I have written in 2009 here about exclusion in science. It continues to be a common theme in research programs to exclude others and to be exclusive. Just recently, I found the interesting 2012 summmary on the pain of social rejection by the American Psychological Association Continue reading Be warned
Maybe it is easier to answer that question if you are a noble winner. The Guardian is reporting two days ago
Leading academic journals are distorting the scientific process and represent a “tyranny” that must be broken, according to a Nobel prize winner who has declared a boycott on the publications…
Randy Schekman, a US biologist who won the Nobel prize in physiology or medicine this year and receives his prize in Stockholm on Tuesday, said his lab would no longer send research papers to the top-tier journals, Nature, Cell and Science.
With the large distribution factor of the internet, I think there is nothing to loose by sending a paper to PLoS or some of the BMC journals. Quality will survive, yea, yea.
For a long time this has been a general rule. Just take the mean and substract two standard deviations and you get some useful reference values. Or whatever algorithm you like. This changed considerably where commercial or any other personal interests come into play. The cholesterin discussion settled only by studies showing that people with a history of cardiovascular disease may derive benefit from statins irrespective of their cholesterol levels.
I see some analogy in the vitamin D field. There is a German dermatologist who believes that 60% of all Germans are vitamin D deficient (the comments following the interview highlight this as an epiphany “totale Erleuchtung”). And a more recent paper showed that “89.9%” of all healthy newborns being insufficient. Really looks like a mix-up of some basic concepts in clinical medicine, yea, yea.
The UCSC Genome Bioinformatics Group ( who is running one of my favorite websites ) just announced
After 15.4 years of CPU run-time in 9,905,594 individual ‘jobs’ and 99 cluster runs for lastz pair-wise alignment…we are excited to announce the release of a 100 species alignment on the hg19/GRCh37 human Genome Browser.
This new Conservation track shows multiple alignments of 100 species and measurements of evolutionary conservation using two methods (phastCons and phyloP) from the PHAST package. This adds 40 more species to the existing 60 species track on the mm10 mouse browser. For more information about the 100 species Conservation track, please see its description page.
Quite some time passed already since my last post (to be exact, more than 5 years) but now there are good news. The FDA issued a warning letter on the 22nd
… The Food and Drug Administration (FDA) is sending you this letter because you are marketing the 23andMe Saliva Collection Kit and Personal Genome Service (PGS) without marketing clearance or approval in violation of the Federal Food, Drug and Cosmetic Act (the FD&C Act) … However, even after these many interactions with 23andMe, we still do not have any assurance that the firm has analytically or clinically validated the PGS for its intended uses … Therefore, 23andMe must immediately discontinue marketing the PGS until such time as it receives FDA marketing authorization for the device …
The response is quite flimsy. Yes, there may be negative side effects of genetic testing and of course tests need to validated first. Slate may be correct that the FDA’s battle with 23andMe won’t mean anything in the long run but now at least, we are set back to science, yea, yea.
Just recently I cam across a long forgotten CIBA Foundation Symposium and they had some nice discussion printed there – conserved for eternity while I think that all these researchgate whatever forums are volatile, yea, yea.
There has been so much written about Frederick Sanger (see nobelprize.org or Sanger Centre itself) while I like most what he wrote himself in Annual Reviews 1988:
These prefatory chapters are usually accounts of biochemists’ experiences in research, teaching, and administration. In my case the last two are easily dealt with as I have done hardly any and have indeed actively tried to avoid both teaching and administrative work. This was partly because I thought I would be no good at them, but also out of selfishness. I do not enjoy them, whereas I find research most enjoyable and rewarding.
Sydney Brenner, another British nobel laureate (2002) thinks:
A Fred Sanger would not survive today’s world of science. With continuous reporting and appraisals, some committee would note that he published little of import between insulin in 1952 and his first paper on RNA sequencing in 1967 with another long gap until DNA sequencing in 1977. He would be labeled as unproductive, and his modest personal support would be denied. We no longer have a culture that allows individuals to embark on long-term—and what would be considered today extremely risky—projects.
Sanger remains one of my heroes – the only scientist from whom I possess an autograph, bought a decade ago on Ebay.
There are so many other inventions in disciplines that I know from hear-say only. When being asked what I would like test, I would point to the ZeHus Bike+ unit, a self contained rear wheel with regeneration during braking and constant movement and electric assistance during acceleration. Continue reading What I would like to test
just in case you want to download also the 1000 genomes data, here is the warning that I received today:
I have been attending yesterday an interesting talk of Stephen Quake. Yes, this was a Leica sponsored event, but not about photography, it was about single cell genomics. I was always interested in that field and quite impressed by the Quake approach. These biology-baptized mathematicians and physicists can easily compete with whole research centers and a 100fold head count.
The commercial spin-off is fluidigm.com while his main research is not only sequencing of the fastest moving bacterium but also an estimate of mutations in his own haploid (sperm) genomes, single cell expression along with single cell methylation patterns.
One of the really exciting questions is the mismatch of single cell RNA and protein content where I need to go for some papers that I wasn’t aware off. Another excellent idea is the clustering of single cell expression profiles. This is already leading to new classes of cells and a probably much more valid approach than using random? surface markers as immunologists usually do, yea, yea.
Do you know what bp;dr means? Here is the solution:
behind paywall; didn’t read
The very first use is being quoted to @NeuroPolarbear. I am using it in emails too but maybe it should be added also to bibliographic references of printed papers, yes, yea.
Nature recently raised an extremely important point
Research metrics are ambiguous — a paper may be cited for positive or negative reasons. Funding agencies and universities focus on positive impact in evaluating research, which increasingly includes alternative metrics. We think that researchers can generate a more complete account of their impact by including seemingly negative indicators — such as confrontations with important people or legal action — as well as those that seem positive.
Yea, yea.
Was Wissenschaft nie beschreiben kann sondern nur die Kunst:
Ich liebe dich nicht, wie ich eine Rose aus Salz lieben würde,
einen Topas, einen Nelkenpfeil, der das Feuer entfacht:
ich liebe dich, wie man die dunklen Dinge liebt,
heimlich, zwischen Seele und Schatten.
Ich liebe dich wie die Pflanze, die nicht blüht und die in ihrem Innern anderer Blumen Licht versteckt,
und dank deiner Liebe lebt in meinem Leibe dunkel das dichte Aroma, das aufstieg aus der Erde.
Ich liebe dich und weiß nicht, wie noch wann noch wo,
ich liebe dich geradezu ohne Fragen noch Übermut,
so lieb ich dich, weil anders ich nicht lieben kann,
vielmehr auf diese Weise, in der ich und du nicht sind,
so nah, dass deine Hand auf meiner Brust ganz mir gehört,
so nah, daß ich in meinem Schlaf deine Augen schließe.
(Übersetzer unbekannt, Neruda Sonnet XVII)
Most people think that you can google for everything you want to know. What an overestimate!! There are so many relationships that will probably never turn out in any graph search ( at least I believe so ). And here is a nice example as I recently heard of a patient with an allergy AGAINST dimethindene maleate ( Fenistil (R), an antihistmaine used TO TREAT allergy. So whenever you enter “fenistil allergy” you get 119.000 hits. Although you get that result in 0,23s it will take you 23y to wade through the results. Hint: You could google for “leroy dimethindene” and you will find that there are only 2 patients so far in the literature plus the one that I know.