genetics
razib | August 18, 2006Many people have posted on this, so I'm going to give a quick link round up.
I linked it early, and then Kawfee Mugg posted a follow up on my other weblog. John-too-good-for-10-assertions then offered up his commentary, and then RPM kicked in his 3 cents. He pointed me to Carl Zimmer's smackdown on the issue.
I think the insight this gives us is similar to FOXP2, yes, we are a lot like other animals (whether it is 98% identity to chimp or not is irrelevant), but, in some ways we are a special breed all our own (i.e., in this case, a lot more evolution seems to have occurred on the human…
razib | August 16, 2006It's been nearly a month since I last posted on The Genetical Theory of Natural Selection. I've been holding off because I didn't know how to approach chapter 2, in many ways it is the most important and ambitious chapter (though not technically the most taxing). I think I will likely post twice on this chapter, and in this entry I'll avoid talking about the difference between "average effect" and "average excess" and what not. Rather, I'll focus on two issues:
1) The Fundamental Theorem of Natural Selection.
2) Fisher's view on the nature of adaptation
Both of these are rather simple…
clock | August 15, 2006Archy is on top of the story, as usual when the story is about people trying to resurrect mammoths!
razib | August 15, 2006I will "house" responses to my 10 assertions about evolution query in this post.
So far, only RPM has taken the bait. He asks some interesting questions in regards to the rather vague scope & nature of this query...but this was purposeful. If you examine RPM's list you see that it is clearly more focused toward the general public than my own list, which ended up highlighting possible differences of opinion within the Faith (e.g., Bora's & my own longstanding debates about levels of selection and what not). This is good, my overall aim is to synthesize a list which focuses on the…
razib | August 10, 2006The American Conservative is having a symposium on the nature of Left & Right, and Heather Mac Donald of the The Manhattan Institute offers up an eyebrow raising piece which is a jeremiad against the perceived necessary connection between conservatism and religiosity. It seems likely that this was prompted by the muddled direction of George W. Bush's directionless religious conservatism.
clock | August 10, 2006I hope PZ will comment on this study:
A humble aquarium fish may be the key to finding therapies capable of preventing the structural birth defects that account for one out of three infant deaths in the United States today.That is one of the implications of a new study published online August 8 in the journal Cell Metabolism. The paper describes a number of striking parallels between a rare but fatal human birth defect called Menkes disease and a lethal mutation in a small tropical fish called the zebrafish that has become an important animal model for studying early development.
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razib | August 10, 2006Blogger NuSapiens offers an intriguing comment on my post about Neandertal introgression:
It's been shown that some mtDNA lines are associated with metabolic adaptations related to climate. This is a serious violation of the neutrality requirement for tracking things, especially far back in time. Adam and Eve are cute stories, but I wonder whether they will be around after another generation.
Neanderthal disappeared during a climate shift in Europe. If Neanderthal mtDNA was adapted to Euro-tundra, I wouldn't expect that to stick around very long during a thaw period. If at all, it might be…
pharyngula | August 8, 2006
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…
razib | August 7, 2006Greg Cochran and John Hawks have a hypothesis about the possibility of a population today that are "living Neandertals." I don't know which population it is, but below the fold, I think I've found strong evidence....
The Boston Irish!
clock | August 7, 2006A short post from April 17, 2005 that is a good starting reference for more detailed posts covering recent research in clock genetics (click on spider-clock icon to see the original).
As I have mentioned before, there was quite an angst in the field of chronobiology around 1960s about the lack of undestanding of circadian and other rhythms at cellular and subcellular levels. Experiment involved manipulation of the environment (e.g,. light cycles) and observing outputs (e.g., wheel-running rhythms), while treating the clock, even if its anatomical location was known, as a "black box".…
razib | August 5, 2006I've decided to jot down some simple* formalisms which I can refer new readers to on this website. So today....
You know that if you have a novel mutation within a population, its probability of fixation if it is neutral is:
1/(2N), where N = effective population, in a neutral scenario where the mutation confers neither advantage or disadvantage. So in a population of 100, a new mutant has a 1 out of 200 chance of fixation, going from 0.5% in the initial generation, to 100% in the generation of fixation. In a population of 1000, a new mutation has a .05% chance of fixation, and so forth.…
razib | August 5, 2006Most of you have likely heard of the paper out in The Proceeding of the Royal Society, Can the common brain parasite, Toxoplasma gondii, influence human culture?. Here is the relevant section from the abstract:
Toxoplasma gondii, explains a statistically significant portion of the variance in aggregate neuroticism among populations, as well as in the 'neurotic' cultural dimensions of sex roles and uncertainty avoidance. Spurious or non-causal correlations between aggregate personality and aspects of climate and culture that influence T. gondii transmission could also drive these patterns. A…
razib | August 3, 2006People often talk about random genetic drift. Like sexual selection it is the deus ex machina of choice when you are shit out of luck in regards to hypotheses. And yet though it looms large in our minds R.A. Fisher dismissed it as an important evolutionary force. Sewall Wright in his Shifting Balance Model tended to emphasize the interactions of genes more than the random fluctuation of frequency as such. Drift only came into its own with the rise of Neutral Theory and molecular evolution. In any case, I'm going throw out an algebraic relation out there that I think is important to keep…
pharyngula | August 2, 2006If 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.
John Rennie speaks out on stem cells on an Australian program, the Science Show.
I reviewed her new book a while ago, and now you can hear Christiane Nüsslein-Volhard lecture on basic developmental biology. She has a very nice light German accent that makes it especially pleasant to listen to, I think.
razib | August 1, 2006RPM points me to a post at Salamander Candy which discusses the usefulness of neutral markers in conservation genetics. Obviously this complements my recent posts about introgression, and in fact, my last entry was a comment on a conservation genetic paper. Here is the important point from Salamander Candy:
The problem is, a growing body of evidence suggests that patterns of variation and divergence in adaptive traits are not well reflected by neutral markers...In the hypothetical species mentioned above, a small amount of gene flow between east and west would be enough to swap small…
razib | July 31, 2006Apropos of our discussion of evolution and dogs, and introgression, here is a new paper I stumbled upon in Molecular Ecology, Detecting introgressive hybridization between free-ranging domestic dogs and wild wolves (Canis lupus) by admixture linkage disequilibrium analysis. Linkage disequilibrium is basically the non-random association of alleles across loci. For example, imagine that you have alleles A1 and A2 at locus A, and B1 and B2 at locus B. Imagine that these two locii are on separate chromosomes (just to make it clearer, though they don't have to be). In a randomly mating…
razib | July 27, 2006I suspect the basic general process of introgression is clear to most of you, though I will get back to it soon. But here are some papers with candidate genes (click "related" for more references):
RRM2P4, dystrophin, xp21.1 and 17q21.31. Also, I should add in the amusing evidence that archaics and moderns had sexual intercourse (amusing, but scientific nonetheless). Finally, a more theoretical paper that just came out.
There are other possibilities, like MC1R, but that could also be frequency dependent selection. More to come soon, I promise....