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Genetics

WordPress as CMS

I have read many useful (and also some less useful) comments how to squeeze WordPress to work as a CMS.

I did not want to make any major changes to scripts that would be lost after an upgrade. I did not want to have extra plugins to change home (for example by creating an overriding home.cfm). I did not want to have any new categories. I did not want to change permalink structure. I still need my directory plugin to work, I still need the blog (some redirects even loose the blog address!) and I wanted to keep the RSS feed.

After several hours I came up with an very simple solution: Take a standard page and rename its title and slug to “Home” – assign a special “Home” template – redirect htaccess to this page. The only trick is to make the “Home” template work: it is basically a copy of the index.cfm in your WordPress theme directory where the line calling loop.php is being replaced with a slightly modifed loop code.

myblog.php
|wj_myblog.php|

 

CC-BY-NC Science Surf accessed 04.11.2025
Genetics

HUGO Changing Offensive Gene Names

Hsien Hsien Lei has a good comment on gene names approved by Human Genome Organisation (HUGO) Gene Nomenclature Committee which are nevertheless offending . Some of the inappropriate names are LFNG – lunatic fringe homolog (Drosophila), MFNG manic fringe homolog (Drosophila) as well as SHH sonic hedgehog homolog (Drosophila). There are many more names that arise only from a particular culture (like death executioner Bcl-2); it seems also a particular kind of humour to call a deaf mouse Beethoven. Yea, yea.

 

CC-BY-NC Science Surf accessed 04.11.2025
Philosophy

Our knowledge springs from two main sources

Immanuel Kant is now also online in English language

Our knowledge springs from two main sources in the mind, first of which is the faculty or power of receiving representations (receptivity for impressions); the second is the power of cognizing by means of these representations (spontaneity in the production of conceptions). Through the first an object is given to us; through the second, it is, in relation to the representation (which is a mere determination of the mind), thought. Intuition and conceptions constitute, therefore, the elements of all our knowledge, so that neither conceptions without an intuition in some way corresponding to them, nor intuition without conceptions, can afford us a cognition.

 

CC-BY-NC Science Surf accessed 04.11.2025
Genetics

Why we should believe professional cyclists

I renember a nice meeting in South Sardinia in 2002 (see my figure below) where a lot of famous people gathered for interesting talks in a wonderful surrounding.
A spin off from this Ogliastra Genetics Park – as the authors called it – is now a paper in PLOS Genetics that examines the heritability of 98 quantitative cardiovascular traits in 6,148 Sardinians.
Although the authors did not measure hematocrit, RBC related counts had an extremely high heritability (MCV 0.76, MCH 0.78). Hemoglobin was somewhat lower (0.47) which might in part be attributable due to some local selection factors. This result comes largely unexpected, as the high heritability of the MCV was not known so far.
In the absence of any assay for exogeneous EPO, hematocrit is used as an indirect parameter for testing athletes. I already wondered why cyclists are having such high values (if we exclude illegal drug use). This seems to be a genetically trait by self-selection – an anemic cyclist will not participate in the Tour de France. Yea, yea.

123-2325_img.JPG

Addendum

Here is an answer to the question what makes a champion ;-)

 

CC-BY-NC Science Surf accessed 04.11.2025
Genetics, Philosophy

On the “Self”

If I would ever find the time, I would write a book on the “self”. Inspired by the Eccles/Popper book that I bought as a student, I always wondered how different the self is being defined in sociology, psychology/psychiatry, philosophy and theology.
As my current focus is more on genetics and immunology, I found a paper by Francisco Borrego on the “missing self” quite interesting as it highlights the genetic self is determined mainly by MHC class I molecules, where only NK cells transfected with H-2Dd were able to confer resistance for being self-attacked. It would be nice if other disciplines could also provide such simple answers, yea, yea.

Addendum

I have another suggestion: Zfp608 protects mouse mothers against immune-mediated attack by fetal cells.

Is there also a “digiself“?

Our identity has, for many years, existed quite independent of our physical incarnation in government, financial and other institutional databases. We are not real to the bank or other authorities unless we can produce something that links our physical self to our “real identity” in their database. We have many versions of this digital identity – or digiSelf, as I like to call it – spread among many databases, each with its unique characteristics, and inferred behaviours. Each one is more real to the institution – and ironically, to the people in that institution – than our physical self, what we consider to be our real self.

 

CC-BY-NC Science Surf accessed 04.11.2025
Philosophy

Genetics making up of Homo sapiens

Lets start a further workup of the evolutionary thread. With the complete human and chimp genome on our harddisks we are now able to compare genome sequence and genome activity of both species. A 2003 review by Sean Carroll summarizes our pre-genome knowledge about pan and homo lineages 6 Million years ago. The most interesting question is which mutations or genome rearrangements (Popesco 2006) are most relevant in the separation of lineages.

