genetics
razib | November 8, 2006I've been talking about introgression for a year right now. I've been waiting for the papers on this topic to come out, and the first has. If you haven't, please read the posts from Greg and John Hawks. Another paper is on the way, and Hawks promises something within this week. I strongly suspect that the Paabo group also has something up their sleeves. As I noted earlier the paper from Lahn et. al. is open access, free to the public. Read it, it's an elegant and compact piece of work, and I think they make a compelling case for introgression of an allele implicated in brain development…
pharyngula | November 7, 2006Here'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 -Â including radical fringe, lunatic fringe and, bizarrely, Indian hedgehog -Â 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…
evolgen | November 7, 2006That's right: if you study human genetics, you suck. In relation to Drosophila geneticists, of course. You see, human geneticists are boring. Drosophila geneticists come up with clever names for genes. When the homologues are identified in humans, the names are deemed offensive and inappropriate. Apparently, patients don't like being told they have a mutation in the lunatic fringe gene. Or sonic hedgehog. Or mothers against decapentaplegia. This is according to an article in Nature.
Maybe I don't know jack about bedside manner, but I can appreciate the amount of thought that goes into naming…
razib | November 7, 2006Previously I discussed the probability of extinction across one generation for a new mutant allele. To review, there is ~1/3 chance that a new mutant will go extinct within one generation of its origination (i.e., a de novo mutation is not replicated and transmitted to the next generation of organisms). If there is positive selection on the mutant allele there is a reduction in the probability of extinction, but only a mild one. Consider that if s is 0.10, a 10% increase in fitness vis-a-vis population median fitness, that is likely to be swamped out in many cases by the stochasticity…
evolgen | November 7, 2006A few months ago, JP posted at GNXP that random mating is not necessary for Hardy-Weinberg Equilibrium (HWE). One round of random mating is still sufficient to achieve HWE genotype frequencies, but there are some non-random mating strategies that will also allow for HWE.
HWE is quite robust to violations of the assumptions. That makes it a poor test for things like natural selection, but it is commonly used to detect population structure. If you sample allele and genotype frequencies from a single population, the genotype frequencies should be in HWE. If, however, you sample from two separate…
razib | October 31, 2006I was going to continue with my review of chapter 5 of Evolutionary Genetics: Concepts & Case Studies today, but time does not permit. This section was to focus on the orgination of advantageous mutations from the stochastic cauldron of generation 1 (which, as we've seen exhibits a 1/3 probability of immediate extinction in th subsequent generation assuming Poisson distribution of reproductive variance and fixed population size), so I will point to my older posts on introgression (of advantageous alleles):
The baby model
My fixations
Archaic-modern hybridization
Intogression-1…
razib | October 30, 2006Heterogeneous Genomic Molecular Clocks in Primates:
The rate at which mutations accumulate in a genome, referred as a "molecular clock," is an instrumental tool in molecular evolution and phylogenetics. Different types of mutations occur via distinctive molecular pathways. In particular, while most mutations occur from errors in DNA replication, spontaneous deamination of methylated CpG dinucleotides is another important source of mutation in mammalian genomes. Molecular clock studies typically combined all types of mutations together. In this paper, the authors analyze molecular clocks of…
razib | October 28, 2006Assume that you have a new mutation, totally novel. What's its probability of going extinct in one generation? That is, it doesn't get passed on....
Consider, you have a population of N individuals. Fix the population size across nonoverlapping generations. So, in generation t you have N individuals and in t + 1 you have N individuals. In the first generation of the mutation the proportion in the population is 1/N, that is, there is one mutant amongst N individuals (ergo, N - 1 other copies). The probability that the mutant is never "drawn" (copied) to the next generation in this fixed…
razib | October 27, 2006I noticed today that I was receiving a lot of search engine queries for black and white twins. Well, I have posted on it several times, but I thought it was a bit much, so I checked the news, and lo & behold, another case just popped up. Like the Australian twins the mother here was biracial (Nigerian and English) while the father was white (in contrast to the earlier British case where the parents were both biracial). I'm sure you're getting tired of this, but I have to comment when I see headlines this: Mum defies million-to-one odds to give birth to black and white boys. I've…
razib | October 26, 2006A reader emailed me asking about the genetics of hair color. Since I've discussed the topic before I simply pointed them to the query of the topic on my other blog. But, I thought it might be good to directly answer two specific questions:
Why do many people have much lighter hair during childhood?
