Friday Five #8 - Welcome 2010

So I was back at work this week, trying to finish a few things prior to the impending end of the decade if it is actually the end of the decade. This a matter of whether you believe if there is a year 0, which is unlikely. So here we go with this Friday's top five.

1) Explaining the Imperfection of the Molecular Clock of Hominid Mitochondria - It should be now surprise at this point that the mtDNA clock isn't all that great of time device, you definitely would not want to set you clock by it.

The molecular clock of mitochondrial DNA has been extensively used to date various genetic events. However, its substitution rate among humans appears to be higher than rates inferred from human-chimpanzee comparisons, limiting the potential of interspecies clock calibrations for intraspecific dating. It is not well understood how and why the substitution rate accelerates. We have analyzed a phylogenetic tree of 3057 publicly available human mitochondrial DNA coding region sequences for changes in the ratios of mutations belonging to different functional classes. The proportion of non-synonymous and RNA genes substitutions has reduced over hundreds of thousands of years. The highest mutation ratios corresponding to fast acceleration in the apparent substitution rate of the coding sequence have occurred after the end of the Last Ice Age. We recalibrate the molecular clock of human mtDNA as 7990 years per synonymous mutation over the mitochondrial genome. However, the distribution of substitutions at synonymous sites in human data significantly departs from a model assuming a single rate parameter and implies at least 3 different subclasses of sites. Neutral model with 3 synonymous substitution rates can explain most, if not all, of the apparent molecular clock difference between the intra- and interspecies levels. Our findings imply the sluggishness of purifying selection in removing the slightly deleterious mutations from the human as well as the Neandertal and chimpanzee populations. However, for humans, the weakness of purifying selection has been further exacerbated by the population expansions associated with the out-of Africa migration and the end of the Last Ice Age.

2) Why Diseased Heart Muscle Cells Don't Communicate Properly An interesting article from Science Daily on a gene associated (EB1) with heart rate gap junctions.

3) Even If Obama Passed Single Payer, Primary Care Doctors Still Wouldn't Get It: A good look at one of the major problems with health care in this country today as physicians treat the disease and not the patient. One of the major reasons that an anthropological perspective would help medical schools and their students.

4) Richard Dawkins on ‘Elders’ (via Neuroanthropology): A good look at Richard Dawkins and why he probably isn't the best spokesman for a defender of evolutionary theory. He tends to look at those who having any sort of faith as the great unwashed masses of ignorance, which is probably not the best strategy for explaining evolution. The point being here that if your goal is to educate it is best not to berate those seeking to learn. I think most of those that seek out Dawkins, already agree with him and this leads to an "O'Reily Show type effect", where those who listen are you perpuating what they already believe. This of course leads them to be less understanding when explaining evolutionary concepts to someone seeking knowledge.

5) Non-Darwinian estimation: My ancestors, my genes' ancestors This article from Genome Research is from a while ago but is an excellent review and rebuke of a number of studies that rely on the idea of identifying ancestry through genetics, particularly the program Structure, but then ignore all of assumptions associated with this technique.

There is widespread interest in characterizing the organization of human genetic variation around the world from a population perspective. Related to this are attempts to describe the pattern of genetic variation in the human species generally, including “recreational” genomics, the genome-based estimation of the ancestry of individuals. These approaches rest on subtle concepts of variation, time, and ancestry that are perhaps not widely appreciated. They share the idea that there are, or were, discrete panmictic human populations such that every person is either a member of such a population or is an admixed descendant of them. Ancestry fraction estimation is biased by assumptions about past and present human population structure, as when we trace ancestry to hypothetical unmixed ancestral populations, or assign an individual's ancestry to continental populations that are indistinguishable from classical “races.” Attempts to identify even individuals' local subpopulations are less precise than most (geneticists included) expect, because that is usually based on a small portion of a person's ancestry, relative to the much larger pool of comparably related ancestors. It is easier to show that two people have some relationship than to show who or where the actual ancestor was. There is an important distinction between individuals' demographic ancestry and the ancestry of their genes. Despite superficial appearances, these interpretations of genetic data are often based on typological rather than Darwinian thinking, raising important issues about the questions that are actually being asked.