Category Archives: Genetics

Allergy, Genetics

liesdamnedlies.com

… quoting Nature Medicine this week

All of this is well and good, but it will hardly be news to those who have pondered these issues. At the Nature journals, for example, data sharing has long been a requirement for publication, and we have gone as far as directly urging authors to fulfill their commitment to sharing when other researchers have requested our involvement.

Ok, I would like to get this full dataset …

 

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Genetics

10:1 for the Victorian method

We had Aulchenko here a year a go or so – now here comes his new paper Predicting human height by Victorian and genomic methods

In a population-based study of 5748 people, we find that a 54-loci genomic profile explained 4–6% of the sex- and age-adjusted height variance, and had limited ability to discriminate tall/short people, as characterized by the area under the receiver-operating characteristic curve (AUC). In a family-based study of 550 people, with both parents having height measurements, we find that the Galtonian mid-parental prediction method explained 40% of the sex- and age-adjusted height variance.

yea, yea.

 

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Allergy, Genetics

Spitalfriedhof Basel, Roopkund Lake, Catacombes de Paris, Central Yakuts

What do all these places share? Spitalfriedhof Basel, Roopkund Lake, Catacombes de Paris and Central Yakuts are all examples where remains are available for genetic studies (even Tutankhamun was undergoing a paternity test recently).
More relevant will certainly be an empirical investigation if reduced selection is leading now to immune disease.

 

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Allergy, Genetics

True, false, true, false, true, false, false

While some of my earlier co-workers continue to praise the achievements of GWAs, some other earlier co-authors now show that the common variants thrown on the current GWA chips are leading to false associations (politely called “synthetic” associations)

We propose as an alternative explanation that variants much less common than the associated one may create “synthetic associations” by occurring, stochastically, more often in association with one of the alleles at the common site versus the other allele. Although synthetic associations are an obvious theoretical possibility, they have never been systematically explored as a possible explanation for GWAS findings. Here, we use simple computer simulations to show the conditions under which such synthetic associations will arise and how they may be recognized. We show that they are not only possible, but inevitable…

The proof comes with a sickle cell anemia study Continue reading True, false, true, false, true, false, false →

 

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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 →

 

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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 05.11.2025
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 →

 

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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?

 

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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 →

 

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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 →

 

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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 →

 

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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? →

 

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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 05.11.2025