Papers 2 – disappointing

I have long been waiting for upgrading Papers 1.9 as it is getting so slow with 10,000+ PDFs; there are notorious bugs that were never fixed (just delete an entry and see what happens). With the big hype around Papers 2, I hoped that all these problems would be cured while I also urgently need OCR, annotation and citation management.
When reading at the new support forum at http://support.mekentosj.com/discussions/problems/3118-papers-2-going-back-to-papers-1 of all the glitches introduced instead, it is probably time to say good bye now to Mekentosj.

 

CC-BY-NC Science Surf , accessed 11.04.2026

50% of all disease genes found, really?

I have been reading now many times in nature genetics that a few newly found SNPs explain about half of the attributable risk by genes while I fear that this probably mixes up different epidemiological concepts.
The population attributable risk is usually defined as the reduction in incidence that would be observed if the population were entirely unexposed. This cannot be meant as I don’t know of any genetic study examining incidence so far. Continue reading 50% of all disease genes found, really?

 

CC-BY-NC Science Surf , accessed 11.04.2026

R cloud computing

A recent article on WPA hacking using the Amzon EC2 cloud computing facility let me wonder whether there couldn’t be more useful projects. For example gene-gene interaction testing would be nice – indeed somebody has already setup a possibility to use R: Robert Grossman, director at the Informatics at the Institute for Genomics and Systems Biology. Great, many thanks!
What’s even better, a

… 60 Genomes dataset can be found here, as part of the public data that Bionimbus makes available to researchers. With the Bionimbus Community Cloud, the data is available via both the commodity Internet, as well as via high performance research networks, such as the National LambdaRail and Internet2 … If you are a member of the Bionimbus Community Cloud, then you don’t need to download the data but can compute over the data directly with Bionimbus. Currently, we are not making the Bionimbus Cloud generally available, but expect to do so beginning in approximately June, 2011.

 

CC-BY-NC Science Surf , accessed 11.04.2026

God is in the house

Last Sunday night, I heard an interesting broadcast at Ö1 on the way back from St. Moritz “Nach dem Willen Gottes. Religion, Erziehung und Gewalt. Gestaltung: Sebastian Fleischer” while couldn’t find the song played during the last 30 seconds.

Finally, here is it, although the Nick Cave version on youtube is still another one than at the Ö1 broadcast. An email clarified it:
Continue reading God is in the house

 

CC-BY-NC Science Surf , accessed 11.04.2026

Handout text 2011 AAAAI Seminar San Francisco Vitamin D deficiency

2011 AAAAI Annual Meeting Handout

Session Number: 3523
Session Title: Vitamin D: Vitamin D Deficiency Causes Asthma -> CON
Session Start: 3/20/2011 12:45 AM
Matthias Wjst, Munich

Welcome to the third major symposium on vitamin D and asthma at the AAAAI. Continue reading Handout text 2011 AAAAI Seminar San Francisco Vitamin D deficiency

 

CC-BY-NC Science Surf , accessed 11.04.2026

Plagiarism or sloppy citation?

We have an interesting discussion here in Germany, how many sloppy citations are being allowed in a dissertation. Does plagiarism only start with central text passages? We all have signed a form like

Ich versichere, dass ich die Arbeit ohne fremde Hilfe und ohne Benutzung anderer als der angegebenen Quellen angefertigt habe und dass die Arbeit in gleicher oder ähnlicher Form noch keiner anderen Prüfungsbehörde vorgelegen hat und von dieser als Teil einer Prüfungsleistung angenommen wurde. Alle Ausführungen, die wörtlich oder sinngemäß übernommen wurden, sind als solche gekennzeichnet.

which is rather clear: “I used only the cited references and nothing else.” Continue reading Plagiarism or sloppy citation?

 

CC-BY-NC Science Surf , accessed 11.04.2026

Science crowd funded?

I already wrote an earlier essay about science as crowd source enterprise. Funding initiatives and funding selection of scientific projects, however, have never been transparent to me (even with all the EU announcements and lobbying before setting out the large framework programmes).
Reading now at david-campbell.orgabout a photo project in Afghanistan Continue reading Science crowd funded?

 

CC-BY-NC Science Surf , accessed 11.04.2026

Placebo works even if you know it’s a placebo

Some fascinating new paper at PLoS ONE

Placebo treatment can significantly influence subjective symptoms. However, it is widely believed that response to placebo requires concealment or deception […] Placebos administered without deception may be an effective treatment for [irritable bowel symptoms]

I have no idea, how this is working…

 

CC-BY-NC Science Surf , accessed 11.04.2026

We are not suggesting that peer review is infallible

Nature medicine recently acknowledged our work as science bloggers by admitting

We are not suggesting, however, that peer review is infallible. Nonetheless, as editors, we hope that anyone accepting an invitation to review a manuscript considers that commitment as being of comparable importance to the other responsibilities of a busy researcher. And although we know that more pressing issues can take precedence over reviewing a manuscript, we still expect that the same level of integrity and objective, critical analysis will be applied to the assessment of the manuscript under review as is applied to the referee’s own work.

In German we say “blauäugig” which translates to “wonderful naive”. There are so many examples of non-integrity and non-objectivity of published research where the peer review failed to a large extent – many examples here and at other sites like retractionwatch or badscience. All these papers by Friedhelm Herrmann, Marion Brach and Roland Mertelsmann with the most recent examples by Carsten Carlberg (“It’s all her fault, and probably today is the worst day of her life when the world sees what she has done”“) and Silvia Bulfone Paus (“it was Elena and Vadim and the journal editors should have caught us“)

With the pervasiveness of the Internet, and the speed of communication it permits, commentary and criticism of research findings can occur almost immediately after their online publi­ cation. This medium should be actively embraced by the research community as a dynamic forum.

There is not even a trackback possibility for that Nature medicine editorial – the whole blogger’s laudatio thing reeks of hypocrisy.

 

CC-BY-NC Science Surf , accessed 11.04.2026

Connect me


The new connectome website has some unusual (artistic) brain pictures that look so much “outward bound”. Although the neuronal direction is well-known for decades, the pictures there are so impressive that I moving that blog entry even in the Science + Theology section, yea, yea.

 

CC-BY-NC Science Surf , accessed 11.04.2026