Genetics

There is something wrong in this world

or should I write “there is no absolute barrier between good and evil”?

One has to realize that there’s no absolute barrier between good and evil. There’s no absolute polarization between the wonderfully good and the horribly evil, and that people who see themselves as trying to do good can inadvertently enter into evil.

I had the opportunity yesterday to watch a documentation about the Lifton interviews of the Nazi doctors by Wolfgang Richter “Wenn Ärzte töten” (SZ , trailer). Richter was accompanied by Christiane Clemm who did all the translations more than 30 years ago. There were moving moments both during the calm narration of the documentation but also afterwards when we could ask Richter and Clemm for more details. Continue reading There is something wrong in this world →

 

CC-BY-NC Science Surf accessed 01.12.2025
Genetics

How to mod your blog to a seminar website

Obviously we want an uncluttered view of our seminar website, so we start by

creating a new page template from the standard page by commenting out headers, footers and sidebars.

We then assign this template to the main seminar page and add some text. By using the ICS calendar plugin lecture dates can be directly imported from iCal by including the

[show-ics-events

command. Next we will create some more subpages in WordPress under the hierarchy of the main seminar page like

— seminar
|—- pdfs
|—- videos
|—- etc…

All subpages need to be set to “private”.

In addition the same hierarchy is produced on the file system while each directory needs an appropriate .htccess file to limit site access. Links to subpages will point towards the file system only. Given appropriate credentials Apache will redirect to the appropriate WordPress page. This trick will secure both content of a directory and access to the mirror WordPress page.

 

CC-BY-NC Science Surf accessed 01.12.2025
Allergy, Vitamins

Allergic sensitization by a food fortifier?

This week the journal “Allergy” printed a report of three cases where allergic sensitization in preterm infants is attributed to the human milk fortifier Similac.

The product contains: Nonfat milk, corn syrup solids, whey protein concentrate, and MCT oil (fractionated coconut or palm kernel oil) as sources of proteins, fat, and carbohydrate (Abbott Laboratories Pediatric Nutritional Products Guide, DIR/98A08, 2008, Mississauga, Canada).

Not listed above but in the Products Guide are 120 IU/100 ml D3 which may indeed function as a sensitizer.

 

CC-BY-NC Science Surf accessed 01.12.2025
Genetics

One mutation every day

At least some people believe that once it’s published in Nature, it must be superior science – even when it’s rather trivial (or even wrong). There is a category “Brief Communications Arising” but when you are trying to get your comments there you will get this message by email:

In the present case, while we appreciate the interest of your comments to the community, we do not feel that they challenge key data or conclusions of the papers by Pleasance et al., and therefore we cannot offer to consider your paper for publication in our Brief Communications Arising section.

Pleasance et al. is a recent paper accompanied by a press release that tells you Continue reading One mutation every day →

 

CC-BY-NC Science Surf accessed 01.12.2025
Genetics, Software

Human language, DNA language?

A new paper in PLoS ONE argues that human languages may adapt like biological organisms. By doing a large-scale analysis of over 2,000 of the world’s languages the authors find striking relationships between the demographic properties of a language—such as its population and global spread—and the grammatical complexity of those languages. Languages with the most speakers (like English) were found to have far simpler grammars than languages spoken by few people and in circumscribed regions. This reminds me to bottlenecks in population history (and founder effects for certain DNA variants) while the authors describe this phenomenon as “Linguistic Niche”. A Hardy Weinberg Equilibrium of declension types?

 

CC-BY-NC Science Surf accessed 01.12.2025
Genetics, Theology

Numbering the hairs on our head

Funny to see this title at PNAS “Numbering the hairs on our head”

Evolution and medicine share a dependence on the genotype–phenotype map. Although genotypes exist and are inherited in a discrete space convenient for many sorts of analyses, the causation of key phenomena such as natural selection and disease takes place in a continuous phenotype space whose relationship to the genotype space is only dimly grasped.

The author was aware of the association to Continue reading Numbering the hairs on our head →

 

CC-BY-NC Science Surf accessed 01.12.2025
Philosophy

Late payment by EU

It is an always increasing problem: the EU doesn’t pay in time for your science. The European Ombudsman now invites observations from the public concerning his own-initiative inquiry into the problem of late payment by the European Commission [link].

 

CC-BY-NC Science Surf accessed 01.12.2025
Allergy, Genetics

Why do we get asthma

A book review of “Why we get sick” at tennov.com writes

Bacteria can evolve as much in a day as we can in 1000 years and there are as many bacterial cells in each of our guts as there are people on earth. That even improbable mutations occur with frequency in populations of pathogens gives them a decided advantage […] As Nesse and Williams emphasize, the end of the war is nowhere in sight. The 20th century was the golden age of relief from infection, but it may be over and this may accurately be considered a “post-antimicrobiol era.”

