All posts by admin

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 25.03.2026
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 25.03.2026
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 25.03.2026
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 25.03.2026
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 25.03.2026
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 25.03.2026
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 25.03.2026
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 25.03.2026
Genetics

Frederick Sanger R.I.P.

Bildschirmfoto 2013-11-20 um 15.45.26

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.

 

CC-BY-NC Science Surf , accessed 25.03.2026
Genetics

Single cell genomics update

talk 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.

 

CC-BY-NC Science Surf , accessed 25.03.2026