these big brains that do amazingly sophisticated processing to interpret the flood of sensory information pouring in through our eyes, our skin, our ears, our noses…but when it gets right down to it, the proximate cause is the arrival of some chemical or mechanical or energetic stimulus at a cell, which then transforms the impact of the external world into ionic and electrical and chemical changes. This is a process called sensory signaling, or sensory signal transduction.

While we have multiple sensory modalities, with thousands of different specificities, many of them have a common core. We detect both light and odor (and our cells also sense neurotransmitters) with similar proteins: they use a family of G-protein-linked receptors. What that means is that the sensory stimulus is received by a receptor molecule specific for that stimulus, which then actives a G-protein on the intracellular side of the cell membrane, which in turn activates an effector enzyme that modifies the concentration of second messenger molecules in the cell. Receptors vary—you have a different receptor for each molecule you can smell. The effector enzymes vary—it can be adenylate cyclase, which changes the levels of cyclic AMP, or it can be phospholipase C, which generates other signalling molecules, DAG and IP3. The G-protein that links receptor and effector is the common element that unites a whole battery of senses. The evolutionary roots of our ability to see light and taste sugar are all tied together.

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And the Nobel goes to…

Andrew Fire and Craig Mello, for the discovery of RNAi. Read Pure Pedantry for an explanation for why this is important.

I’ll also mention that Carl Zimmer presents his take on this award…and wouldn’t you know it, evolution has its greasy fingerprints all over it.

I must also promote an excellent comment from Andy Groves:

I’ve said it before, and I’ll say it again for the benefit of ID supporters out there – this is what a real scientific revolution looks like. Fire and Mello published their paper in 1998 (two years after “Darwin’s Black Box” came out, for those who are interested). Since then, the number of primary research papers on RNAi, siRNAs and miRNAs stands at 12399, using the search terms

(RNAi OR siRNA OR miRNA) NOT review

12400 papers in eight years. That’s 1550 a year, or just over four papers a day. Would Bill Dembski, the Isaac Newton of information theory, care to comment?

Hmmm?

Every science paper, every bit of recognition given to working scientists, seems to be a rather nasty rebuke to the promulgators of creationism.

Hox complexity

Here’s a prediction for you: the image below is going to appear in a lot of textbooks in the near future.

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(click for larger image)
Confocal image of septuple in situ hybridization exhibiting the spatial expression of Hox gene transcripts in a developing Drosophila embryo. Stage 11 germband extended embryo (anterior to the left) is stained for labial (lab), Deformed (Dfd), Sex combs reduced (Scr), Antennapedia (Antp), Ultrabithorax (Ubx), abdominal-A (abd-A), Abdominal-B (Abd-B). Their orthologous relationships to vertebrate Hox homology groups are indicated below each gene.

That’s a technical tour-de-force: it’s a confocal image of a Drosophila embryo, stained with 7 fluorescent probes against different Hox genes. You can clearly see how they are laid out in order from the head end (at the left) to the tail end (which extends to the right, and then jackknifes over the top). Canonically, that order of expression along the body axis corresponds to the order of the genes in a cluster on the DNA, a property called colinearity. I’ve recently described work that shows that, in some organisms, colinearity breaks down. That colinearity seems to be a consequence of a primitive pattern of regulation that coupled the timing of development to the spatial arrangements of the tissues, and many organisms have evolved more sophisticated control of these patterning genes, making the old regulators obsolete…and allowing the clusters to break up without extreme consequences to the animal. A new review in Science by Lemons and McGinnis that surveys Hox gene clusters in different lineages shows that the control of the Hox genes is much, much more complicated than previously thought.

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Wells: “Darwinism is Doomed” because we keep making progress

There are days when I simply cannot believe how dishonest the scoundrels at the Discovery Institute can be. This is one of them. I just read an essay by Jonathan Wells that is an appalling piece of anti-scientific propaganda, an extremely squirrely twisting of some science news. It’s called “Why Darwinism is doomed”, and trust me, if you read it, your opinion of Wells will drop another notch. And here you thought it was already in the gutter!

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Squid Hox genes

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It’s April (not anymore—it’s September as I repost this), it’s Minnesota, and it’s snowing here (not yet, but soon enough). On days like this (who am I fooling? Every day!), my thoughts turn to spicy, garlicky delicacies and warm, sunny days on a lovely tropical reef—it’s a squiddy day, in other words, and I’ve got a double-dose of squidblogging on this Friday afternoon, with one article on the vampire squid, Vampyroteuthis infernalis, and this one, on squid evolution and cephalopod Hox genes.

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Evolution of alcohol synthesis

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We need to appreciate beer more. Alcohol has a long history in human affairs, and has been important in purifying and preserving food and drink, and in making our parties livelier. We owe it all to a tiny little microorganism, Saccharomyces cerevisiae, which converts complex plant sugars into smaller, simpler, more socially potent molecules of ethanol. This is a remarkable process that seems to be entirely to our benefit (it has even been argued that beer is proof of the existence of God*), but recent research has shown that the little buggers do it all entirely for their own selfish reasons, and they’ve been busily making alcohol that has gone undrunk by humankind for tens of millions of years.

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