The same fact in Mel Greaves’ writing (p 216)

Natural selection will have operated against individuals who inherited fatal conditions that strike early in life, and for those whose immune systems were bext equipped to restrain the ravages of plagues. The geneticist and polymath, J B S Haldane, was surely correct in suggesting that infections have been the most powerful ‘natural’ selective pressure acting on human populations.

Unaware of the Haldane quote Continue reading Why do we get asthma →

 

CC-BY-NC Science Surf accessed 01.12.2025
Genetics

Evolutionary Medicine – A brief history

According to Gluckman et al. 2009 (page 22) the beginnings of evolutionary ideas appeared at the end of the 18th century with natural science on the rise driven by Carl Linnnaeus and Georges-Louis Leclerc – the great cataloguers of a living species – and Erasmus Darwin and Jean-Baptiste Lamarck – the new interpreters of the tree of life. Of course there are more influential French scientists (Georges Cuvier, Etienne Geoffrey Saint-Hilaire) that had an impact on Darwin and Wallace and also Robert Chambers who argued for evolution under divine guidance. The main contribution, however, is the Origin of Species by Charles Darwin, the mutability of the genome, the importance of genetic variation and the importance of selection mechanisms. There was quite some silence after that lightning strike . Although mutation events were not questioned, William Bateson (as well as Thomas Morgan) believed more in saltatations, eg. undirected mutations. Only the great mathematicians Ronald Fisher, JBS Haldane and Sewall Wright ussed population genetics to unite modern genetics and evolutionary thoughts. While the mid 20thies biologists like Dobzhansky and Ernst Mayr enforced a naturalist’s perspective, a direct relationship to clinical medicine is being established only now with Continue reading Evolutionary Medicine – A brief history →

 

CC-BY-NC Science Surf accessed 01.12.2025
Genetics, Software

PLINK: Bug or feature?

I am struggling now for 4 weeks with some unusual behaviour in PLINK that gives me different results with a trait of the alternate phenotype files either by calling that trait directly

plink –file mydata –tdt –pheno pheno2.txt –mpheno 1

or from a loop over all traits

plink –file mydata –tdt –pheno pheno2.txt –all-pheno

It seems that I am working with different numbers at both occasions – click to enlarge the log Continue reading PLINK: Bug or feature? →

 

CC-BY-NC Science Surf accessed 01.12.2025
Philosophy, Theology

Supra/Super/In Excelsis science

Yes, again some thoughts about the limits of science and the horizon of religion, triggered by The Mermaid who writes about cause and effect and is itself

triggered in part by watching a video of a BBC television series called The Impressionists. It is a very fine dramatization of the 19th century French impressionism movement in art: Degas, Manet, Monet, Cezanne and others. At the same time these painters were working, realist painters were working as well (and there was conflict between the two groups, of course). So why did impressionism arise? Why is impressionist art so impressive (to some, at least)?

There are different ways to describe reality – and clearly the impressionist’s painters have developed their own way – neither better nor worse, just different.
But why are there so many materialistic scientists who want us to show that all religion is either caused by genes (VMAT2 – the “god gene”), by neuro-anatomy (Ramachandran’s god modul) by psychology (Freud’s “phantasy structure”) or just politics (“Opium des Volkes”). Why is it unacceptable that religion may be just the “impressionistic” way that may be even advantageous in some if not many situations?

 

CC-BY-NC Science Surf accessed 01.12.2025
Genetics, Philosophy

Formal proof is difficult if not impossible

At least in medicine but also in many other fields, formal proof of a scientific hypothesis is difficult if not impossible. Reading again Greaves’ cancer book, I discover even more insights there. Talking about the hormonal stress leading to breast cancer he makes the point that

there is no ’cause’ in the straightforward, singular, or usually perceived meaning of the word; no tubercle bacillus equivalent. Neither is a mutant gene the common cause. Chronic hormonal stimulation driving persistent epithelial stem cell division seems to be a major factor (cycles driving cycles) and this reflects in large measure our social divorce from evolutionary adaptations for reproduction … Superimpose some degree of inherited predisposition and chance itself on this prescription and a very plausible causal network imbued with evolutionary principles becomes evident.

This is a very different view to the current sequencing headlines like “Lung cancer and melanoma laid bare“.

 

CC-BY-NC Science Surf accessed 01.12.2025