Living near highways

A new study now shows directly that personal exposure of particles is linked to asthma symptoms. Children carried pollution monitors in their backpacks on the way to school where PM2.5 ranged from 20 to 50 micrograms per cubic meter. Although only around 10 percent of the total mass of particles was diesel soot, it was this that was most closely linked to the children’s asthma. This nicely complements results of our study in Munich in 1989/1990 which was the first survey indirectly linking car exhaust and airway symptoms in children. Mechanisms how this happens are not very well known – for a discussion of the biphasic response see our paper of a mouse model, yea, yea.

On display – the masterclass

During my professional career I have never been told how to make good graphics although extracting essential information from datasets is an advanced (and necessary skill). Fortunately, however, there are some excellent books that cover graphical display. The first one I came across was Michael J Campbell and David Machins’ “Medical Statistics – A commonsense approach” (see pages 44ff and 58 for “increasing data ink”) that gives a lot of useful advices how to improve figures. The next book that I found influential was Bill Cleveland’s 1993 book “Visualizing Data” who introduced into R and S multidimensional lattice graphics (also covered 2005 in “R Graphics” of Paul Murrell published by Chapman & Hall/CRC). I used this technique extensively in my 2005 PLoS paper on the worldwide distribution of allergy. At the moment I am reading the new book “Graphics of large datasets” by Antony Unwin, Martin Theus, Heike Hofmann which seems to be finally the masterclass of displaying data. Yea, yea.

Addendum 1

An examples how to improve a barchart (yes – I resisted to start with a 3D barchart but the cluttering colors and grids are hopefully good to see).

demo.gif

Addendum 2

A new Nature Nascent entry: “The way we present genomic and proteomic data on the web sucks

Foucault pendulum

I visited the Deutsche Museum yesterday, where one of best attractions is the Foucault pendulum a 30 kg weight at a 60 m rope (the original at the Panthéon was 67 meter long and weights 28 kg). We could see, that the pendulum swings on a an elliptic course, hitting the conses always from the back. As we were told, the deviation of the pendulum is a function of latitude. The horizontal axis is the latitude from 90 degrees to 0 degrees latitude. The vertical axis shows the rate of precession in degrees per hour; positive for clockwise precession, negative for counterclockwise precession (the Coriolis effect seems to have a minor role). I wondered what might be the reason for the spin or chirality seen so often in nature. Most DNA has a right-hand screw (nevertheless there are hundreds of images on the net and many scientific papers) that show left-handed DNAs). Yea, yea.

Ethnographic studies at Oktoberfest

Having many years of experience with ethnographic studies at Oktoberfest München, I am fascinated by a new Cell paper that shows distinct behavioral responses to ethanol. This is something that I alread assumed (although I did not known about this particular RhoGAP18B isoform only about ADH deficiency). Will the knowledge of more and more mutations in the lifestyle area raise ethical problems? Yea, yea.

False Memory

The German magazine Spiegel has a nice paper about the false memory debate and the “implanted” memory of events that never happened. They cite Hans Markowitsch from Bielefeld that the autobiographical memory is not very good in recalling past events, being much much more adapted to orientation of current and future events. Has anyone examined blogs and if their content can be recalled by the author? Nai, nai.

Once again genetic testing

I have argued earlier that the free decision of an individual to allow genetic testing, will also reveal data on genetic relatives that have never consented to that procedure.
A new review by Bruce Weir now confirms that “it is reasonably straightforward to find the probability of the genotypes of individuals when their relationship is known…” My current work lets me also assume that with 500,000 SNP data at hand, much individual characteristics of the donor can be reconstructed – there are no anonymous DNAs datasets as some people still believe.
I even fear that genetic testing will increase for example in “homeless” (in vitro fertilized) individuals as these people will want to prevent sibling marriage – see for example the a-China DNA project. Other people may be curious about their genealogy, others about drug side effect prediction, lifestyle, assurance questions…
With every new dataset, available datasets will gradually decrease their anonymity level. I fear that anonymity is not so much a dichotomous property, it is much more a likelihood ratio to stay unknown under the probability to be known. Yea, yea.

Addendum

Time online of Dec 17, 2006 reports that the British police is holding the DNA records of more than 1m innocent people — eight times more than ministers have previously admitted. I wonder if this will affect participation rate of the UK Biobank that targets health of lifestyle, environment and genes in 500,000 people.

Sleep well

Just came to my attention that there is research of sleep related genes, the usual stuff of protein kinases, dopaminergic receptor, and serotonine transporter. Also this research community seem to have the common difficulty of the complex disease gene mappers – to understand a phenomenon (not a trait) as systemic function, an intrinsic property of a multicellular and multiwired brain, yea, yea.

Addendum

More strange phenotypes orgasm frequency, pain, human memory performance.

Addendum

Read also the what-we-could-have-learned-from-linkage-studies.

Heritable mutation or not?

moblog – Tsun Leung Chan is now reporting a heritable germline epimutation of MSH2 in a family with hereditary colorectal cancer another case of “paranormal” inheritance. They find a mosaic germline methylation pattern (which might even be a symptom of another mutation that affects the demethylation-de novo methylation pattern of MSH2 during embryogenesis?). If my hypothesis is true these families should even show more genes with different methylation patterns, yea, yea.

Addendum 28/5/08

Another attempt to answer this question comes by a study of the MLH1 promotor

Pro: MLH1 promoter methylation was found in a patient and his mother giving evidence for a familial predisposition for an epimutation in MLH1. Contra: a de novo set-up of methylation in one patient, a mosaic or incomplete methylation pattern in six patients, and no evidence for inheritance of MLH1 promoter methylation in the remaining families.

Science projects, glue projects

Reading about science projects, glue projects and platform projects, all with minority, gender, public communication and ethics modules while including large administrative overheads, travel and meeting costs, I even wonder how much money is finally going to real research – careful experimentation and thoughtful interpretation. Some people seem to spend more time on creating logos than in study design, yea, yea.

What could have been learned from linkage studies

What makes the difference between genetic linkage and association studies? Simply speaking, for linkage you need to inherit a particular marker allele from your parents where it does not matter if a child in another family inherits another allele (pending it shares it with its affected sibling). With association studies this matters.

As we found with the much relaxed linkage strategy so many minor diverse loci, I assume a rather heterogeneous origin of complex diseases. There is no doubt about the importance of genes, but about the sharing of the same genetic abnormality. An (anonymous) position paper on basic Asthma Research Strategy II in Clin Exp All 2006; 36: 1326 says

The average size of effect on asthma and related traits from common SNPs is small. For instance, seven common SNPs in the IL13 gene jointly accounted for only 0,5% of the variance of total IgE … With a heritability of circa 60% for total IgE this implies that hundreds of genes, each with small effects, may be involved in IgE regulation.

Families presenting with a complex system disease will all have unique patterns how they arrive at the same clinical endpoint. Alpha-delta-gamma asthma, theta-kappa-jota schizophrenia or $%&# diabetes – are they combining lets say 3000 variations in 300 genes of 30 metabolic-signalling pathways to 1 disease of variable onset, severity and prognosis? Yea, yea.