genetics

Dave Munger has a post up about discernment when it comes to wine. The Munger sayeth: Researchers have known for some time that not everyone has the same ability to detect tastes. Some people -- "super-tasters" -- are especially sensitive to a wide range of tastes. As it turns out, whether or not you're a super-taster may come down to your ability to detect a single molecule: 6-n-propylthiouracil, or PROP for short. Those who can taste PROP find it incredibly bitter, but super-tasters are also extra sensitive to saltiness, sweetness, and even tactile sensations in the mouth. I've posted on…
As I have noted before one of the consequences of genomic analysis techniques becoming relatively cheap and accessible is that they are now viable tools toward exploring a host of fundamentally non-genetic questions. That is, instead of exploring the dynamics of evolutionary biology, they can be used to shed light upon other sorts of dynamics. Sometimes the questions are fuzzy and the techniques can be laborious; e.g., the extraction and analysis of ancient DNA and their subsequent insertion into an explanatory framework where the non-genetic data are patchy. On other occasions, the…
I really like the PLoS journals. Their mission -- to make research freely available -- is totally awesome. And, on top of that, the journals publish very interesting research. PLoS Biology is a top notch journal, with papers on par with those in Science and Nature. And the specialty journals, like PLoS Genetics and PLoS Computational Biology, consistently have articles that I find quite attractive. But the website is totally fucked. I can't access most of the articles in PLoS Genetics. Thankfully, the articles are all mirrored on PubMed Central, but it's a major pain to track those down after…
There is a new paper out suggesting that the Flores hominids, known as Hobbits, were "human endemic cretins." From the abstract of this paper: ... We hypothesize that these individuals are myxoedematous endemic (ME) cretins, part of an inland population of (mostly unaffected) Homo sapiens. ME cretins are born without a functioning thyroid; their congenital hypothyroidism leads to severe dwarfism and reduced brain size, but less severe mental retardation and motor disability than neurological endemic cretins. We show that the fossils display many signs of congenital hypothyroidism, including…
Yann points me to a new paper, Complex signatures of selection for the melanogenic loci TYR, TYRP1 and DCT in humans: Diversity patterns clearly evidence adaptive selection in pigmentation genes in Africans and Asians. In Europeans, the evidence is more complex, and both directional and balancing selection may be involved in light skin. As a result, different non-African populations may have acquired light skin by alternative ways, and so light skin, and perhaps dark skin too, may be the result of convergent evolution. As noted above the paper, which is provisional and subject to later…
Or, perhaps, the truth is more complicated, as revealed in the comments of that post.
David B gives an excellent overview of some of the issues with Stephen Oppenheimer's The Origins of the British.
There's a new paper which is getting some press buzz; here's a typical headline, Immune system differences found. That's as banal as can be: of course immune systems differ, there's a reason that MHC loci are very polymorphic. Our own immune diversity is the only way we can equalize the unfair "arms race" with the bugs who are always an adaptive peak ahead of us. It seems very likely that on the MHC loci many alleles become more fit as their frequency declines to very low levels because the pathogens which are optimized to "beat" them in the game of life can't find hosts and disappear. At…
Evolgen points me to a new blog, Computational Biology and Evolution. Only quibble, http://bioinf.cs.auckland.ac.nz/ isn't a memorable domain....
