genetics
razib | April 26, 2007Via Dienekes, a new possible historical genetic story on the horizon: the extent of "European"-origin settlers in pre-modern China. The biography of the individual sequenced:
Yu Hong (d. 592 [C.E.]) was a high-ranking member of a community of Sogdians who had settled on the northern border of China at the beginning of the fourth century. While barely in his teens, Yu Hong began his career in the service of the most powerful nomadic tribe at the time, known as the Ruru, and was posted as an emissary to several countries, including Iran.
Now, the genetics:
...we discuss our analysis of the…
razib | April 18, 2007A few days ago I posted about how overdominance, the fitness advantage of a heterozygote (an Aa genotype instead of an AA or aa genotype), can maintain polymorphism (genetic variation) within a population at a locus. Roughly, the equilibrium ratio between the two alleles is determined by their respective fitnesses in the homozygote state. For example, if AA & aa are of equal fitness and of lower fitness than the heterozygote then the final equilibrium frequencies will be 0.5.
Heterozygote advantage is intuitively comprehensible to many people, after all we've all heard of "hybrid vigor…
grrlscientist | April 18, 2007tags: cancer, chromosomes, aneuploidy
There is an article about cancer in this month's issue of Scientific American written by pioneering the virologist, Peter Duesberg. For those of you to whom his name sounds vaguely familiar, Duesberg became famous by claiming that HIV doesn't cause AIDS. Fortunately, this article does not go into his radical ideas about HIV. Instead, this piece explores his more plausible hypothesis regarding the cause of cancer, which proposes that the source for many cancers is aneuploidy: a condition where the cell's chromosomes are scrambled -- duplicated, broken,…
evolgen | April 17, 2007A lot of interesting evolutionary genetics research gets published, and I don't have time to write an insightful commentary on all of it (some may argue that I have never written an insightful commentary on anything). Here's a brief overview of the stuff I have missed in the past few weeks:
A population of sheep was started with the introduction of two individuals on a remote island in the southern region of the Indian Ocean. Surprisingly, genetic diversity has increased over time in this population (reported here). This increase in heterozygosity (measured by the amount of microsatellite…
razib | April 16, 2007One of the classic ways to maintain genetic variation with a population is "overdominance," in short, a state where heterozygotes exhibit greater fitness than the homozygote genotypes. Imagine for example a locus, A, with two alleles, A1 & A2. Now, assume the fitness is distributed like so across the genotypes:
A1A1 = 0.75
A1A2 = 1.00
A2A2 = 0.75
In a random mating population the equilibrium genotypes given particular allele frequencies are described by the Hardy-Weinberg Equilibrium like so:
p2 + 2pq + q2
In a diallelic scenario q is by definition 1 - p, resulting in some algebraic…
razib | April 16, 2007The times has a mildly stupid article up, Chimps are ahead of humans in the great evolutionary race, which just goes to show that the people writing the headlines often have no comprehension skills, or just don't bother reading more than the first paragraph of a story. As confused as the article is it contradicts such a stark assertion. Here's the important point:
They found 154 human genes that showed evidence of the rapid positive selection that marks out adaptive traits, but 233 chimp genes with the same qualities.
Read the article with great caution, some of the sentences are very…
razib | April 13, 2007I promised I'd go over the recent PNAS paper, Group selection and kin selection: Two concepts but one process. This is one of those articles where most of the heavy lifting is in the technical appendix. I've decided that it isn't worth the effort to restate this verbally in detail, I looked over the algebra and I didn't catch anything glaring (though I could have looked more closely), and would have felt ridiculous pointing out where they used "the chain rule here." The main point that I gathered from this paper is that Martin Nowak's model used groups which did not split very often, but…
evolgen | April 13, 2007According to Physorg.com, this study on epigenetic inheritance in chickens "shake[s] Darwin's foundation". Who knew inheritance in a flightless bird could induce an earthquake in northern Australia? That's not what they're referring to? They're not claiming that a neo-Lamarckian process could produce seismic activity?
For everyone running around like a chicken with its head cut off (where's my damn rim-shot?), this result is more of a shot at Mendel than Darwin. And it's not all that surprising. Don't get me wrong, it's cool to see the inheritance of acquired characteristics (unless Reed…
clock | April 11, 2007As you know, the last several days saw quite a flurry of blog posts about framing science. I posted my thoughts here and I keep updating my post with links to all the new posts as they show up (except the expected drivel by William Dembski, some minor creaitonists and Lubos Motl). Some of the other bloggers ignored my post, many linked to it without comment, and many linked to it with positive commentary - with two exceptions.
One was Larry Moran (who probably skimmed it quickly, found what he did not like in it with his own frame of mind at the time, and used it as a starting point to…
grrlscientist | April 11, 2007tags: bipolar disorder, mania, manic mouse, psychiatric research
Some of you, like me, suffer from bipolar disorder or might know someone who does, so I thought I'd take this opportunity to write a little about the creation of a mouse model to study the genetics that are thought to underlie the manic phase of bipolar disorder -- a phase that has not been well understood so far.
