genetics
razib | May 29, 2008Just got a copy of Short Guide to the Human Genome, put out by Cold Spring Harbor Laboratory. It's a fun little review; appropriate for browsing during your "in-between" time. As the title emphasizes this guide is characterized by extreme brevity, under 200 pages. Nevertheless it attempts a survey of the major results which have come to light over the past decade in human genomics. This isn't really a primer, it assumes you know what UTR stands for and why spliceosomes are important. In other words, return on investment is probably only there if you are reasonably familiar with the basics…
gregladen | May 28, 2008 Photograph of Francis S. Collins Just passing along the details from Associated Press:
WASHINGTON (AP) -- The government is losing its gene guru: Dr. Francis Collins, who helped lead the breakthrough unraveling of the human genetic code -- and found common ground between the belief in God and science -- is resigning.
Collins, arguably the nation's most influential geneticist, announced Wednesday that he will leave the National Institutes of Health this summer, to write a book and explore other opportunities.
The folksy geneticist helped translate the complexities of DNA into everyday…
evolgen | May 28, 2008Francis Collins, head of the National Human Genome Research Institute (NHGRI), will be stepping down from that position in August. Collins has overseen the sequencing of the human genome, the HapMap project, the ENCODE project, and many other large advances in genomics. The NHGRI has had a major impact in the field of genetics while Collins was at its helm.
Collins also has a history of putting his foot in his mouth -- not that it's a bad thing to do so (lord knows my foot's spent more time lodged in my face than on the ground). He's been incorrect about morality and human evolution, to name…
edyong | May 21, 2008
The era of genetic sequencing has revealed as much about the ties that bind us to other animals as the differences that set us apart. Often, comparing the genomes of different species shows that large changes in body size, shape and form are not mirrored by similar changes at a genetic level. New adaptations typically come about through small changes that redeploy existing genes to different ends, rather than raw innovation.
Snakes are an exception. A new study by Todd Castoe and Zhi Jiang at the University of Colorado has shown that the lifestyle of serpents is so unique that some…
razib | May 21, 2008One of the main facts about American life is hypodescent, "the practice of determining the lineage of a child of mixed-race ancestry by assigning the child the race of his or her more socially subordinate parent." Barack Obama & the Kenyan politician Raila Odinga (who, probably falsely, claims to be Obama's first cousin) are both "black," despite the fact that when compared to each other Obama's substantial European ancestry is rather clear. I recall years ago watching the Oprah Winfrey television show where they were discussing the issue of self-hatred with a young black woman who was…
razib | May 20, 2008Notes on Sewall Wright: Wright's F-statistics:
A preliminary question is one of terminology. What, if anything, does the letter 'F' stand for? One plausible answer is that it stands for 'fixation', since among other things the F-statistics can be used to measure the rate at which alleles tend to be 'fixed'. Wright himself in his later writings sometimes refers to F as an 'index of fixation'.
Believe it or not, Fst is one of thos population genetic concepts you've almost certainly encountered no matter your background.
Related: On Reading Wright, Notes on Sewall Wright: Path Analysis and…
gregladen | May 20, 2008 Could even this bird be reanimated, gene by gene? When you are extinct you're extinct. Everything about you is dead and gone. There are no more of you, every individual in your species is kaput, non existent, used up, as the Pima Indians would say, you are hokum (like a car with a flat tire). In fact, you are hohokum (like a car with no tires). Your existence is erased. You are as blotto as a budgie in Burbank.
Indeed, every bit of your being, every gene in your genome, every base pair in your DNA, is no longer extant.
...
Or is it?
Well, scientists have recently taken a bit of…
razib | May 19, 2008A Genome-Wide Association Study Identifies Novel Alleles Associated with Hair Color and Skin Pigmentation:
It has been a longstanding hypothesis that human pigmentation is tightly regulated by genetic variation. However, very few genes have been identified that contain common genetic variants associated with human pigmentation. We scanned the genome for genetic variants associated with natural hair color and other pigmentary characteristics in a multi-stage study of more than 10,000 men and women of European ancestry from the United States and Australia. We identified IRF4 and SLC24A4 as loci…
razib | May 19, 2008Will Saletan makes an analogy between cousin marriage and delayed (i.e., 40something) motherhood:
If Bittles' numbers are correct, they substantiate a somewhat embarrassing point made by defenders of cousin marriage. Embarrassing, that is, to all of us good Western folk who turn up our noses at the practice. The British Down's Syndrome Association has posted a chart showing the risk of producing a baby with the syndrome at various maternal ages. From age 20 to age 31, the risk doubles. From 31 to 35, it doubles again. From 35 to 38, it doubles again. From 38 to 41, it more than doubles again…
razib | May 19, 2008OK, the title is deceptive; but the reality is kind of cool in my opinion (you may not share my normative filter; some people prefer the dead). PLOS One is publishing a paper which takes Tasmanian Tiger genetic material, and re-expresses it in vivo in mice! The reasoning for this is pretty straightforward; there are phylogenetic questions which extant lineages can't always answer. With the emergence of the whole field of ancient DNA extraction and sequencing an entirely new avenue of scientific analysis is opening up. This paper cites the work from last year on Neandertal MC1R; if we're…
razib | May 15, 2008Since everyone is talking about the fact that the Polar Bear how become a protected species, I thought I'd point to this cool study, Mitochondrial DNA Phylogeography of the North American Brown Bear and Implications for Conservation. Additionally, check out the figure below....
