I wondered if Chorea Huntington may be unintentionally diagnosed by current SNP chips used in research projects of other diseases. On a first glance, this seems to be unlikely – we are dealing with repeated CAG repeats in huntingtin located on chromosome 4p16.3 that are not easily accessible by SNP panels. Continue reading Will current SNP chips unintentionally diagnose Huntington?
The new Lancet has a paper from our own group as well as another one from ISAAC. We have already suggested earlier that asthma is a iatrogenic disease- the ISAAC paper now confirms at least the long suspected association with paracetamol use – gratulations to my London friend who had been working so long on this hypothesis. The accompanying editorial puts in into context:
Furthermore, although many important potential confounders were included in multivariate analyses, confounding by underlying respiratory disease, differences in hygiene, and use of other antipyretics might also explain the findings.
To put it more on a general level – more iatrogenic factors cannot be excluded, yea, yea.
A recent opinion article (Nature, Aug 14) has an interesting retrospective look on Gödel’s proof, the 1958 secondhand description of Gödel’s 1931 finding that rules of logic for quoting axioms eg. substituting variables and formulating deductions are themselves mathematical operations – pretty much the same of todays object oriented programming Continue reading Gödel’s proof
Public Rambling discusses post-publication journals:
These ideas of sorting based on measures of usage is already being tested by the new Frontiers journals. These are a series of open access journals published by an international not-for-profit foundation based in Switzerland. As PLoS ONE, these journals aim to separate the peer-review process of quality and scientific soundness from the more subjective impact evaluation. In practice they are doing this by publishing research in a tiered system with articles submitted to a set of specialty journals.
I am already in favor Continue reading Dealing with noise
Edge has a wonderful article about statistics:
… statistical and applied probabilistic knowledge is the core of knowledge; statistics is what tells you if something is true, false, or merely anecdotal; it is the “logic of science”; it is the instrument of risk-taking; it is the applied tools of epistemology [and epidemiology Continue reading The logic of science?
PLoS medicine publishes today a piece that we wrote already last summer. As we have removed the narrative abstract (PLoS uses keypoints instead of an abstract) here is it – pleading for an update of traditional informed consent. Continue reading Informed Consent 2.0
For the first time, I found some data about “bench to bedside” transit times. Of 101 promising claims between 1979 and 1983, there have been only 5 clinical interventions in 2003 and only 1 had extensive clinical used; mean lag time 24 years, yea, yea.
for living then longer … This might be a good rule for private life (and even for a scientific career) but not so much for the progress of science.
There is another allergy gene paper on FCER1A and RAD50. FCER1A has some tragedy as the authors believed for many years in FCER1B (and others in FCER2).
Another tragedy comes with the second gene – Continue reading Try to stay away from rants and comparisons
Can we really control our thoughts? A PLoS ONE paper is looking into neural correlates of distraction by comparing 12 Zen meditators and 12 control subjects that were offered a “real English word” or “not a real English word” while resting in a 3 Tesla Siemens Magnetom. Outcome has been the time of refocusing attention to the breathing. The results are quite convincing (and not really unexpected) that the Zen meditators showed a reduced duration of their neural response to distraction probably by cutting down emotional self-reflectance and other associations coming up. I would be happy to participate also in a trial where somebody could record my EEG while driving on the of these new 185 kW Tesla roadsters.
It seems that CEA just published my rather critical view of the recent ORMDL3 association paper. My letter had been first submitted to “Nature” but rejected after review.
A rebuttal seemed to be necessary as the authors repeatedly highlight ORMDL3 as a new asthma gene – in the printed Nature paper, in the Nature podcast and in the accompanying press releases. They even continue with reviews saying that
Completion of the human genome sequence and the advent of genome-wide association studies have resulted in the identification of two novel asthma susceptibility genes, ORMDL3 and CHI3L1, in the past year.
Continue reading ORMDL3 – more inconsistencies in the Nature paper
Physics gets now a lot of attention with the largest experiment ever done with the LHC (pictures+data).
* largest machine (26.659 m diameter)
* largest freezer (60 tons helium)
* fastest runaway (99,99999 % speed of light)
* highest energy consumption (7 TeV)
* most lonely place – vaccum (10^-13 at)
* hottest place 100.000-fold temperature of the sun
* coldest place onearth (-271,3°C)
* largest supercomputer
Gratulations from the biomedical field that produced much less records in this week.
Genowatch (paper|website) is doing pretty well by annotating large SNP sets that would require otherwise numerous hours to map their position on genes, biological function and pathways. Continue reading SNP batch annotation of GWAs
Galaxy, one of my favorite bioinformatics websites now offers the conversion of existing history into a work flow. Obviously source data (by UCSC or Ensembl) may be produced in the same format but everything else can then be delegated to a workflow – just a set of instructions how to modify your data.
The authors put a question mark at the end of the above statement while I would not hesitate to put an exclamation mark there. Writing this as a comment to a new study in the IJE they summarize the evidence that the “epidemics” of asthma in Western countries has begun to decline – as hygiene standards are not declining this might indicate the end of the hygiene hypothesis. Continue reading The end of the hygiene hypothesis
Having a free copy of the Lancet at the moment, I found a nice book review about “Dissent over Descent” by Steven Rose.
[He] takes a pleasure, which in part I share, in puncturing the often hyperbolic claims of natural scientists to be unimpeachable purveyors of absolute truth Continue reading Dissent over descent