This is not a joke – we can easily drop the last 3 or 4 nature genetics volumes for ignorance of basic facts. I have written here many times about the usefulness of current GWAs but missed the details of a Cell paper by McClellan & King that I am wholeheartedly supporting (although not all other science bloggers) Continue reading Drop the last 3 nature genetics volumes from the libraries
The New Scientist started a new essay this week
In 1856, geologist Charles Lyell wrote to Charles Darwin with a question about fossils. Puzzled by types of mollusc that abruptly disappeared from the British fossil record, apparently in response to a glaciation, only to reappear 2 million years later completely unchanged, he asked of Darwin: “Be so good as to explain all this in your next letter.” Darwin never did.
While preparing my new lectures on evolutionary medicine, Continue reading Be so good as to explain all this in your next letter
A Nature correspondence letter laments
Universities are experiencing a crisis of purpose, focus and content, rooted in a fundamental confusion about all three. The crisis is all the more visible as their pace of social, intellectual and technological change falls increasingly out of step with that outside. Furthermore, universities are largely reactive where they should be visionary and critical.
Of course, that’s right – how to study “biology”? What’s should be purpose, content and focus? Maybe that’s easier with “medicine” Continue reading A crisis of purpose, focus and content
I tried out everything but only one trick worked. Continue reading R timeout with read.table() and large datafiles
is my favorite quote of a scientist – the late Frederick Sanger. I would so much love to get an interview with him.
I have no idea where genetics is heading now. A Nature paper last week on the “population relevance of 95 loci for blood lipids” at least ends somewhere in the nowhere. Take not only 100 thousand participants but 100 million participants and you will get 95,000 loci – sorry to all my friends on the author list – that’s crap. Another, more interesting development during my recent absence in the Alpes comes by the Royal Society
In 1993 the world’s population was 5.5 billion; it is now 6.8 billion and is due to hit 7 billion by early 2012. A major new study looking at the implications of the changes in global population is being launched by the Royal Society with an expected conclusion in early 2012. […] Continue reading Does population matter?
At the Lindau Nobel site we can submit questions to Nobel prize winners. Most of them are trivial or even boring – basically how to make a career or what rank did you have in your university studentship. My proposal to ask there: “Is another information layer on top of the known DNA sequence?” You may want vote for my question, thanks!
One of the best questions so far is “Many people consider the peer-review system broken. If you share that opinion, do you have a solution?” by Clay Barnard.
Roy Glauber, Nobel Laureate in Physics 2005: The current system is pretty poor. So now it’s not a question of spending a lot of money, as it can be resolved very easily without. Good papers last and bad papers don’t. Individuals should rate the papers, although this may not need to be done in an official way.
Sir John Walker, Nobel Laureate in Chemistry, 1997: The peer review system does have problems, but it is the best we have got and I am very much opposed to replacing it with a numerical assessment system. It is a lousy way of assessing people and the pressure to change this system comes from science bureaucrats. This is because it is scientsists making decisions about scientists’ work and the bureaucrats don’t like that; they want to have control.
Jean-Marie Lehn, Nobel Laureate in Chemistry, 1987: That’s an interesting question! I have been interested in it for a very long time. I think we need to have a control otherwise things get in the literature that should not be there …
Here comes my most favorite paper in 2010 so far, clearly written and elegant in it’s simplicity. It is printed in this week’ Nature magazine
One reason for this is that epigenetic factors are sometimes malleable and plastic enough to react to cues from the external and internal environments. Such induced epigenetic changes can be solidified and propagated during cell division, resulting in permanent maintenance of the acquired phenotype.
Petronis sees heritability as multiple layers (like a Russian matryoshka doll) which is a far more appropriate view than the current DNA sequence based view.
The paper touches many points that I will also include in a forthcoming review where I am describing epigenetics as a buffering system before changes are permanently written in the genome, yea, yea.
I need to refer here to a post 3 years ago and the medical literature that genes frequencies may have changed rapidly between generations.
Any empirical proof of this hypothesis, however, is scarce so far. Or I have to say, until this week, when I found a study published earlier in PLoS ONE that tackles this problem: Selection for Genetic Variation Inducing Pro-Inflammatory Responses under Adverse Environmental Conditions in a Ghanaian Population Continue reading Genes on the fast lane
Took me some time to find the famous Forbes June 2007 reference but here it is
“The risk is that 20 years from now everyone gets tested and learns they have a 5% risk for developing 10 diseases and a 2% risk for 20 other diseases– and what we do is increase neurosis instead of improving health,” frets Yale University geneticist Richard Lifton.
(at least for scientists) is the possibility to annotate PDFs. Sorry, the screenshot originates from one the most stupid papers that I read over the past years but it nicely shows Continue reading The most significant improvement in Snow Leopard
The first GWAS of human vitamin serum D level finds the most important SNPs:
In a genome-wide association study (GWAS) of 4,501 persons of European ancestry drawn from five cohorts, we identified single nucleotide polymorphisms (SNPs) in the gene encoding group-specific component (vitamin D binding) protein, GC, on chromosome 4q12-13 that were associated with 25(OH)D concentrations: rs2282679 (P=2.0 x 10–30), in LD with rs7041, a nonsynonymous SNP (D432E; P=4.1 x 10-22), and rs1155563 (P = 3.8 x 10–25).
Funny, rs7041 is the same variant Continue reading rs4711, uh rs7041
This is an update of the recent TCRA post herewhere I argued that TCR studies shouldn’t be done with genomic DNA from peripheral blood cells. Instead, I was arguing for buccal DNA as epithelial cells will not have undergone somatic recombination. Only last week, however, I came across an earlier letter about DNA-based assessment of chimerism after allogeneic blood stem cell transplantation (BSCT). Continue reading Is buccal DNA really buccal DNA?
While I never found it difficult to test for bacterial micro-evolution (like in the already famous 2009 E coli paper) I have considerable problems to see this also in contemporary human populations. As an epidemiologist I am now attracted by a new PNAS paper that addresses this problem (for the first time?).
Our aims were to demonstrate that natural selection is operating on contemporary humans … To do so, we measured the strength of selection, estimated genetic variation and covariation, and predicted the response to selection for women in the Framingham Heart Study … We found that natural selection is acting to cause slow, gradual evolutionary change. The descendants of these women are predicted to be on average slightly shorter and stouter, to have lower total cholesterol levels and systolic blood pressure, to have their first child earlier, and to reach menopause later than they would in the absence of evolution.
Athough the abstract is quite clear, Continue reading Evolution at work
There seems to be more evidence for the fake food hypothesis that I raised here some years ago. It says in brief that our
food recognition process is largely fooled by pre-processed food that contains additives changing appearance, taste and smelling.
while an empirical proof is still missing. But wait there is a new study about functional ankyrin-B mutations(which are believed to be a food sensing molecule although such a link is not so strong. Anykyrin-B made by the ANK2 gene is described by Vann Bennett in Science Signalling 3/113 to be associated with type II diabetes. What’s about obesity?