3 R tips for loops

Tip 1: Avoid loops.
They are generally slow – use a function instead. Even with the need of variable and fixed columns in a loop, a function may be constructed like
apply(data,2,function(col2){table(col1,col2)

Tip 2: Always show current state.
Include options(warn=1) and show current state with cat(“message\n”);flush.console();

Tip 3: Avoid merging steps.
Use instead datasets in same order and with the same subset of the larger table before updating anew column with data from the second table.

DNA for DNA

It might be fun to read here on a genetics board about DNA (Direct Note Access) which is a technology implemented in Melodyne that can extract notes from polyphonic music.
So far, it does not use a library of musical instruments according Peter Neubäcker, head of development, in an interview published in c’t 8/2008, p 34. It separates “musical content” defined by periodicity, similar overtones and meaningful musical distance like halftones. Although that’s something bioinformatics is trying for some while for DNA (desoxyribonucleic acid), I wonder if the decomposition concept in DNA would works also for DNA, yea, yea.

That’s one small step for (a) man, one giant leap for mankind

The BBC headline yesterday is close to the famous quote of Neil Amstrongs’ with reporting the United States blocking now genetic discrimination.

Or as Kennedy put it forward “the first new civil rights bill of the new century”. Unfortunately, we are lagging behind in Europe. My recent initiative to promote such a legislative in Germany was futile; the most recent goverment proposal only earned a lot of criticism.

A protestantic view of science

The 2006 document on perspectives of the German Protestant Church (EKD) briefly touches also the relation to science on p. 44 Continue reading A protestantic view of science

Personal Genome Explorer

Laborjournal 4/2008 reports a new software tool for DNA addicted people: the Personal Genome Explorer which is based on SNP annotation by SNPedia. So, what I tried to institutionalize on a sound level as “Genome Explained” possibly within the framework of HGVS is now being done by a street initiative fueled by early adopters like Cross, Arlington, Halamka and Smolenyak. It looks very much like an unholy alliance of profit interests and technical curiosity than good science and responsible counseling, yea, yea.
Addendum: If you believe in support vector machines, you can even let your laptop screen the medical literature for genetic associations with GAPscreener. <irony> No more lengthy training in genetics, statistics, epidemiology and bioinformatics, no more years of collecting all relevant papers & abstracts, just let your laptop score your DNA variants </irony>

Our lives are unrepeatable experiments lacking a control

a prosaic quotation from the recent Nature correspondence section that highlights why genetics has been leading us into nowhere.

Our lives are unrepeatble experiments lacking a control. Myriad external factors interact with genetic and epigenetic factors and with chance to determine whether we are well or ill, smart or dull, successes or failures.

Yea, yea.

Herrmann von Helmholtz on the cure of hayfever

It was difficult to find but I knew it should be there: a letter of Herrmann von Helmholtz about his private attempt to cure hay fever. Published in the increasingly important Nature magazine on May 14, 1874 von Helmholtz describes the vibrio like bodies in his own nasal fluid and the successful local treatment with quinine.

Unfortunately there is a consecutive letter that did not confirm this effect. I also do not know how this treatment would have worked. Fiction, placebo or true antiparasitic side-effect? We even know of quinine induced allergy, making even reverse causation possible.

G. Kanny, J. Flabbée, M. Morisset M, D. Moneret Vautrin. Allergy to quinine and tonic water. Eur J Intern Med 14 (2003), p. 395-396.
R. Cundall, Idiosyncrasy to quinine in bitter lemon. Br Med J 20 (1964), p. 1638.

How we are reshuffling our genome

is an exciting question that will have a large disease relevance. I think this is not so much about cytogenetic abnormalities but the general understanding which genetic modules are recombining, e.g. are compatible in terms of function, and which need to be tight together. Continue reading How we are reshuffling our genome

We are the model organisms

Genomeweb today reports Sidney Brenner (Nobel Prize winner 2002 and pioneer in the use of Caenorhabditis elegans as a model organism) speaking on a conference. These days he’s pushing a new model organism: humans.

“We don’t have to look for a model organism anymore,” Brenner said. “Because we are the model organisms.”

Vitamin, germs and allergy – 41 years ago

Do you still have some doubts on a recent experiment in mice that were sensitized under vitamin D co-exposure?
Here is another nice paper from Nature, Jan, 21, 1967 where rabbits are fed allergen & vitamin in a germ-free environment Continue reading Vitamin, germs and allergy – 41 years ago

To be honest

Bruce Alberts, the new editor-in-chief of Science magazine, has in his March, 21 editorial a nice comment that I would like to highlight here

Scientists share a common way of reaching conclusions that is based not only on the evidence and logic, but also requires honesty, creativity, and openess to new ideas.

Struggling in an area where no (or only seldom) conclusions ar being reached, I agree Continue reading To be honest