Alternative Impact Factors

There is no need to say that impact factors have largely failed to measure scientific value – even within selected groups (look for the Wikipedia article).

But are there any alternatives to ISI-Thompson? I haven’t found so many, the Hirsch factor, Google Scholar page rank, or Elseviers Scopus. Of course download figures of open access journals help to define popularity. But is this impact?

The latest development are citation management systems like CiteULike or Connotea that require to make all your readings public. Maybe its true what 80-year-old Garfield wrote in the BMJ: “there is no substitute for judgement, quality, and relevance. Impact and other citation measures merely report facts.” So blogs are even more important, yea, yea.

Merlin

Merlin by Goncalo Abecasis is probably the most widely used linkage program. By using sparse tree approach it is extremely fast. I only wonder why its name is not Excalibur (the name of the famous sword that helped Artus to marry Guineva, to banish the Saxons and eventually becoming king of Brittania). Goncalo moved to the US – are you still working on that? Yea, yea.

Gadfly

Just learned from the brandnew (German) book of Hannes Stein “Endlich Nichtdenker / How to become a non intellectual” that Americans call their renegate – apostate – dissident or unconventional intellectuals gadflies. Yea, yea.

Bereshit bara Elohim et hashamayim ve’et ha’arets…

The genesis – the common book of Jewish and Christian faith – reports the begining of the world. Interestingly , the creation of living things include also genes in the same instance: “1.11 let the earth spawn grass and leaves that make seeds…” We have been told that reverse genetics may not be used any more. Whats about forward genetics? Yea, yea.

Munich, Pettenkofer, Nazis and Public Health: An obligation

Reading the biography of Max Pettenkofer you will discover unexpected turns (starting his career as a third class actor in Augsburg) but also recognize him as one of the founders of Public Health (with a big impact on Munich city development by canalization and foundation of a fire department). Munich had been on the forefront even before the foundation of the famous Boston Public Health school.

With Volksgesundheit the idea of Public Health became perverted by the Nazis. With Erbgesundheit in mind the Nazis even tried to eradicate genes from the gene pool. Munich became Hauptstadt der Bewegung, and its university even awarded Mengele (the later physician in Auschwitz) a PhD degree.

During post-war period there was probably no epidemiological research in Munich, with Public Health only an unimportant discipline in the medical curriculum. When doing a first major epidemiological study in Munich at the end of the 1980ies and a first genetic population based study in the mid 1990ies, I felt a particular obligation for informed consent where any misuse of genetic data should be avoided.

Unfortunately, these goals are being threadened by an increasing ignorance of informed consent and missing legislative framework for genetic testing in Germany.

10 commandments

  1. There is only one human genome.
  2. You should not misuse it for any other purpose than continuing human lineage
  3. Observe the order of exons and introns and nongenic sequences.
  4. Recognize recombination and preserve it for a long lifespan.
  5. Do not knockout genes.
  6. Do not mix genomes.
  7. Do not steal sequences from other genomes.
  8. Do not assign wrong functions to genes.
  9. Do not use chromosomes in other cells.
  10. Do not be jealous on your neighbours sequence nor on your neighbors wife sequence nor on your neigbours children sequence.

Yea, yea.

Siddur, mantra, prayer

The Jewish siddur, the Buddist mantra and Christian prayer all contain repeating elements. Why does our genome also has has so many long and short interdispersed repeats – to give life a stable background on an ever changing environment? Yea, yea.

SQL injection and retrovirus infection

What is similiar to SQL injection (in webforms) and retrovirus infection (of mammals)? I think there is always a vulnerable situation (tainted variable by unexpected data entry – or double strand break and ligation) that allows foreign code to be inserted. What is different? Retrovirus insertion is probably position specific while SQL injection can even determine its own target. Yea, yea.

Avalanche – backstage story

-moblog- The next Lancet will publish my editorial on the b2AR and asthma association – “Has all been said?” This is to honour my favorite comedian Karl Valentin “It has all been said – but not by everybody”.

I have to confess that I wanted a completely different title “Search and rescue after the avalanche” where I described the tedious work to find all buried corpses under tons of snow – in analogy for the many genetic association studies – fearing already the next avalanche of genomewide SNP scans. Renember – very dangerous – steep 45o slopes, North West and new snow. Yea, yea.

Reading behind the lines

-moblog– Eran Segal et al. describe in Nature a genomic code for correct nucleosome attachment of genomic DNA. DNA must be positioned for access to functional sites of gene activity where 147 bases are wrapped around each nucleosome core. AT is favored where phosphodiesterase backbones face inward and GC where it faces outward. Distance between nucleosomes may be variable – as the accompanying editoral by Timothy Richmond explains (the enigmatic histone H1 question). Do genomes use nucleosome DNA preference to target transcription factor towards appropriate sites? This might expain why current transcription factor models are rather poor as they are using only sequence binding matrices. It reminds me to steganograpy, algorithmic procedures that can be used to hide secret messages in in pictures without affecting the visual impression. Yea, yea.