Our knowledge springs from two main sources

13.11.2006 admin

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.

Uncategorized

GfH, Bonn

13.11.2006 admin

http://www.gfhev.de/

Genetics

Why we should believe professional cyclists

13.11.2006 admin

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.

Addendum

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

Genetics, Philosophy

On the “Self”

13.11.2006 admin

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.

Joke, Philosophy

Sex, drugs and DNA: Science’s Taboos Confronted

11.11.2006 admin

Highly recommended by a friend, I have ordered “Sex, drugs and DNA” by Michael Stebbins. Also Publishers Weekly finds
Continue reading Sex, drugs and DNA: Science’s Taboos Confronted →

Philosophy

Dr. Google

11.11.2006 admin

Googling for a diagnosis? The results are not too bad if you believe in a new BMJ report. The authors measured the percentage of correct diagnoses from Google searches compared with the correct diagnoses of 26 cases published in the New England Journal of Medicine. Google searches revealed the correct diagnosis in 15 (58%) cases.
Continue reading Dr. Google →

Uncategorized

Bioinformatics München

10.11.2006 admin

http://www.bioinformatik-muenchen.de/

Uncategorized

NGFN Heidelberg

10.11.2006 admin

http://www.science.ngfn.de/index_479.htm

Genetics

A simple POP answering machine

10.11.2006 admin

A script that I used for many years…

popreply.cfm
|wj_popreply.cfm|

CC-BY-NC

Philosophy

Genetics making up of Homo sapiens

9.11.2006 admin

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.

Philosophy, Theology

Solomon’s Decision

9.11.2006 admin

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, 125â€“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, 76â€“82; 2000).

Yea, yea.

Genetics

Don´t leave orphan links

9.11.2006 admin

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.

Genetics

A low-cost system for a PDF literature archiv II

8.11.2006 admin

With Google Desktop you will have the archiving capabilities that would have cost 10,000$ only a few years ago. Things become more tricky if want to share your archive on a workgroup level. Here is an idea that I have found in the German Laborjournal

Shut down your firewall
Install the freeware DNKA available from dnka.com. It will act as a web server by interacting as a layer between Google Desktop Search and the user
use http://127.0.0.1:4664 to configure your webserver and offer http://yourIP to your working group.

Need more information? Check geekzone and a nice indexer interface at TweakGDS.

Genetics

Snapshot of your working directory

7.11.2006 admin

We need two open source programs: Gzip is a compression utility with a high compression rate and free from patented algorithms. GnuPG is a complete and free encryption solution to protect confidential communication and digitally stored information. Create a /backup directory in each of your working directories.

backup.cmd
|wj_backup.cmd|

Write the above code in a file, put it somewhere in your path and assign an icon (I am running this from the buttonbar of TotalCommander (R)). One click – and your current directory is being saved as zip file and signed with your key.

Genetics

Convert an Access(R) database into mySQL format

7.11.2006 admin

That should be a pretty straightforward task: Open in Access(R) the export function, select ODBC and send the tables to your local MySQL installation. This fails, however, on my system without any useful error message.

Access2MySQL(R) of DMSoft(R) does the job, costs 55$. The trial version stops after transfering 10 datasets; nevertheless the newly created database allows an hazzle-free phpMyAdmin import of .csv exported data.