I'm easily annoyed. A lot of things piss me off. Here are the things that irked me today: Fake St. Patrick's Day. A large drinking school schedules Spring Break the same week as St. Patty's Day, and they do it two years in a row. This pisses off the students because it costs them an official drinking day (they'll be drunk on spring break regardless if it's St. Patrick's day). So, the students schedule their celebration of St. Patrick's day for the weekend before Spring Break. There's a few hundred drunk douchebags walking around town in green shirts and stupid hats today. It's goddamn…
The flu is caused by the influenza virus, of which there are several types. H1N1 is known as the "Spanish Flu," H2N2 as the "Asian Flu" and so on. These funny letters and numbers refer to specific genotypes. The H1N1 is the version of the flu that caused the Great Influenza Pandemic of 1918 and 1919, which was responsible for the death of between 50 and 100 million people. Considering that the difference between a bird or pig flu that may be hanging around in the background and a human pandemic causing flu can be a few dozen changes in the genome, understanding the evolutionary patterns…
Photograph of a chicken. Click to see larger version. From PLOS article cited in blog post. Where and when were chickens domesticated? From whence the humble chicken? Gallus gallus is a domesticated chicken-like bird (thus, the name "chicken") that originates in southeast Asia. Ever since Darwin we've known that the chicken originated in southeast Asia, although the exact details of which one or more of several possible jungle fowls is the primal form has been debated. The idea that more than one wild species contributed to the early chicken has been on the table for a long time,…
In my post below about a possible locus to look at to explain the normal variation in hair form we see around us a reader asked: I was once suckered into giving a course on animal ecophysiology (I was told it was basic ecology until after it was too late to back out) which was a traumatic experience as I've only taken one university-level animal physiology course in my life. One of the students asked what the advantage is of kinky hair. I wondered if it might be a better insulator against the heat of the sun but that's just guessing. I also said that perhaps the question should be the other…
Severe Acute Respiratory Syndrome (SARS) is caused by a coronavirus that is now believed to have originated in bats. In 2004, thousands of palm civets (a cat like carnivore) were killed off in China because it was believed that they were the main reservoir of this disease. Ooops. It appears now that the civets had contracted the disease from humans, rather than the other way around. Nearly a thousand people among the 8,000 or so infected died during that outbreak, and no human infections are known since early 2004. A number of different researchers who have been looking at the source…
tags: researchblogging.org, bipolar disorder, clinical depression, mental illness, mood disorder, functional genomics, blood test, biomarkers Image: Florida Department of Law Enforcement. According to the United States Department of Health and Human Services, serious mental illnesses affect approximately 44 million Americans. Serious mental illnesses include mood disorders; depression and bipolar disorder. Unfortunately, correctly diagnosing mental illnesses, such as bipolar disorder, appears to be a sort of voodoo science that depends upon the skill of the mental health professional…
A DNA phylogeny based on over 200 species of lemurs and related species is now available. Lemurs are part of the large group known as the strepsirrhine primates (yes, three r's...)From the abstract of this paper, coming out in March in Genome Research: ... strepsirrhine primates are of great interest ... due to their phylogenetic placement as the sister lineage to all other primates. Previous attempts to resolve the phylogeny of lemurs employed limited mitochondrial or small nuclear data sets, with many relationships poorly supported or entirely unresolved. We used genomic resources to…
I saw this paper in Nature Genetics, Disruption of P2RY5, an orphan G protein-coupled receptor, underlies autosomal recessive woolly hair: The genetic determinants of hair texture in humans are largely unknown. Several human syndromes exist in which woolly hair comprises a part of the phenotype; however, simple autosomal recessive inheritance of isolated woolly hair has only rarely been reported...In all cases, we discovered pathogenic mutations in P2RY5, which encodes a G protein-coupled receptor and is a nested gene residing within intron 17 of the retinoblastoma 1 (RB1) gene. P2RY5 is…
Parallel Selection on TRPV6 in Human Populations (Open Access): ...The selective footprints, however, are significantly differentiated between non-African populations and estimated to be younger than an ancestral population of non-Africans. The possibility of a single selection event occurring in an ancestral population of non-Africans was tested by simulations and rejected. The putatively-selected TRPV6 haplotype contains three candidate sites for functional differences, namely derived non-synonymous substitutions C157R, M378V and M681T. Potential functional differences between the ancestral…
Excitement on science blogs! Karen James of the Beagle Project Blog has just today published a paper in PLoS ONE: Diversity Arrays Technology (DArT) for Pan-Genomic Evolutionary Studies of Non-Model Organisms: Background High-throughput tools for pan-genomic study, especially the DNA microarray platform, have sparked a remarkable increase in data production and enabled a shift in the scale at which biological investigation is possible. The use of microarrays to examine evolutionary relationships and processes, however, is predominantly restricted to model or near-model organisms.…
John Hawks has commentary on a new paper, A genome-wide signature of positive selection in ancient and recent invasive expansions of the honey bee Apis mellifera. John's point is that evolutionary dynamics are evolutionary dynamics. I'm sure as a species which spans multiple continents and all the latitudes and longitudes we might be able to learn a bit about ourselves from examining other lineages of great geographic range.