genetics
razib | March 15, 2006In my post below there is a reference to fast evolution in a relatively slow-breeding species, H. sapiens. For this to be plausible you need high selection coefficients, that is, the difference between mean population fitness and the fitness of those who are carrying the favorable allele. How plausible is this? R.A. Fisher argued against selection coefficients of large effect because he believed that mutations of large effect would usually "overshoot" the idealized fitness peak, and it was mutations of small gradual effect which were the real drivers of evolution. But recent work has…
razib | March 12, 2006I am going to cut & paste whole a comment from Jemima Harrison of Passionate Productions, who is behind the upcoming documentary about the family who exhibits quadruped locomotion:
The mutation on 17p has been identified by a Turkish/German team in Berlin headed by Professor Stefan Mundlos. They suggest, some would say controversially, that this mutation could have knocked out a gene that plays a role in bipedal walking, atavastically exposing an earlier form of walking.
Professor Humphrey believes, however, that this mutation has merely caused the cerebellar hypoplasia confirmed by MRI…
razib | March 11, 2006I commented on the "throwback family" a few days ago, well, The Times (of London) has two articles which reduce the likelihood of this being a hoax in my mind. It seems clear that there is a family, highly inbred, which lives in Turkey where a number of the children walk on all fours and exhibit other forms of impairment.
Nevertheless, the exact details of what is going on here is problematic to me. As usual, the newspapers tend to garble and confuse many issues. Consider this sentence: "All five are brain-damaged because of a mutation in a gene 17p, located on chromosome 17, which…
razib | March 10, 2006An author of the paper on recent human evolution was interviewed for the last 15 minutes of the first hour of Science Friday. The audio archive will be available soon. Also, I hear that you'll see a new article on this paper in The New York Times this weekend, so check for Nick Wade's byline.
evolgen | March 10, 2006Today's evolgen Double Entendre Friday deals with the genetic phenomenon known as incomplete penetrance. Ok, maybe this one isn't a double entendre, but more of a pseudo-homonym (can you guess what it sounds like?). When students in an introductory biology course are taught about dominance they learn about recessive and dominant alleles and maybe some special cases (codominance, incomplete dominance, etc). Incomplete penetrance refers to the unpredictability of certain dominance relationships. Take, for example, two alleles of a single gene ('A' and 'a') in which A is dominant to a. We…
pharyngula | March 9, 2006
Remember Snuppy, the cloned puppy? He's been living under a cloud for a while now, since one of his creators was Woo-Suk Hwang, the Korean scientist who was found to have faked data and exploited his workers, and there was concern that perhaps the dog cloning experiment was also tainted.
Put those fears to rest. Two groups of researchers have independently analyzed Snuppy and its putative clone parent, and both agree that it is most likely a clone. The nuclear markers between the two were identical, while mitochondrial markers were different—exactly what you'd expect in this kind of clone,…
razib | March 9, 2006Which sense do you value the most? I think many people, if they had to choose, would stick to their vision as the must-have sense. One thing that I want to get beyond on this blog is the tendency to find the one-gene-that-causes-all phenomenon. This tendency to fix on genes of large and singular affect, traditional Mendelian phenotypes like cystic fibrosis (a recessive disease), has been dictated by the lack of power of and limitations in studying quantitative traits, where I think the real uncharted territory is going to be with the next few decades. Nevertheless, a new paper in Nature…
evolgen | March 8, 2006Kevin White (aka, Mr. Drosophila microarray data) has a paper coming out in tomorrow's issue of Nature. The paper (which is not available on the Nature website yet) compares the expression of over 1,000 genes from humans, chimpanzees, orangutans and rhesus monkeys. From a news write up of the findings:
When they also looked for human genes with significantly higher or lower expression levels, they found 14 genes with increased expression and five with decreased expression. While only ten percent of the genes in the total array were transcription factors, 42 percent of those with increased…
pharyngula | March 7, 2006
I'm teaching my developmental biology course this afternoon, and I have a slightly peculiar approach to the teaching the subject. One of the difficulties with introducing undergraduates to an immense and complicated topic like development is that there is a continual war between making sure they're introduced to the all-important details, and stepping back and giving them the big picture of the process. I do this explicitly by dividing my week; Mondays are lecture days where I stand up and talk about Molecule X interacting with Molecule Y in Tissue Z, and we go over textbook stuff. I'm…
razib | March 6, 2006Evolgen points me to the fact that even our hosts here at Seed are spreading the "blondes are going to go extinct" hoax/meme which first cropped up 3 years ago. I also noticed that someone as informed about biology as John Wilkins was was taken in. An altered iteration of this hoax/meme that focused on redheads was also spreading last year. As Evolgen notes, this meme has been thoroughly debunked. To make it short, if you assume that blondness is a monogenic recessive trait (a gross simplification), its expression in the population will be q2, derived from Hardy-Weinberg Equilibrium p2 +…
evolgen | March 5, 2006Polymorphism and Divergence
This is the eighth of multiple postings I plan to write about detecting natural selection using molecular data (ie, DNA sequences). The introduction can be found here. The first post described the organization of the genome, and the second described the organization of genes. The third post described codon based models for detecting selection, and the fourth detailed how relative rates can be used to detect changes in selective pressure. The fifth post dealt with classical population genetics methods for detecting selection using allele and genotype frequencies…
razib | March 3, 2006I saw this post about human population diversity the other day...and though it was interesting, there was something that stuck in my craw:
Actually, this will be sharper for genes under selection, since selection should be weaker in bottleneck populations.
