“the possibility does not necessarily lead to materialization”
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Why do we possess introns?
This seems to be a question with not so many good answers. “The origins of genome architecture” (Sinauer, 2007) has a nice chapter on “Genes in pieces” covering
- the spliceosome fisson-fusion model: Did a single ancestral spliceosome diverge into different lineages or is there an endogeneous origin within a single species?
- the introns early-introns late debate: Were introns present in the first prokaryotic cell or not?
Mechanisms about intron gain center about AGGT tetramer duplication that result in new splice sites —AG|gt … ag|GT— with the segment in lower cases being the new intron. (What I found a funny fact, when working for the first time with genomic sequences around 1994 is the “codon ignorance” and “domain ignorance” of introns while on the other hand allowing for alternative splicing). Another mechanism of intron gain may be transposable elements although retrotransposons cannot deliver introns as they are spliced out. More likely are already released introns and ectopic reintegration. Another (not mentioned mechanism) could be random mutations activating cryptic splice sites.
The key question remains Continue reading Why do we possess introns?
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1, 2, 3
A new review [Allergy (2009) vol. 64 (3) pp. 348-353] examines the evidence that
(1) failure to up-regulate the interferon gamma (IFNg) response during infancy is an important determinant of the risk of allergic disease
(2) expression of the IFNg gene in naive T-cells is regulated by epigenetic mechanisms, and
(3) failure to up-regulate IFNg gene expression of naive T-cells associated with low early life microbial exposure.
If we replace “microbial exposure” with Continue reading 1, 2, 3
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I can not confirm that
When I could not replicate results from original data of a recent study I thought this to be my private problem. It seems, however, that I am not alone here when reading another reanalysis attempt:
We reproduced two analyses in principle and six partially or with some discrepancies; ten could not be reproduced.
Continue reading I can not confirm that
CC-BY-NC Science Surf , accessed 10.04.2026
Pasteur and the hygiene hypothesis
I have just finished the revision of a paper describing the history of allergy development. While a temporal coincidence (introduction of vitamin D) will not provide any proof, the absence of such a coincidence (like key features of the hygiene hypothesis) is a rather strong argument Continue reading Pasteur and the hygiene hypothesis
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Danger of continuous information flow
Nassim Taleb points in his black swan book (p181 in the German edition 2008) towards the “toxicity” of continuously added information. He is citing experiments from the 1960ies where students were offered increasingly sharp pictures of water pipes. Students in the group with slightly inceasing sharp pictures had much more problems to recognize the pipe in constrast to the group being offered the same picture without any interim pictures. Together with the experiments of Stuart Oskamp it seems more difficult to discover real breakthroughs when being too deeply involved (and obsessed by getting the complete literature in a particular field). This even questions my daily Pubmed alerts; I will change them now to monthly update.
CC-BY-NC Science Surf , accessed 10.04.2026
Le Doubs
Bert Brecht
… Ich, sagte er uns
Bin der Zweifler, ich zweifle, ob
Die Arbeit gelungen ist, die eure Tage verschlungen hat.
Ob, was ihr gesagt, auch schlechter gesagt, noch für einige Wert hätte. Continue reading Le Doubs
CC-BY-NC Science Surf , accessed 10.04.2026
Forget about genes III
Here is another opinion from a widely read German magazine (Spiegel online, 25. Mai 2009, Jörg Blech, Wahrsager im Labor) about our too great expectations in genetics:
Während die einen noch mehr und noch größere Vergleichsstudien fordern, halten Skeptiker wie Goldstein dies für reine Zeitverschwendung: “Wenn man 30.000 Patienten mit Diabetes Typ 2 untersucht hat, dann halte ich es für sinnlos, die Zahl auf 60.000 oder 100.000 zu erhöhen.”
good bye to the “common variant hypothesis”!
CC-BY-NC Science Surf , accessed 10.04.2026
I am a scientist
Widely cheered in the blogosphere, Science magazine asked if we as scientists “are ready to be become a number”.
So, in general, I think there’s plenty of agreement that this sort of author ID system is past due. It can do everything from ease the process of manuscript submission to help researchers mine the existing volume of scientific data.
Sure, a unique DOI like ID Continue reading I am a scientist
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Die Aerzte sind die Kranken
Life expectancy of physicians is lower in most countries – an argument why Karl Kraus may be right:
Was ist’s mit den Analysen? Kann da ein Zweifel bleiben? Die Methode ist bewiesen an jenen, die sie treiben. Daß man mit euch nur scherzte – welch törichter Gedanke! Im Gegenteil: die Ärzte sind Kranke.
While just recovering from an orthopedic procedure (see picture below) my impression is that the quality of medical care has very much approved during the years. The performance of a surgeon can be always immediately verified ;-)
CC-BY-NC Science Surf , accessed 10.04.2026
Ill will, good will – free will?
Neuroscientists largely see the “free will as an illusion” – according to a recent essay in Nature. As the author of this interesting essay, I have a major problem to give up the idea of a “free will” (mainly for theodicy reasons that needs a free will of humans). Maybe our will is being influenced by many factors, it is not always a conscious decision and it can of course be altered by chemicals or diseases. Nevertheless the subjective, sudden and not anticipated impetus to do something – for example writing a blog about free will – is a symptom of free will even with all existing antinomies, yea, yea.
CC-BY-NC Science Surf , accessed 10.04.2026
Surfer’s asthma
Here comes the link to a case report of surfer’s asthma (could not resist)
… We present the case of a 42-year-old man with a 2-year history of wheezing, chest tightness, and upper respiratory symptoms that were associated with surfing. Continue reading Surfer’s asthma
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Forget about genes II
Blood pressure seems to have a complicated regulation according to a recent nature medicine editorial
If you ask a physiologist what organs are involved in blood pressure regulation, you will probably be told the kidney, the brain or the blood vessels. The kidney is responsible for handling sodium … The brain integrates afferent signals from peripheral sites such as the kidney … systemic vascular resistance is elevated in almost all adults with hypertension, suggesting that arteriolar vasoconstriction has an important role in this disease.
The editorial accompanies a new mechanistic report how a high-salt diet leads to interstitial hypertonic Na+ accumulation by activation of tonicity-responsive enhancer binding protein (TonEBP) binding the promoter of the gene encoding vascular endothelial growth factor-C (VEGF-C). As far, as good, Continue reading Forget about genes II
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Forget about genes I
An AJHG paper that is already resting some longer time on my desk says that
Nonsense SNPs introduce premature termination codons into genes and can result in the absence of a gene product … Continue reading Forget about genes I
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Science flies
Still in the spirit of the last few posts, here comes something exciting: sciflies.org aims at
We look forward to receiving your application for funding of initial proof-of-concept STEM research projects in the range of $5,000 to $12,000. To participate in this unique online grassroots-funded opportunity, please complete the questionnaire about your project, including details of its possible outcome/impact and profiles of the researchers or research team.
but, sorry, I have to warn you – the website does NOT save your project – it took me 20 minutes to figure that out.
CC-BY-NC Science Surf , accessed 10.04.2026