genetics
razib | April 16, 2009The New England Journal of Medicine has a series of articles up on the impact of new genomic techniques on medicine, specifically in the domain of pinpointing genetic markers which are correlated with increased risk of a particular disease. David Goldstein has a skeptical take up on the future returns of genomewide association studies, while Joel Hirschhorn is more hopeful. There is another review which takes a middle path, emphasizing the relatively marginal predictive power of many of the risk alleles, but suggesting that techniques and results are bound to improve.
Probably the most…
grrlscientist | April 15, 2009tags: performance horses, polo, racing, tendon injury, stem cell research
Horses clear a jump during the Challenge Cup Handicap Steeplechase
on the second day of the Cheltenham Festival in the UK.
Image: BBC News.
Those of you who follow my writings about racehorses and other high-performance horses will be interested to learn that several companies that I've been following have been redirecting their stem-cell research that they originally developed to help injured horses to help people recover from Achilles tendon injuries.
After a tendon or ligament tear, both horses and people…
pharyngula | April 15, 2009I've been busy — I'm teaching genetics this term, and usually the first two thirds of the course is trivial to prepare for — we're covering Mendelian genetics, and the early stuff is material the students have seen before and are at least generally familiar with the concepts, and all I have to do is cover them a little deeper and with a stronger quantitative component. That's relatively easy.
The last part of the course, though, is where we start moving into uncharted waters for them, and every year I have to rethink how I'm going to cover the non-Mendelian concepts, and sometimes my ideas…
razib | April 15, 2009Genetic Evidence of Geographical Groups among Neanderthals:
The Neanderthals are a well-distinguished Middle Pleistocene population which inhabited a vast geographical area extending from Europe to western Asia and the Middle East. Since the 1950s paleoanthropological studies have suggested variability in this group. Different sub-groups have been identified in western Europe, in southern Europe and in the Middle East. On the other hand, since 1997, research has been published in paleogenetics, carried out on 15 mtDNA sequences from 12 Neanderthals. In this paper we used a new methodology…
edyong | April 14, 2009On November 1st, 1700, an entire dynasty of kings came to a crashing end with the death of Charles II of Spain. Charles had neither a pleasant life nor a successful reign. He was physically disabled, mentally retarded and disfigured. A large tongue made his speech difficult to understand, he was bald by the age of 35, and he died senile and wracked by epileptic seizures. He had two wives but being impotent, he had no children and thus, no heirs. Which is what happens after 16 generations of inbreeding.
Charles II was the final king of the Spanish Habsburg dynasty (see family tree), part of a…
razib | April 14, 2009
The Hapsburgs are one of those royal families who are relatively well known, and in the minds of the public are to a great extent the emblems of the downsides of inbreeding. To painting to the left is of Charles II, king of Spain, the last of the Spanish Hapsburgs, and an imbecile whose premature death at the age of 39 ushered in a period of dynastic chaos which led to the War of Spanish Succession These conflicts between France and other European powers were one of those turning points in history, a sad capstone to the long reign of the Sun King, Louis the XIV. France's position as the…
razib | April 14, 2009Accelerated Adaptive Evolution on a Newly Formed X Chromosome:
Sex chromosomes originated from ordinary autosomes, and their evolution is characterized by continuous gene loss from the ancestral Y chromosome. Here, we document a new feature of sex chromosome evolution: bursts of adaptive fixations on a newly formed X chromosome. Taking advantage of the recently formed neo-X chromosome of Drosophila miranda, we compare patterns of DNA sequence variation at genes located on the neo-X to genes on the ancestral X chromosome. This contrast allows us to draw inferences of selection on a newly…
razib | April 13, 2009Over at Secular Right I point out that Romania is set to decriminalize consensual sexual relations between adult first-order kin. That is, incest. There are a few angles that this story offers. First is the moral-ethical one. From a rational individualist perspective how reasonable are laws which ban consensual sex between adults who just happen to share distinctive genetic information? The love that dare not speak its name because of alleles which are identical by descent?
Of course all this rational talk is irrelevant for most people. Incest is gross, repugnant and immoral. Not because…
razib | April 13, 2009Over at Gene Expression Classic p-ter points to an interesting paper, Genetic Architecture of Tameness in a Rat Model of Animal Domestication:
A common feature of domestic animals is tameness - i.e. they tolerate and are unafraid of human presence and handling. To gain insight into the genetic basis of tameness and aggression, we studied an intercross between two lines of rats (Rattus norvegicus) selected over more than 60 generations for increased tameness and increased aggression against humans, respectively. We measured 45 traits, including tameness and aggression, anxiety-related traits,…
razib | April 11, 2009Science News has an interesting piece up, Shared Differences: The architecture of our genomes is anything but basic. The main focus is on genetic variation, the possibility that there might be important information in copy number variance, and that the common disease-common variant hypothesis is dead. At least for complex traits that we're interested in like schizophrenia. If any of this is unfamiliar or confusing, I recommend the article, it even has references to the primary literature that you can follow up on.