I don't think this is true. Selection isn't weaker, random genetic drift is stronger. Consider the probability of fixation of a new mutation. If the mutation is neutral so selection is non-existent its frequency is being buffeted only by random genetic drift. As you probably know, the probability of fixation is 1/(2Ne), where Ne is…
pharyngula | February 28, 2006Creationists sometimes try to argue that what we consider straightforward, well-demonstrated cytological and genetic events don't and can't occur: that you can't get chromosome rearrangements, or that variations in chromosome number and organization are obstacles to evolution, making discussions of synteny, or the rearrangement of chromosomal material in evolution, an impossibility. These are absurd conclusions, of course—we see evidence of chromosomal variation in people all the time.
For example, A friend sent along (yes, Virginia, there is a secret network of evilutionists busily sharing…
evolgen | February 27, 2006I have a little bit of an infatuation with copy number polymorphism (CNP), which describes the fact that individuals within a population can differ from each other in gene content. Some genes, such as olfactory receptors (ORs), have many different related variants in any animal genome. New copies spring up via duplication events (a type of mutation), so one could imagine that individuals from a single population differ in the number of copies of these genes. In fact, this is the case with any gene or gene family (a group of related genes) in the genome -- there may be duplications…
razib | February 26, 2006Just found this web site that has a good bibliography of R.A. Fisher's work. Good supplement to the R.A. Fisher digital archive. Why do I obsess with Fisher? First, ANOVA is ubiquitous. Second, stories like this would shock & awe a lot less if people read The Correlation Between Relatives on the Supposition of Mendelian Inheritance (PDF of full paper). Now, the text of the paper can be rather opaque, and the dancing flow of algebraic manipulations and moments magic can elude your grasp, but the gist is simple: the variance components of the offspring of heterozygous parents can be…
evolgen | February 26, 2006My advisor received an email from a fairly prominent geneticist regarding some results published by Dobzhansky over fifty years ago. The geneticist had done some back of the envelope calculations and noticed some trends that had been overlooked for a half of a century. We happened to have the animals to replicate the experiments (and I was planning on doing some similar experiments) so my advisor had me perform the crosses. I ended up with a negative result -- I did not see the same trends that Dobzhanksy and colleagues observed. I guess you could say my negative result was a positive…
razib | February 22, 2006I have a review of Nick Wade's Before the Dawn: Recovering the Lost History of Our Ancestors coming out in the May/June issue of Science & Spirit magazine. Wade's book covered the intersection of genetics and human evolution, so it was a quick and interesting read.
razib | February 21, 2006Biology is sloppy. I always say "all parameters held equal" or "all variables controlled" because there are so many factors to consider. I am now reading a classic, The Genetics of Human Poulations, by L. L. Cavalli-Sforza and W. F. Bodmer, and here is an interesting bit from the chapter on population structure: consanguineous rates of marriage were extremely low throughout much of Europe up until the 19th century, at which point their frequency rose sharply, before dropping again during the 20th century. What was happening here? The authors note that the 19th century abolition of…
razib | February 19, 2006Tim posts on the recent PLOS paper Gene Losses during Human Origins published by the Wang et al. If that gets you all excited, check out The Origin of Subfunctions and Modular Gene Regulation and Preservation of Duplicate Genes by Complementary, Degenerative Mutations. I might lionize the contributions of R.A. Fisher, Sewall Wright and J.B.S. Haldane to evolutionary biology, but as I posted before, tools need tasks, and the mass of data being unveiled by genomics is uncovering many surprises. Science isn't about a priori inference, it is about venturing into the wilds, and by the grace of…
pharyngula | February 18, 2006
Once upon a time, I was one of those nerds who hung around Radio Shack and played about with LEDs and resistors and capacitors; I know how to solder and I took my first old 8-bit computer apart and put it back together again with "improvements." In grad school I was in a neuroscience department, so I know about electrodes and ground wires and FETs and amplifiers and stimulators. Here's something else I know: those generic components in this picture don't do much on their own. You can work out the electrical properties of each piece, but a radio or computer or stereo is much, much more than a…