Bipolar disorder, or manic-depressive illness, is a psychiatric condition that affects a person's moods. Typically, a person who suffers from a classical bipolar disorder (Also known as bipolar affective disorder,…
razib | April 10, 2007A few months ago I was posting on R.A. Fisher's Genetical Theory of Natural Selection. I stopped because I was a bit confused as to what to do about the chapter on dominance, which was basically an exposition on a theory which has been falsified by the preponderance of data. In sum, R.A. Fisher contended that the dominance of an allele emerged via evolutionary processes, while his primary interlocutor Sewall Wright contended that this phenomenon was an emergent property of physiological dynamics. Fisher noted that "Wild Type" phenotypes are invariably dominant. He suggested that…
grrlscientist | April 10, 2007tags: dog breeds, IGF1, insulin-like growth factor 1, cancer, growth disorders
One gene mutation makes all the difference in body size between a big dog and a little dog.
Image: NY Times.
There are several things that I think are amazing about dogs, Canis familiaris. First, there is a huge discrepancy in body size between different breeds -- greater than for any other mammal, in fact, and second, these vastly different dog breeds still recognize each other as being of the same species. Yet, according to a recently published research paper, this huge differential in the body size of dogs…
clock | April 7, 2007Here, have a go at it. Even better, if you can get the actual paper and dissect it on your blog, let me know so I can link to that. Have fun!
Good Behavior, Religiousness May Be Genetic:
A new study in Journal of Personality shows that selfless and social behavior is not purely a product of environment, specifically religious environment. After studying the behavior of adult twins, researchers found that, while altruistic behavior and religiousness tended to appear together, the correlation was due to both environmental and genetic factors.
According to study author Laura Koenig, the…
pharyngula | April 6, 2007Jonathan Wells apparently felt the sting of my rebuttal of his assertions about Hox gene structure, because he has now repeated his erroneous interpretations at Dembski's creationist site. His strategy is to once again erect a straw man version of biologist's claims about genetic structure, show that biologists have refuted his dummy, and claim victory. The only real question here is whether he actually believes his historical revisions of what we've known about Hox genes, in which case he is merely ignorant, or whether he is knowingly painting a false picture, in which case he is a malicious…
grrlscientist | April 4, 2007Scientists at the National Institute on Drug Abuse (NIDA) have identified genes that might increase a person's ability to quit smoking. This research was conducted by George Uhl at NIDA's Intramural Research Program and a team led by Jed Rose at the Center for Nicotine and Smoking Cessation Research at Duke University Medical Center.
"This research marks the first time we've been able to identify genes involved in the ability to quit smoking," says NIDA Director Nora Volkow. "It marks a movement from identifying the genetics of addiction vulnerability to identifying the genetic basis of…
pharyngula | April 3, 2007This evening, I am watching an episode of that marvelous and profane Western, Deadwood, as I type this; it is a most excellently compensatory distraction, allowing me to sublimate my urge to express myself in uncompromisingly vulgar terms on Pharyngula. This is an essential coping mechanism.
I have been reading Jonathan Wells again.
If you're familiar with Wells and with Deadwood, you know what I mean. You'll just have to imagine that I am Al Swearingen, the brutal bar-owner who uses obscenities as if they were lyric poetry, while Wells is E.B. Farnum, the unctuous rodent who earns the…
evolgen | April 2, 2007
Alex has posted the (lucky) thirteenth edition of Mendel's Garden at the Daily Transcript. It's (not) an April Fools Day edition, but it would have been if it had come out yesterday. And there's a theme of magic fish flakes for you favorite model organism, but I don't think they're safe to incorporate into my fly food. What are you still doing reading this? Get over to Alex's place and read about genetics.
clock | March 29, 2007On The Scientist website you can find their new experimental feature - an article with questions to the public that will be used in forming the articles for the print version of the magazine next month. Go see Special Feature: Stem cell cloning needs you: In a unique experiment we're inviting you to participate in a discussion that will help shape our next feature on stem cell research and post comments:
We're inviting people to give us their thoughts and questions on whether we need to rethink the scientific and ethical approach to stem cell cloning to help shape a feature that we'll be…
pharyngula | March 28, 2007
A creationist, Rob McEwen, left me a little comment here which lists a number of his objections to evolution. It’s a classic example of the genre, and well illustrates the problem we have. The poor fellow has been grossly misinformed, but is utterly convinced that he has the truth. I’m not going to dismantle his entire line of blather (thanks to Loren Petrich, who has already briefly pointed out the flaws in his thinking), but I do want to show what I mean with one example.
Here’s what Mr McEwen says:
Mutations have NEVER produced additional DNA structures. NEVER! Even as scientists study…
razib | March 26, 2007The American Journal of Human Genetics has an article up examining population substructure within Europe (or, more precisely, the varation of genes), Measuring European Population Stratification with Microarray Genotype Data. From the discussion:
PC1 [the largest principle component of variance] largely separates northern from southeastern individuals...and is consistent with the clines observed in classic gene-frequency...Y-chromosome...mtDNA...and whole-genome...studies of European diversity. PC2 [the second largest principle component of variance] reflects mainly east-west geographic…