genetics
razib | February 1, 2008The story about HERC2 & OCA2 is getting a lot of press; that is, the genetics behind how people have blue eyes. But see this in ScienceNow:
There are still large questions, though. Why did blue eyes persist? Scientists say it is difficult to see how eye color would have an environmental advantage, as skin color does. Some theories suggest that women may have played a role in driving the selection. Perhaps, Kayser says, "the females thought it more exciting to have a male with blue eyes."
I already posted this before: the SNPs which are used to predict blue eyes also track skin color…
clock | January 31, 2008Someone did it.
Get a prize if you correctly identify which one is intelligently designed.
In both cases, the designer was an intelligent.....human. Of course. No media reports yet of bioengineering labs run by chimps, dogs, elephants or dolphins.
razib | January 31, 2008Sound familiar? Well, good things come in pairs. A few days ago I posted on a paper which used a linkage analysis to come to the conclusion that an SNP on HERC2 was responsible for the variation in eye color in Europeans. Some background, a gene, OCA2, was implicated in the variation in eye color, and it turns out that a few haplotypes on this locus can be used to predict with reasonable accuracy the phenotype in question. The paper I blogged a few days ago was a extension of the work of this work; the same group found that one SNP on HERC2 could actually better explain the variation (…
razib | January 30, 2008ScienceDaily has a most-retarded title up for a report on some new research, Blue-eyed Humans Have A Single, Common Ancestor. I already blogged the paper at my other blog. The paper roughly confirms the previous finding that I blogged that an SNP on the gene HERC2 might regulate expression of OCA2 so that there is depigmentation; in particular in the iris. I have another post coming up tomorrow morning on another study on HERC2 (it's in schedule).
Anyway, the title is stupid, because yes, the HERC2-OCA2 region probably has increased in frequency from a single gene copy, but blue-eyed…
gregladen | January 30, 2008Color is funny. Anthropologists have long known that different cultures have different relationships, linguistically and in day to day practice, to the color spectrum. For example, the Efe Pygmy Hunter-Gatherers of the Ituri Forest describe things as white, black, or red, and that's it. They live in a world of green. Going with the model for "Eskimos" having a hundred words for snow because snow is so important in their environment, one would expect that the Efe would have a hundred words for green. On the other hand, the Efe Hunter-Gatherers must have a fairly primitive culture,…
razib | January 30, 2008Give the lady her due, Olivia Judson can lay down some serious exposition when she's on:
There are a couple of interesting things about this discovery. The first is that the molecular basis of the change from pelvis to no pelvis does not involve a mutation to the protein-coding region of the Pitx1 gene itself. In other words, the protein made from the gene hasn't changed. What has changed is the way the gene is expressed. This is in contrast to the sorts of mutations one often reads about as being involved in evolution, which typically involve changes to the protein itself.
A second…
retrospectacle | January 29, 2008Wouldn't it be great if there was some magical institution which mapped out the developmental expression of mouse genes, and then made it freely available on the internet? And wouldn't it be cool if all that data was compiled in an easily-searchable database that was being constantly updated with new genes and new experimental data?
Well, dream no more, because the folks at Department of Molecular Embryology at the Max-Planck Institute of Experimental Endocrinology have done just that by creating GenePaint. If there was a "You Might Be a BioDork If..." list, I think up there on the list…
razib | January 29, 2008Last year a group out of Australia published a paper which purported to explain eye color variation based upon a polymorphism around the OCA2 locus. The paper was A Three-Single-Nucleotide Polymorphism Haplotype in Intron 1 of OCA2 Explains Most Human Eye-Color Variation, and I blogged it here. Basically the paper showed that three SNPs arranged on several haplotypes could be plugged into a function to generate a relatively good prediction of eye color. Why does this matter? First, because eye color is one of the first things you learn about "genetics" in high school, but we're still stuck…
razib | January 28, 2008Chapters read:1, 2, 3, 4, 5, 6 and 7.
So I'm reading Stephen Jay Gould's magnum opus, The Structure of Evolutionary Theory. I figure if I read this I won't have to read anything else by the guy; if he couldn't squeeze it into 1,464 pages, it really wasn't worth mentioning I'm assuming. Here are impressions from the 90 page first chapter, which is a general overview of his ideas and biography....
1) There is the fact of evolution (descent with modification), and the mechanism of evolution promoted by Charles Darwin (gradual phyletic change operating through natural selection at the level of…
mikethemadbiologist | January 28, 2008When I read Olivia Judson's post about hopeful monsters, I didn't think she used the term correctly (here are some good explanations why), but I was surprised by Jerry Coyne's response.
First, the personal attack on Judson is unwarranted: when we reach the point where the serious challenge to evolutionary biology is the misuse of a discredited decades-old idea, as opposed to the politically powerful anti-science creationist movement, we're in a pretty good place. She made a mistake--I don't think her motives were self-aggrandizing. Second, if you're going to launch an ad homeniem attack,…
razib | January 28, 2008Over at Greg's place, Brian Switek notes:
Thanks for the link Greg (and thanks for the compliment, Steve). I've generally been unimpressed with Coyne's popular articles, especially given that he seems to go out of his way to attack Gould and evo-devo whenever it seems fit to do so (which is just about anytime, apparently). Criticism and controversy is fine (even expected), but the way Coyne reacted to Judson's post was a bit too harsh and condescending. Part of the problem, I think, is that there doesn't seem to be a good definition of what a hopeful monster is or is not, what a saltation is…
gregladen | January 27, 2008This is my reply to a post by Coturnix called The Hopeless Monster? Not so fast!
