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Philosophy

When is the critical rate of discoveries that warrants any further experiment?

We were recently dicussing that problem too what Nature writes about the Encode project:

The question is, where to stop? Kellis says that some experimental approaches could hit saturation points: if the rate of discoveries falls below a certain threshold, the return on each experiment could become too low to pursue

As always – the scientific method once invoked – creates beautiful results but when it comes to justification of programs or methods it’s all about personal preferences, irrational beliefs, common misunderstandings, conformance to general trends, and whatsoever non-scientific influences.

 

CC-BY-NC Science Surf , accessed 25.03.2026
Philosophy

The true reason for retractions?

Retractions are increasing anytime I look around retraction watch. A new PNAS paper now has the most thorough analysis of retractions:

A detailed review of all 2,047 biomedical and life-science research articles indexed by PubMed as retracted on May 3, 2012 revealed that only 21.3% of retractions were attributable to error. In contrast, 67.4% of retractions were attributable to misconduct, including fraud or suspected fraud (43.4%), duplicate publication (14.2%), and plagiarism (9.8%) …fraud has increased ∼10-fold since 1975.

So, fraud is the most frequent cause – and it usually does not come isolated Continue reading The true reason for retractions? →

 

CC-BY-NC Science Surf , accessed 25.03.2026
Genetics

An enormous step forward in whole genome sequencing

The idea might not be new – we already diluted DNA already a decade ago ( see this 2003 paper ). A new Nature paper by Peters ( Accurate whole-genome sequencing and haplotyping from 10 to 20 human cells… ) now shows that diluting DNA into 384 wells, adding unique tags, and pooling again before sequencing everything on a Hiseq, will result in an enormous reduction of sequencing errors – a problem that we are fighting now for a year. IMHO the paper isn’t primarily about the low number of cells that can be sequenced, but also about error reduction in WGS. The two key facts are certainly

To ensure complete representation of the genome we maximized the input of DNA fragments for a given read coverage and number of aliquots. Unlike other experimental approaches this resulted in low- coverage read data for each fragment in each of the wells a fragment is found in.

plus an intelligent phasing algorithm Continue reading An enormous step forward in whole genome sequencing →

 

CC-BY-NC Science Surf , accessed 25.03.2026
Software

Add geolocation barcodes to travel guides, conference leaflets, etc please

There are so cute little files while I am constantly looking up addresses in travel guides, madly identifying them at google earth before transferring location bookmarks to my mobile devices.

Why can’t publishers produce just some small geo.kml or geo.rdf files, deposit them somewhere on their web server and link them with barcodes that are printed each time a geolocation is referred too (example link Groebenzell)?

The iPhone needs a slightly different form (without kml) as well as an app like i-nigma that is pointed by this barcode

QRCode

to maps://?geocode=&q=gr%C3%B6benzell&ie=UTF8&client=safari&oe=UTF-8&hnear=Gr%C3%B6benzell,+Oberbayern,+Bayern&gl=de&t=m&z=14”>Groebenzell.

 

CC-BY-NC Science Surf , accessed 25.03.2026
Philosophy

Warning: Reply to all

Nature 486, 157 (14 June 2012) warns:

Scientists discussing their work through written media, including e-mail, should be aware that they could at any time be asked to reveal their conversations.”You are commanded to produce…any and all documents, data, and/or communications.” Towards the end of last year, those orders appeared in a subpoena that landed at the Woods Hole Oceanographic Institution in Massachusetts.

so please write me private things only in a closed letter. Maybe it’s not such a problem Continue reading Warning: Reply to all →

 

CC-BY-NC Science Surf , accessed 25.03.2026
Genetics, Philosophy, Software

A broken contract

Erika Check Hayden ( who asked me by email before she wrote that piece ) has a new article about “A broken contract – as researchers find more uses for data, informed consent has become a source of confusion. Something has to change“. While I largely agree with her analysis of the current situation, her points for change are somewhat weakly described ( BTW that paper already generated a heated discussion at The Mermaid’s Tale: “Informed consent — who’s it supposed to protect, anyway?” ). Continue reading A broken contract →

 

CC-BY-NC Science Surf , accessed 25.03.2026
Software

A Word file that crashes the Macbook hard disk

Believe it or not, I was editing this week a document that I received by email. After 3 minutes Word Mac 2011, Version 14 crashed, leaving only a temporary file back on my OSX 10.7.4 desktop.

As restarting Word did not work, I used disk utility, that recommended to be started from another disk.

When doing so, it recommended to reformat my hard disk (which I did). Continue reading A Word file that crashes the Macbook hard disk →

 

CC-BY-NC Science Surf , accessed 25.03.2026
Philosophy

What is life?

There is an interesting discussion going on starting with Trifinov’s ( whom I met here last year ) seminal paper in J Biomol Struct Dyn 2011

Analysis of the vocabulary of 123 tabulated definitions of life reveals nine groups of defining terms of which the groups (self-)reproduction and evolution (variation) appear as the minimal set for a concise and inclusive definition: Life is self-reproduction with variations… Over 100 of definitions of life exist today– learned opinions each one of which is, or has been in the past, defended not without a reason though generally met with skepticism. Continue reading What is life? →

 

CC-BY-NC Science Surf , accessed 25.03.2026
Vitamins

Prevision

In my recent review on vitamin D and allergy I introduced the rather new concept of epigenetic priming of the offspring’s vitamin D system. I could find only a limited number of studies supporting this view. Fortunately, there is a new study published today that gives me some support. Using a twin design the authors (AJCN. First published ahead of print May 30, 2012 as doi: 10.3945/ajcn.112.035683) find

Our results suggest that maternal circulating 25(OH)D is the most significant regulator of neonatal circulating 25(OH)D concentrations, with underlying genetic factors playing a limited role.

 

CC-BY-NC Science Surf , accessed 25.03.2026