razib | May 15, 2008I know I've posted on this topic before, but I thought I'd revisit it again. You do know that sometimes population bottlenecks can actually result in more variation being freed up for selection? This may strike you as a bit strange; after all, the power of selection to effect phenotypic change is proportional to genetic variance, specifically, additive genetic variance. Population bottlenecks imply a reduction in effective population size, the increase of sample variance across generations, that is, random genetic drift. As population size drops the stochastic change in gene frequencies…
razib | May 13, 2008Ron Bailey in Reason, The Genetics of Ensoulment:
Advances in stem cell research may be provoking a kind of "God of the Gaps" retreat on the moral status of embryos. People who subscribe to God of the Gaps thinking believe that the hand of God can be seen in those things which science cannot explain. In this case, the closing gaps in the details of molecular biology are forcing pro-lifers into an uncomfortable corner where they have to decide whether or not a cell can be imbued with a soul by turning a single gene on or off.
razib | May 12, 2008Another article about cousin marriage in the UK. The issue here is simple; you have a National Health Service which covers everyone, and doctors are noticing that Pakistanis are overrepresented in many cases of recessive diseases. The culprit is probably cousin marriage. Here are two points which are both valid:
'In our local school for deaf children, half the pupils are of Asian origin though Asians only form about 20 per cent of the population,' said Ann Cryer, MP for Keighley. 'I also know of several sets of parents in my constituency who are cousins and whose children are severely…
razib | May 12, 2008Last year p-ter put up a post pointing to useful online tools such as Haplotter. One of the great things about biology today is that so much of the data from genomics is being thrown out there within reach of the plebs. And a lot of value is being added through user interfaces which smooth the connection between you and these databases. So check out NextBio; from the FAQ:
NextBio is a life science search engine that enables researchers and clinicians to access and understand the world's life sciences information. With NextBio, in just one click you can search through tens of thousands of…
clock | May 11, 2008It takes 38 minutes for the E.coli genome to replicate. Yet, E.coli can bo coaxed to divide in a much shorter time: 20 minutes. How is this possible?
Larry poses the riddle and provides the solution.
The key is that complex biochemical processes are taught sequentially, one by one, because that is how we think and process information. Yet, unless there is a need for precise timing (in which case there will be a timer triggering the starts and ends of cellular events), most processes occur all the time, simultaneously, in parallel. How do we teach that?
pharyngula | May 10, 2008
Finals week is upon me, and I should be working on piles of paper work right now, but I need a break … and I have to vent some frustration with the popular press coverage of an important scientific event this week, the publication of a draft of the platypus genome. Over and over again, the newspaper lead is that the platypus is "weird" or "odd" or worse, they imply that the animal is a chimera — "the egg-laying critter is a genetic potpourri — part bird, part reptile and part lactating mammal". No, no, no, a thousand times no; this is the wrong message. The platypus is not part bird, as…
razib | May 9, 2008Over at The Scientist Neil S. Greenspan has an article up, Darwin and deduction:
One of the most remarkable but insufficiently noted features of Charles Darwin's conception of evolution is that its logical implications are still being worked out. I am not merely claiming that experimental and observation studies continue to make use of and bear on Darwinian ideas and principles. I am calling attention to the fact that after almost a century and a half, new deductions are still being teased out of his very fertile axioms of descent with modification and natural selection.
One of the primary…
mikethemadbiologist | May 9, 2008As I've mentioned before, one of the things that always mystifies me about creationists (most, anyway) is that they seem to be stuck in a scientific time warp: there's no recognition that any new progress has been made since 1859.
Of course, if creationists did recognize the progress that's been made since 1859, then they might not be creationists anymore. The reason I raise this is that John Timmer, at Ars Technica, summarizes what he learned about natural selection at a Rockfeller symposium about evolution:
Natural Selection: Explore Evolution [the Discovery Institute's 'biology' textbook…
razib | May 8, 2008Notes on Sewall Wright: Genetic Drift:
Continuing my series of notes on the work of Sewall Wright, this one deals with the subject of genetic drift. I had originally planned to call this note 'Inbreeding and the decline of genetic variance', but anyone interested in the matters covered here, and searching for them on the internet, is far more likely to search for 'genetic drift'. This is one of the subjects most closely associated with Wright, to the extent that genetic drift was formerly often known as the 'Sewall Wright Effect'. My main aim is to help people follow Wright's own derivation…