First, the phylogeny of the discussion.
Olivia Judson wrote this:
The Monster Is Back, and It's Hopeful
Which was responded to here:
Hopeless Monsters--A Guest Post from Dr. Jerry Coyne
That dyad of posts was passed around by Carl Zimmer, who asked for commentary. This is the set of posts of which I'm aware that resulted:
Why wither Goldschmidt?
Nature makes no leaps...
Jerry Coyne smacks down Olivia Judson
Coyne is on the Loom
Macromutations and Punctuated Equilibria
Hopeful Monsters and Hopeful Models
Then…
razib | January 27, 2008In The Hopeless Monster? Not so fast! Bora says:
In a back-and-forth with a commenter, Coyne defends himself that he is talking about the changes in genes, not evolution. This just shows his bias - he truly believes that evolution - all of it - can be explained entirely by genetics, particularly population genetics. His preferred definition of evolution is probably the genocentric nonsense like "evolution is a change of gene frequencies in a population over time". I prefer to think of it as "evolution is change in development due to ecology" (a softening of Van Valen's overly-strong…
gregladen | January 27, 2008The loss of sight in cave dwelling species is widely known. We presume that since sight in utter darkness has no fitness value, the mutation of a gene critical to the development of the sense of sight is not selected against. Over time, any population living in darkness will eventually experience experience such mutations, and these mutations can reach fixation.
Astyanax mexicanus: Top is the surface, sighted form, bottom is the cave-dwelling, blind form. From the Jeffery Lab.Beyond this, we may hypothesize that a mutation "turning off" sight could be beneficial. By definition, an…
clock | January 26, 2008Olivia Judson wrote a blog post on her NYTimes blog that has many people rattled. Why? Because she used the term "Hopeful Monster" and this term makes many biologists go berserk, foaming at the mouth. And they will not, with their eye-sight fogged by rage, notice her disclaimer:
Note, however, that few modern biologists use the term. Instead, most people speak of large morphological changes due to mutations acting on single genes that influence embryonic development.
So, was Olivia Judson right or wrong in her article? Both. Essentially she is correct, but she picked some bad examples,…
gregladen | January 24, 2008A hopeful monster is a mutant born with a genetically determined and large novel trait (compared to its parents) which confers enhanced fitness on that individual. This enhanced fitness increases the likelihood that the new mutant gene that determines this trait will be passed on and spread throughout the evolving population, so in a single generation a rapid process of speciation is initiated. For example, a fish with a mutation that causes both its eyes to grow on one side of its head could become the flounder of a new generation of flatfish. Well, just for the halibut, it might be fun…
razib | January 24, 2008Wow. Well, Jerry Coyne has never been one for weak words. A few days ago evolutionary biologist & journalist Olivia Judson posted The Monster is Back, and It's Hopeful on her blog The Wild Side. Jerry Coyne, a prominent evolutionary biologist at the University of Chicago and co-author of the magisterial Speciation, has posted a strongly worded response over at Carl Zimmer's weblog:
Judson commits two errors of reasoning when arguing a la Goldschmidt (or Gould). The first is what I call the "macromutationist fallacy," for this error is so common that it deserves a name. It is this: we…
razib | January 22, 2008Variation in neural V1aR predicts sexual fidelity and space use among male prairie voles in semi-natural settings:
Although prairie voles (Microtus ochrogaster) are socially monogamous, males vary in both sexual and spatial fidelity. Most males form pairbonds, cohabit with one female, and defend territories. Wandering males, in contrast, have expansive home ranges that overlap many males and females. In the laboratory, pairing is regulated by arginine vasopressin and its predominant CNS receptor, vasopressin 1a receptor (V1aR). We investigated individual differences in forebrain V1aR…
razib | January 22, 2008In the Fatosphere, Big Is in, or at Least Accepted:
Blogs written by fat people -- and it's fine to use the word, they say -- have multiplied in recent months, filling a virtual soapbox known as the fatosphere, where bloggers calling for fat acceptance challenge just about everything conventional medical wisdom has to say about obesity.
...
Ultimately, these bloggers argue, being skinny may have far more to do with the luck of the genetic draw than with lifestyle choices.
When I was visiting Bangladesh in 2004 I noticed that peasants in the rural areas were shorter, wirier and "tighter" in…
razib | January 21, 2008Why elephants are not so long in the tusk:
The average tusk size of African elephants has halved since the mid-19th century. A similar effect has been spotted in the Asian elephant population in India.
Researchers say it is an example of Darwinism in action, caused by the mass slaughter of dominant male elephants - but whereas evolution normally takes place over thousands of years, these changes have occurred within 150 years.
Zoologists at Oxford University fear that poaching and hunting of the largest male elephants, which also have the largest tusks, has changed the natural breeding…