Category Archives: Genetics

Genetics

Scientist lost their way

LA Times’ Michael Hiltzik reports yesterday

Researchers are rewarded for splashy findings, not for double-checking accuracy. So many scientists looking for cures to diseases have been building on ideas that aren’t even true.
…
A few years ago, scientists at the Thousand Oaks biotech firm Amgen set out to double-check the results of 53 landmark papers in their fields of cancer research and blood biology.
The idea was to make sure that research on which Amgen was spending millions of development dollars still held up. They figured that a few of the studies would fail the test — that the original results couldn’t be reproduced because the findings were especially novel or described fresh therapeutic approaches.
But what they found was startling: Of the 53 landmark papers, only six could be proved valid.

I can confirm that finding.

 

CC-BY-NC Science Surf accessed 05.11.2025
Genetics

Nämlich wenn Sie erfinden

Wann Wissenschaftler kreativ sind? Vasari schreibt über die Entstehung Leonardo da Vinci’s Abendmahl (letzte Woche war ich in Mailand und natürlich auch in der Santa Maria della Grazie)

Leonardo kannte den klaren Verstand und den Takt des Fürsten, und deshalb entschloss er sich, mit ihm über die Sache ausführlich zu reden, was er mit dem Prior nie getan hatte. Er äußerte sich weitläufig über die Kunst und machte anschaulich, daß erhabene Geister bisweilen am meisten schaffen, wenn sie am wenigsten arbeiten, nämlich wenn sie erfinden und vollkommene Ideen ausbilden.

Nach der Meinung eines Universalgenies ist also etwas wichtig, das im lieben langen Wissenschaftstag nicht vor kommt?

 

CC-BY-NC Science Surf accessed 05.11.2025
Genetics

How much DNA molecules are in a PCR

Size of diploid human genome: 2 x 3 billion bp = 6 billion bp
Average size of of nucleotides:  487 + 159 g/mol = 646 g/mol
Single cell DNA amount: 6 billion * 646 g/mol = 3.87 pg
In 25 ng PCR human genomic DNA : 25000 pg / 3.87 pg = 6459 copies

 

CC-BY-NC Science Surf accessed 05.11.2025
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 05.11.2025
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 05.11.2025
Genetics

The fall of scientific celebrities

„Wenn 500 Menschen berühmt sind, ist keiner berühmt. Um also erkennbare Persönlichkeiten, herausragende Gestalten zu schaffen, muss man von den 500 mindestens 490 in den Hintergrund drängen. Dabei handelt es sich nicht um ein wohlwollendes Übersehen – jenen 490 muss aller Lohn für ihre Mühen entzogen werden, um ihn den 10 Glücklichen zukommen zu lassen.“

Richard Sennett,
Verfall und Ende des öffentlichen Lebens

“… if 500 people are famous, no one is, and so to find someone you can call a recognizable personality, a man who stands out, at least 490 must be pushed into the background. This is not benign neglect. Those 490 must be positively unrewarded in the same measure the 10 are rewarded; by denial as much as approval, a few people will then be brought forward as recognizable individuals.”

Richard Sennett,
The Fall of Public Man

 

CC-BY-NC Science Surf accessed 05.11.2025
Genetics, Philosophy

Too much to read too little time

I didn’t find so much time to update the blog during the past few months – there are too many attractions out there, and so many interesting things to do. The never ending problem is that there is too much to read and too little time. This is, however, what also other people find, for example genomeweb.com

Pedro Beltrao at the Public Rambling blog says there never seems to be enough time to keep up with all the literature researchers keep churning out. In 2009, 848,865 papers were added to PubMed, he says — that’s something like 1.6 papers per minute. While there’s definitely no scarcity of outlets to publish, is anyone even paying attention?

Or the Latest Everything blog

From a half-forgotten Einstein quote to the complete works of J. S. Bach, everything is instantly available. But what can we really do with it all? A HALF-CENTURY ago Marshall McLuhan wrote: “We are today as far into the electric age as the Elizabethans had advanced into the typographical and mechanical age. And we are experiencing the same confusions and indecisions which they had felt when living simultaneously in two contrasted forms of society and experience.”

who republishes theNew Scientist article (04 April 2011) pp. 1-3 in Surfing the data flood: Continue reading Too much to read too little time →

 

CC-BY-NC Science Surf accessed 05.11.2025
Allergy, Genetics

Will the bacterial flora protect you from you allergies?

Here is another post as the field seems to progress so fast with a new study on enterotypes of the human gut microbiome from

22 newly sequenced faecal metagenomes of individuals from four countries with previously published data sets, here we identify three robust clusters (referred to as enterotypes hereafter) that are not nation or continent specific.

The 3 clusters are Bacteroides (enterotype 1), Prevotella (enterotype 2) and Ruminococcus (enterotype 3) – no idea if these are under selective pressure from the host (genes!), from enviroment (antibiotics!) or from microbial competitors. When we look, however, at another study published also last week at Science magazine, it seems that at least one cluster has it’s own trick to get the right of residence by synthesizing a symbiosis factor. Continue reading Will the bacterial flora protect you from you allergies? →

 

CC-BY-NC Science Surf accessed 05.11.2025
Genetics, Noteworthy, Philosophy

LIMIT TO 5! What about a maximum of 5 papers per year per scientist?

Undoubtly, there is an avalanche of poor research – as the Chronicle wrote last June, “we must stop the avalanche of low-quality research”

the amount of redundant, inconsequential, and outright poor research has swelled in recent decades, filling countless pages in journals and monographs. Consider this tally from Science two decades ago: Only 45 percent of the articles published in the 4,500 top scientific journals were cited within the first five years after publication. In recent years, the figure seems to have dropped further

Also Genomeweb writes

Pedro Beltrao at the Public Rambling blog says there never seems to be enough time to keep up with all the literature researchers keep churning out. In 2009, 848,865 papers were added to PubMed, he says — that’s something like 1.6 papers per minute.

Continuing a discussion Continue reading LIMIT TO 5! What about a maximum of 5 papers per year per scientist? →

 

CC-BY-NC Science Surf accessed 05.11.2025