human genetics
mikethemadbiologist | October 26, 2010A problem in genome-wide association studies ("GWAS") is the"missing heritability" issue--identified genetic variation can only account for a small fraction of the estimated genetic contribution to variation in that trait. Razib has a good roundup of several explanations (and I added some speculation about nearly-neutral mutations).
GWAS also have problems accurately characterizing the trait. For example, not all heart diseases (note the plural) are alike, so we have to be certain that we accurately assess the trait of interest. But what is very rarely discussed is the environmental…
mikethemadbiologist | March 31, 2010A while ago, I described how previous decisions allowing the patenting of human genes--and thereby making cheap, affordable diagnostics impossible--flew in the face of the goal of federally-funded research. There's no reason to patent something and charge thousands of dollars for something a high school student could do (PCR and sequencing). From The NY Times (italics mine):
Judge Sweet, however, ruled that the patents were "improperly granted" because they involved a "law of nature." He said that many critics of gene patents considered the idea that isolating a gene made it patentable "a '…
razib | March 16, 2010Dienekes has reposted some of the abstracts from the meeting of the American Association of Physical Anthropologists. This one caught my eye, Genetic analyses reveal a history of serial founder effects, admixture between long separated founding populations in Oceania, and interbreeding with archaic humans:
Genetic anthropologists continue to debate whether human neutral genetic variation primarily reflects a continuum of demes connected by local gene flow or colonization and serial founder effects. A second unresolved issue concerns the genetic contribution of archaic species to the modern…
razib | February 4, 2010Highly Punctuated Patterns of Population Structure on the X Chromosome and Implications for African Evolutionary History:
It is well known that average levels of population structure are higher on the X chromosome compared to autosomes in humans. However, there have been surprisingly few analyses on the spatial distribution of population structure along the X chromosome. With publicly available data from the HapMap Project and Perlegen Sciences, we show a strikingly punctuated pattern of X chromosome population structure. Specifically, 87% of X-linked HapMap SNPs within the top 1% of FST…
razib | November 23, 2009Cannibalism is a controversial topic. It is routine for particular societies to accuse "barbarians", enemies, or evil mythological figures, of cannibalism. When it comes to the archaeological record some skeptics have claimed that like "sacred objects" too often human remains found in peculiar circumstances are ascribed to human sacrifice or cannibalism. In Did Adam and Eve Have Navels? Martin Gardner lays out the skeptical case for why cannibalism is rare to non-existent, and rather something which emerges from the imaginations of ethnographers and archaeologists, or is rooted in…
razib | October 14, 2009Reading the papers on Ardipithecus ramidus which just came out in Science one of the take-home points that jumps out at me is that extant apes may be very misleading analogs to extinct hominins. Here is Owen Lovejoy:
In retrospect, clues to this vast divide between the evolutionary trajectories of African apes and hominids have always been present. Apes are largely inept at walking upright. They exhibit reproductive behavior and anatomy profoundly unlike those of humans. African ape males have retained (or evolved, see below) a massive SCC and exhibit little or no direct investment in their…
razib | September 22, 2009Sometimes I wonder if the period between the publication of The History and Geography of Human Genes and The Journey of Man, roughly from the mid-90s to the early 2000s, will be seen as a golden age for historical population genetics in hindsight. A few weeks ago I pointed to new data based on DNA extraction which really confuses the picture of how Europe was populated over the past 25,000 years. It seems the more data we get, the more interesting things get. In the late 1990s the emergence of powerful technologies to extract and amplify genetic material and sequence it shed light on several…
razib | September 12, 2009The Evolutionary Origin of Man Can Be Traced in the Layers of Defunct Ancestral Alpha Satellites Flanking the Active Centromeres of Human Chromosomes. The authors are Russian, so I think the somewhat grand and archaic first portion of the title can be explained as a mater of translation. Here's the author summary:
The primate centromere evolves by amplification of alpha satellite sequences in its inner core, which expands and moves the peripheral sequences sideways, forming layers of different age in the "pericentromeric" area. The expanding centromere model poses two main questions: (1)…
razib | May 26, 2009On this week's Science Saturday John Horgan interviews Richard Wrangham. The second half of the conversation focuses on Wrangham's new book, Catching Fire: How Cooking Made Us Human. I've heard pieces of the arguments mooted in the back & forth before, but it looks like in this book they're all brought together. Humans are a large animal with a very small gut, so we need to maximize the bang-for-the buck when it comes to what we eat. Unlike gorillas and to a lesser extent chimpanzees we just aren't able to process enough low quality vegetable matter to keep ourselves going. Part of this…
razib | May 19, 2009400-500 years ago in the midst of the Great Dying somewhere the indigenous inhabitants of the New World suffered mortality rates on the order of 90-95%. This was almost certainly due to the facts of evolutionary history; the indigenous peoples had little defense against Eurasian pathogens. A result has been the reality that most of the New World is inhabited by European, African or mixed populations. But there are exceptions. In Mesoamerica there is still an indigenous dominated region from southern Mexico into the highlands of Guatemala. More substantially the highlands of the Andes, and…
razib | May 11, 2009Dienekes reports on an abstracts for paper presentations at the ESHG 2009. This was is particularly interesting:
European Lactase Persistence Allele is Associated With Increase in Body Mass Index