razib | April 11, 2009The leader author of the PLoS Genetics paper Inferring the Demographic History of African Farmers and Pygmy Hunter-Gatherers Using a Multilocus Resequencing Data Set, which I blogged a few days ago left a clarifying comment:
I just have few remarks. I do not expect that the Bantu expansions are responsible for the separation of Western and Eastern Pygmies. In a recent article in Current Biology, Paul Verdu and colleagues showed that the separation of Pygmy groups, but only those from the Western part of sub-Saharan Africa, diverged concomitantly with Bantu expansions (3,000-5,000 years ago…
razib | April 10, 2009Signatures of natural selection are not uniform across genes of innate immune system, but purifying selection is the dominant signature:
We tested the opposing views concerning evolution of genes of the innate immune system that (i) being evolutionary ancient, the system may have been highly optimized by natural selection and therefore should be under purifying selection, and (ii) the system may be plastic and continuing to evolve under balancing selection. We have resequenced 12 important innate-immunity genes (CAMP, DEFA4, DEFA5, DEFA6, DEFB1, MBL2, and TLRs 1, 2, 4, 5, 6, and 9) in healthy…
razib | April 9, 2009Inferring the Demographic History of African Farmers and Pygmy Hunter-Gatherers Using a Multilocus Resequencing Data Set:
The transition from hunting and gathering to farming involved a major cultural innovation that has spread rapidly over most of the globe in the last ten millennia. In sub-Saharan Africa, hunter-gatherers have begun to shift toward an agriculture-based lifestyle over the last 5,000 years. Only a few populations still base their mode of subsistence on hunting and gathering. The Pygmies are considered to be the largest group of mobile hunter-gatherers of Africa. They dwell in…
razib | April 9, 2009Jonah's interview of Judith Rich Harris is much recommended. Clearly related to my post on adoptive parents.
razib | April 9, 2009Via Dienekes, Differential parental investment in families with both adopted and genetic children:
Stepchildren are abused, neglected and murdered at higher rates than those who live with two genetically related parents. Daly and Wilson used kin selection theory to explain this finding and labeled the phenomenon "discriminative parental solicitude." I examined discriminative parental solicitude in American households composed of both genetic and unrelated adopted children. In these families, kin selection predicts parents should favor their genetic children over adoptees. Rather than looking…
razib | April 8, 2009Women May Be Sniffing Out Biologically-relevant Information From Underarm Sweat:
Sniffed alone, the underarm odors smelled equally strong to men and women. When fragrance was introduced, only two of 32 scents successfully blocked underarm odor when women were doing the smelling; in contrast, 19 fragrances significantly reduced the strength of underarm odor for men.
...
Not only were women better smellers the men, but male odors were harder to block than female odors. Even though underarm odors from the two sexes didn't differ in how strong they smelled, only
So women have a better sense of…
razib | April 8, 2009I only know about Phenylketonuria (PKU) because it is an elementary example of an autosomal recessive disease. Newborns are routinely tested, because those with PKU may develop mental retardation on a normal diet. That's about all I knew, but this from Wikipedia:
If PKU is diagnosed early enough, an affected newborn can grow up with normal brain development, but only by eating a special diet low in phenylalanine for the rest of his or her life. This requires severely restricting or eliminating foods high in phenylalanine, such as meat, chicken, fish, nuts, cheese, legumes and other dairy…
razib | April 3, 2009A new paper on the genetics of height, Meta-Analysis of Genome-Wide Scans for Human Adult Stature Identifies Novel Loci and Associations with Measures of Skeletal Frame Size:
Recent genome-wide (GW) scans have identified several independent loci affecting human stature, but their contribution through the different skeletal components of height is still poorly understood. We carried out a genome-wide scan in 12,611 participants, followed by replication in an additional 7,187 individuals, and identified 17 genomic regions with GW-significant association with height. Of these, two are entirely…
razib | April 1, 2009Richard Dawkins: 'There is something illogical about the fear of death':
The comfort of a dying soldier, the succour for a grieving mother or belief in the after-life of a widower - is it still possible to see the utility of certain psychological aspects in some religious beliefs or customs? [Interviewer - R]
I do see a psychological value, if it does have a real value. I would not wish to be the person who destroys that person's psychological succour. I would not compromise with my public speaking out in the public forum and writing. But if I was visiting someone who was recently bereaved, I…
razib | March 31, 2009Estimating the number of unseen variants in the human genome:
...Consistent with previous descriptions, our results show that the African population is the most diverse in terms of the number of variants expected to exist, the Asian populations the least diverse, with the European population in-between. In addition, our results show a clear distinction between the Chinese and the Japanese populations, with the Japanese population being the less diverse. To find all common variants (frequency at least 1%) the number of individuals that need to be sequenced is small (â¼350) and does not differ…