Philosophy

A Science career should not be like a Mastermind game

You do an experiment or a clinical study and you are the code braker not knowing the peg positions and colors ( set by a code maker ).

The codebreaker tries to guess the pattern, in both order and color, within twelve (or ten, or eight) turns. Each guess is made by placing a row of code pegs on the decoding board. Once placed, the codemaker provides feedback by placing from zero to four key pegs in the small holes of the row with the guess. Continue reading A Science career should not be like a Mastermind game →

 

CC-BY-NC Science Surf , accessed 13.04.2026
Software

How browsers render elements

This is a bit of mystery for me but fortunately there is some information out there, mainly the article “How browsers work” by Tali Garsiel.
I was a bit annoyed by the current Twentyfourteen WordPress Template that renders first some lines before getting towards the final layout. I am experimenting therefore with keyframe encapsulating as I did not find any better method. Continue reading How browsers render elements →

 

CC-BY-NC Science Surf , accessed 13.04.2026
Philosophy

Value replicability not journal impact

There is an excellent comment on research misconduct at the brand new Pubmed Commons site by Dorothy Bishop:

…
Instead of valuing papers in top journals, we should be valuing research replicability. This would entail a massive change in our culture, but a start has already been made in my discipline of psychology (see http://www.nature.com). Continue reading Value replicability not journal impact →

 

CC-BY-NC Science Surf , accessed 13.04.2026
Software, Video

Filtered net, self-censored opinion, what can we belief?

This piece is about filtering

and this about censoring

Rupert Sheldrake is a fascinating member of the scientific world. His TED talk named “The Science Delusion” was controversially censored by the TED community after being aired. Rupert shares that humanity has become stuck in turning science into another belief or dogma vs. allowing the method to be what it is. Rupert Sheldrake outlines 10 dogmas he has found to exist within mainstream science today. He states that when you look at each of these scientifically, you see that they are not actually true.

Some views are strange of course, while others are not (replace for example “morphogenetic fields” with “DNA methylation”). Even with a few interacting factors, a causal proof is nearly impossible. More at SFGATE or The Guardian.

 

CC-BY-NC Science Surf , accessed 13.04.2026
Philosophy

Giants in Medicine

The JCI has a nice series of video interviews with Marc Feldmann, Thomas Südhof, John T Potts, Aaron Ciechanover, Bruce Beutler, Jon Oates, Christine Seidman, Stephen O’Rahilly, Bruce Spiegelman, Paul Greencard, Jeffrey Friedman, Eugene Braunwald, Thomas Starzl, Francis Collins, Paul Marks, Joan Wilson, Donald Seldin, Tadataka Tachi Yamada, Llloyd Hollingsworth Smith, Robert Lefkowitz, Joseph Goldstein, Michael Brown, Harold E. Varmus.
The next generation is at the WALS board.

 

CC-BY-NC Science Surf , accessed 13.04.2026
Allergy, Vitamins

The best vitamin D paper in 2013

I have probably two candidates here. The first one is by the Cantorna group in October 2013 and provides for the first time a link between between the gut microbiome and oral vitamin D exposure. We all thought that vitamin D has no influence on bacteria as they cannot utilize it. But that doesn’t seem to be true as the composition of the microbiome may change.

Mice that cannot produce 1,25(OH)2D3 [Cyp27b1 (Cyp) knockout (KO)], VDR KO as well as their wild-type littermates were used. Cyp KO and VDR KO mice had more bacteria from the Bacteroidetes and Proteobacteria phyla and fewer bacteria from the Firmicutes and Deferribacteres phyla in the feces compared with wild-type. In particular, there were more beneficial bacteria, including the Lactobacillaceae and Lachnospiraceae families, in feces from Cyp KO and VDR KO mice than in feces from wild-type … Our data demonstrate that vitamin D regulates the gut microbiome and that 1,25(OH)2D3 or VDR deficiency results in dysbiosis, leading to greater susceptibility to injury in the gut.

So while I always thought, oral vitamin D supplementation may have a direct effect on the gut mucosal system, this paper opens a completely new avenue. Continue reading The best vitamin D paper in 2013 →

 

CC-BY-NC Science Surf , accessed 13.04.2026
Philosophy

On risk taking

Here is a recent interview transcript of Bruce Beutler

JCI: Would you advise any of your trainees to have the same drive and motivation you did to go after one singular problem with the same kind of tenacity that you had?
Beutler: I was often told by people, including by my father, that I was putting all of my eggs in one basket. But I must say in retrospect, if we hadn’t been focused and committed to one problem, we probably wouldn’t have got there. It was risky but I would counsel people to undertake high-risk projects and do them serially, rather than to work in parallel with a number of low-risk projects.

 

CC-BY-NC Science Surf , accessed 13.04.2026
Philosophy

Should we boycott top science journals?

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.

 

CC-BY-NC Science Surf , accessed 13.04.2026
Philosophy, Vitamins

Reference values should be based on reference populations and not on politics

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.

 

CC-BY-NC Science Surf , accessed 13.04.2026
Allergy, Genetics

New species alignment

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.

 

CC-BY-NC Science Surf , accessed 13.04.2026
Genetics, Noteworthy

Finally! 23 and the FDA warning

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.

 

CC-BY-NC Science Surf , accessed 13.04.2026