BTW I have still doubts about any positive effects of mutations (although this might be possible). Yes, I wonder also where are the exact pan-homo transitions (although the Sahelanthropus tchadensis might be a good candidate). Furthermore, I have doubts in survival of the fittest where non-survival of the non-fittest seem to be more relevant ;-) “Survival of the Sickest” is a CD of Mad Sin and a book of Sharon Moalem 2007.

Neuroanatomy might have provided some clues of a larger frontocortex in homo sapiens although the detailed cytoarchitecture could be as relevant. Noise of neutral substitutions could have confounded previous findings. It is also not clear to me if expansions and contractions of whole gene families are even more relevant. We may also renember that most quantitative traits have a polygenic background.

In any case FOXP2 could be associated with speech and language disorders (Vargha-Khadem 2005) where another prominent gene was now found in the 49 regions that are different between chimp and human but otherwise conserved (Pollard 2006). This new gene called “HAR1” is even expressed in the developing neocortex making it a prime candidate for species differentiation. Is there anybody able to convince me that the 18 fixed mutations in HAR1 have indeed a beneficial effect on brain development? A “leading edge” comment in Cell argues that all substitutions are upgrades from weak to strong base pairing:

Curiously, this weak-to-strong substitution bias in HAR1 extends over 1.2 kb, a region far larger than HAR1 itself. Such changes which also appear to characterize the HARs as a group undoubtely serve to strengthen RAN helices against dissociation…

I would also like to mention that male humans share more identity with male chimps than with female humans, at least on a genetic level, yea, yea.

Addendum

Even blogs have a half-life of less than 1 week. A new PNAS paper by Michael Oldham shows a more integrated view of human brain evolution by examining gene coexpression networks in human and chimpanzee brains. This seems to be another promising approach.

 

CC-BY-NC Science Surf accessed 04.11.2025
Philosophy, Theology

Solomon’s Decision

There is a never ending stream of popular press articles in Germany about creation versus evolution (ZEIT Wissen 1/2006:58 reports that 50,4% of all German believe in creation). Much of the controversy between ID-activists and evolutionary anthropogists is about timescales. Why can creationist not accept that

Ps 90:4 For a thousand years in your sight are like a day that has just gone by, or like a watch in the night.

Anthropogists may find a new review on coalescence methods interesting that finds

If the importance-sampling distribution is well chosen, the algorithm will perform well, otherwise, it will perform poorly. Unfortunately, unless we have a good idea of the correct answer from some alternative source, it is not obvious whether the algorithm is working well. Once again there is significant scope for intuition when choosing the importance-sampling distribution. The method is as much art as science. [sic!]

or another review:

… new results contradict early but still influential conclusions that were based on analyses of gene trees from mitochondrial DNA and Y-chromosome sequences

where the search for the most recent common ancestor by haploid marker is expected to result in shallower times. A recent letter in Nature on “Dogma, not faith, is the barrier to scientific enquiry” offers a nice compromise, that can be read twice:

In a famous article, “Nothing in biology makes sense except in the light of evolution” (Am. Biol. Teach. 35, 125–129; 1973), Dobzhansky described his religious beliefs: “It is wrong to hold creation and evolution as mutually exclusive alternatives. I am a creationist and an evolutionist. Evolution is God’s, or Nature’s, method of Creation.”
In contrast to modern creationists, Dobzhansky accepted macroevolution and the documented age of Earth. He argued that “the Creator has created the living world not by caprice (supernatural fiat) but by evolution propelled by natural selection”.
He collaborated for many years with Ernst Mayr, who, when asked about his religious views, replied: “I am an atheist. There is nothing that supports the idea of a personal God. On the other hand, famous evolutionists such as Dobzhansky were firm believers in a personal God. He would work as a scientist all week and then on Sunday get down on his knees and pray to God” (Skeptic 8, 76–82; 2000).

Yea, yea.

 

CC-BY-NC Science Surf accessed 04.11.2025
Genetics

Don´t leave orphan links

Tim Berner Lee argued in his article “Cool URLs don´t change” to set always a server redirect if you have moved a page.
The frequently seen page reload using the header tags <META HTTP-EQUIV=REFRESH CONTENT="0;URL=http://new.server.de/tips_tricks/">
 is only suboptimal as spider will not follow them. Put instead one of the following lines in your your Apache con/http.conf or into the .htaccess file of your directory.

.htaccess
|wj_htaccess.txt|


Preventing bots from increasing your server load is another suggestion.

 

CC-BY-NC Science Surf accessed 04.11.2025