The same reason that European babies are often with blue eyes or dark skinned babies are born with light skin, we get darker as we age (with the partial exception of females during puberty). The darkening of hair is simply a symptom of a general trend toward increased melanin as we age (or as…
clock | October 25, 2006The honeybee genome project has been finished and a bunch of papers are coming out tomorrow. As soon as they become available online I will comment, at least on the one paper that shows that the molecular machinery of the bee circadian clock is much more similar to the mammalian clock than the fruitfly clock - something that makes me very excited.
In the meantime, you can read more about the bees and their genome on The Loom, The Scientist, Scientific American and EurekAlert.
razib | October 25, 2006One of the things I regret during my tenure blogging is that I started doing "10 questions" too late to get in touch with John Maynard Smith. If you haven't, I highly recommend this interview by Robert Wright from a few years ago. Also, Smith wrote one of the more readable introductory texts on Evolutionary Genetics, as well as pioneering the use of game theory in evolutionary biology, introducing the concept of the ESS.
razib | October 22, 2006Hsien-Hsien Lei points me to another story about black and white twins. First, the "black" twin is clearly mixed race, her skin color is between the modal complexion of Europeans and sub-Saharan Africans on the von Luschan scale. The "white" twin on the other hand does seem to exhibit the color of someone of European descent. What's going on here? This is somewhat different than the other case of black and white twins, in that case both parents were mixed-race, in this case the father is white (German) and the mother is mixed-race (Jamaican & English). The two cases are different even…
razib | October 19, 2006David B continues his series on R.A. Fisher's opinions regarding population size and evolutionary genetics (part I).
Update: Links fixed. Thanks John.
pharyngula | October 18, 2006Human 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…
evolgen | October 18, 2006
We're in need of a host for the 9th Edition of Mendel's Garden, scheduled for 6 November. Mendel's Garden is blog carnival devoted to genetics, from evolutionary to molecular. If you would like to host the upcoming edition or any future edition, please contact Paul Decelles via the Blog Carnival Submission Page.
Also, we're switching from a biweekly schedule to a monthly schedule. A new edition of Mendel's Garden will be published on the first Monday of each month (starting November 6). Your entries are due by the Sunday before the first Monday (i.e., the day before the carnival comes out).
clock | October 17, 2006Razib and commenters are commenting on this article which appears to be 19th century SF-fantasy repackaged as "serious science" about the future evolution of the human species. Actually, the article is so silly, Razib does not even want to waste time on it and points out only one of the obvious fallacies of the argument, the one about skin color. On the other hand, Lindsay does a thorough and delightful fisking that you may enjoy!
I don't even know in which 'channel' to put this post. I guess it is "biology" but only nominally... as we do not have a "nonsense and having fun with it"…
razib | October 17, 2006This is the shape of things to come for mankind is an article which claims that "Variations in skin colouring are expected to be smoothed out, with most humans moving towards a brown tone." The source of this is an evolutionary psychologist, Dr. Oliver Curry, but, it seems to me that Dr. Curry is passing off what he read in science fiction as science. Genetics is not blending. I have posted on skin color enough to make clear why humans won't turn uniformly as beautifully brown as some privileged people! A small number of loci (4-5) control skin color variation, and though random mating…
razib | October 16, 2006JP has an interesting post, Why the regulatory changes vs. coding sequence changes debate is inane:
Here's the question we're supposed to answer: which are more important-- protein-coding changes or regulatory changes? And here's the problem with that question: how do you define important? Let's make a list of the ways humans differ from chimpanzees-- we walk on two feet, we have bigger brains, we have less hair, etc. etc. You can add your own if you like. If a protein-coding change gives us the bigger brain, but a regulatory change the lack of hair, who wins? Sure, you could argue about…
evolgen | October 15, 2006
Sandy has posted the eight edition of Mendel's Garden at Discovering Biology in a Digital World. Go read the best genetics blogging from the past couple of weeks. If you have written something about genetics and would like to be included in the next edition of the carnival, you can submit your work here.