All posts by admin

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.

 

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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?

 

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Allergy, Vitamins

The first proven risk factor for allergy

After more than a century of research, the first successful clinical trial of an allergy risk factor has been performed. It looks like the authors even did not anticipate such an effect (known as triple blind design). But read what the Pubmed article about the Norizoe et al. paper says

To elucidate whether maternal vitamin D supplementation during lactation improves infantile eczema and other subsequent allergic disorders, a randomized, double-blind, placebo-controlled trial was performed.
Mothers (n=164) of infants with facial eczema at one-month checkup were randomly assigned to receive vitamin D3 supplements (n=82; 800 IU/day) or placebo (n=82) for 6 weeks from May 2009 to January 2011. The primary outcome was infantile eczema quantified by Scoring Atopic Dermatitis (SCORAD) index at the three-month checkup, and the secondary outcomes were atopic dermatitis, food allergy, and wheeze diagnosed by doctors up to 2 years of age.
There was no significant difference in SCORAD at 3-month checkup between two comparative groups. Doctor-diagnosed food allergy was significantly more common up to age 2 years in vitamin D group (10/39: 25.7%) than in placebo group (3/40: 7.5%; RR=3.42, 95%CI=1.02 to 11.77, P=0.030). Moreover, at least one secondary outcome was also significantly more common in vitamin D group (17/39: 43.6%) than in placebo group (7/40: 17.5%; RR=2.49, 95%CI=1.16 to 5.34, P=0.012).
These results suggest that vitamin D supplementation may not decrease the severity of infantile eczema at three months of age, but may rather increase the risk of later food allergy up to two years of age. Because a large number of subjects was lost to follow-up, further study is needed to confirm the findings.

Of course, there may be some weakness in the study design, a large loss to follow-up and the way how food allergy was diagnosed will be critized. I think, however, that this is a major breakthrough that raises the hope that we will finally understand how allergy develops.

Addendum Dec 23th, 2013

I should have added “true” risk factor, as there are positive trials on probiotics and atopic dermatitis. The meta-analysis by Lee immediately lead to a rebuttal

Their review fails to meet published standards for the quality of systematic reviews on several criteria, and this has led to inappropriate conclusions. […] These defects in methodologic rigor have led to an exaggeration of the clinical benefits of probiotics for eczema prevention.

The Cochrane Summaries are also negativ

There is not enough evidence to recommend using probiotics for the treatment of eczema.

Same situation with asthma

We found no evidence to support a protective association between perinatal use of probiotics and doctor diagnosed asthma or childhood wheeze

 

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Philosophy, Video

Ich habe doch nichts zu verbergen !???

Wie oft habe ich den Satz in den letzten Wochen schon gehört… und er wird durch die häufige Wiederholung nicht richtiger. Denn natürlich habe ich etwas zu verbergen, wie die meisten Menschen, ich bin sogar vom Staat zum Arztgeheimnis verpflichtet worden.
Hier kommt jedenfalls ein sehr detailliertes Video für alle “die nichts zu verbergen haben”.

 

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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

 

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Theology

Gott braucht Dich (nicht)?

Es ist ein großartiges Buch, das Esther Maria Magnis geschrieben hat. Sprachmächtig, mit starken Bildern, nimmt uns Esther Magnis mit in die Tiefe ihres Erlebens.

Es ist eine der stärksten Stellen am Ende des Buches, wo nie die Rede davon war, dass es auf der Erde witzig sein wird und unser Glauben, der Glauben der Christen einen Schrecken hat, nämlich das Wissen um den ganzen Dreck der Welt.

Vielleicht ist auch Esther in Wirklichkeit ein Pseudonm, ein Pseudonym für Ijob? Die unglaublich direkte Anklage Gottes. Und Ijob, der sich zur Wand dreht und nicht mehr leben will. Erst durch Elihu fasst er wieder Mut. Dabei stellt Elihu das Recht des Menschen in Frage, das göttliches Wirken zu beurteilen, und zwar grundsätzlich, da die Frage nach dem Grund für das Leid nur als Frage zu dem Zweck des Leides formuliert werden kann.

Unnachahmlich auch Ihre Sicht der Evangelien, die sie als extrem schräg bezeichnet – viermal nebeneinander wie Zeugenaussagen nach einem Unfall, der in der Tat ziemlich echt wirkt. Von den vielen beschaulichen Jesus Büchern, von Schweitzers Geschichte der Leben Jesu Forschung bis zu Ratzingers Jesus von Nazareth, hat das kaum jemand so sehr auf den Punkt gebracht.

Und sie traut sich was.

Und wenn Du schreist “Es gibt keine Wahrheit”, dann beweis mir die Wahrheit an dem Satz, und wenn Du es nicht kannst, dann geh zurück in die Gräber… Und Du wirst nicht viele finden, die darauf bestehen, dass Wahrheit relativ ist, wenn es darum geht, ob man ihre Kinder foltern, ficken und fressen darf. Sie werden relativ klar, sie werden ziemlich bestimmt den Anspruch haben, die Wahrheit zu sagen, dass das ein Verbrechen wäre. Sie werden sogar <böse> sagen und es überkulturell, überkonfessionell, über den Zeiten und oberhalb der Meinungen ansiedeln. Ich weiss nicht viel. Ich weiss nicht was gut und böse ist. Ich habe Ahnungen, ich habe die Wahrheit nicht.

Magnis, Esther Maria: Gott braucht dich nicht. Eine Bekehrung, Rowohlt Verlag, 238 S., ISBN 978-3-498-06406-8, 16,95 Euro

Interview

Rezension

 

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Joke, Philosophy, Software

Bad news are good news

e! Science News reports a new study in EPJ Data Science by Marcel Salathé showing that anti-vaccination sentiments spread more easily than pro-vaccination sentiments.

We find that the effects of neighborhood size and exposure intensity are qualitatively very different depending on the type of sentiment. Generally, we find that larger numbers of opinionated neighbors inhibit the expression of sentiments. We also find that exposure to negative sentiment is contagious

Read the full paper for the tricky design – at least the results fully underpin daily life experience. It’s certainly much easier to do Twitter than Facebook studies on the other hand these rather short messages are certainly not the main channel of many great “opinionated” people.

 

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Philosophy, Vitamins

The best vitamin D paper in 2012

The turn of the year may not only indicate many new chances but also allow a higher standpoint. IMHO the best paper in the vitamin field was published by Rousseau Gama in the BMJ 2012;345 :e5706.

We measured serum C reactive protein and 25-hydroxyvitamin D concentrations before and two days after elective knee or hip surgery in 30 patients. After surgery the mean serum concentration of C reactive protein increased (5.0 (SD 5.5) v 116.0 (81.2) mg/L; P <0.0001), whereas serum 25-hydroxyvitamin D decreased (56.2 (30.3) v 46.0 (27.6) nmol/L; P <0.0006).

The reasons are not fully clear but the results are consistent with two other studies reporting a fall in serum 25-hydroxyvitamin D concentration during a systemic inflammatory response. So, it looks like 1 simple study will make 1000 other studies useless. That seems to be the beauty of science… although I do not understand how that related to a serum half-life of two weeks?
So far I argued that vitamin D is always a lifestyle proxy e.g. pubmed/22698792) but there maybe also biological reasons.
BTW I would also have a candidate for the worst vitamin D paper, just in case, ….

 

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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.

 

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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 18.01.2026