J. A. Kettunen et al.
The global prevalence of obesity, usually indexed by body mass index (BMI) cut-offs, has increased significantly in the recent decades, mainly due to positive energy balance. However, the impact of a selection for specific genes cannot be excluded. Here we have tested the association between BMI and one of the best known genetic variants showing strong selective pressure: the…
razib | May 5, 2009In the comments below on the post on human population structure there was some request for a bigger global perspective. Below the fold I've placed a table with FST values which compare each population to the other. This an older population genetic statistic derived from the work of Sewall Wright, but you are almost certainly familiar with the talking point that "85% of variation is within races, and only 15% between." That is an FST insight. The higher the FST the greater the proportion of genetic variation which can be attributed to between population differences, so it serves as a rough…
mikethemadbiologist | March 11, 2009A while ago, economist Paul Krugman described the institutional loss of knowledge in the discipline of economics:
And the latter group, the equilibrium macro side, was so convinced of the logical correctness of its position that schools dominated by that view stopped teaching demand-side economics. (Schools dominated by new Keynesians, on the other hand, did teach real business cycle theory.) I haven't been able to dig up the quote, but somewhere along the line Ed Prescott declared that his students wondered who Keynes was, because he was never mentioned in their courses.
And those trained…
mikethemadbiologist | February 13, 2009A recent paper in PLoS argues that variation in genes that regulate dopamine (5-HTTLPR) and serotonin neurotransmission (DRD4) influences financial risk taking: at the 5-HTTLPR gene, one homozygous form (two identical copies or alleles) took on 28 percent less risk, while those who had the '7-repeat' form of the DRD4 gene took 25 percent more risk. The Mad Biologist has issues regarding this study.
To me, the total amount of money the subjects could win (or not win) could influence the results. Someone who is risk adverse at $23 might be risk accepting at $2,300: if the participant were…
mikethemadbiologist | January 14, 2008According to the Boston Globe, bisphenol A levels lower than those found in 93% of people led to obesity in mice:
Thousands of chemicals have come on the market in the past 30 years, and some of them are showing up in people's bodies in low levels. Scientists studying obesity are focusing on endocrine disrupters - which have already been linked to reproductive problems in animals and humans - because they have become so common in the environment and are known to affect fat cells.
...A recent US Centers for Disease Control and Prevention study found that about 93 percent of the US population…
mikethemadbiologist | June 22, 2007With Massachusetts having prevented the attempt to de-legalize gay marriage, there is much discussion about the topic. But this story about a splinter Mormon group highlights the importance of outlawing one type of marriage: marriages between close relatives. By way of Lance Mannion, from Reuters (italics mine):
In a dusty neighborhood under sheer sandstone cliffs studded with juniper on the Arizona-Utah border, a rare genetic disorder is spreading through polygamous families on a wave of inbreeding.
The twin border communities of Hildale, Utah, and Colorado City, Arizona, have the world…
mikethemadbiologist | June 7, 2007I like much of Matt Yglesias' writing. But he still doesn't appreciate how science and evolution affect public policy issues. As many of you know, three out of ten Republican presidential candidates stated that they don't believe in evolution at one of the presidential debates. Yglesias comments on Huckabee's response:
I see that Jamie Kirchick didn't care for the reply at all: "Sorry, but if someone believes in fairy tales, I think that's pretty relevant to their qualifications as president." But why? The core of Huckabee's answer is here:
It's interesting that that question would even…
mikethemadbiologist | March 14, 2007You might not know this, but your body produces a whole bunch of antibacterial compounds, one of which is lactoferrin. It's found in breast milk and mucosal substances such as tears and saliva. Lactoferrin hasn't really been investigated as a medical antibiotic because many disease-causing bacteria (e.g., E. coli) also live on (and in) people as harmless commensals, and consequently, have evolved resistance to lactoferrin. However, a new paper suggests that some lactoferrin might kill these pathogens.
The authors found that people with a single amino acid change in lactoferrin "were more…
mikethemadbiologist | September 3, 2006Over at Pandagon, Pam's aunt had her ancestry traced using mitochondrial DNA ('mtDNA'). The results given to her aunt were that she is:51% Sub-Saharan Africa (she didn't get any information as to country)
37% European (we have known ancestry in Ireland and England)
12% Native American (likely a NY or Connecticut tribe; we thought Shinnecock, but have not been able to confirm)
How is it even possible to conclude that one is 'percent-anything' based on a mtDNA haplotype? Is there something about the test that I'm missing here?
One really can't say that an mtDNA haplotype is 50% X and 50% Y,…