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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 02.04.2026
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 02.04.2026
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 02.04.2026
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 02.04.2026
Genetics

A low-cost system for a PDF literature archiv II

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

  1. Shut down your firewall
  2. 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
  3. use http://127.0.0.1:4664 to configure your webserver and offer http://yourIP to your working group.

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

 

CC-BY-NC Science Surf , accessed 02.04.2026
Genetics

Snapshot of your working directory

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.

 

CC-BY-NC Science Surf , accessed 02.04.2026
Genetics

Convert an Access(R) database into mySQL format

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.

mysqlrev.png

 

CC-BY-NC Science Surf , accessed 02.04.2026
Genetics

A database driven epidemiological questionnaire

During a past project I moved from a paper-based questionnaire directly to a database version. This has the advantage of generating at the same time an online version (with some interface scripts) and an offline version (by using a serial paper printing).

The whole package is written in standard HTML with some Cold Fusion(R) extension (where you need the Railo(R) or Blue Dragon(R) interpreter too).

Download (md5:1922125540), create a datasource “aerzte” and attached the included Access(R) database. Then run the following script in your browser.

frage.cfm
|wj_frage.cfm|

 

CC-BY-NC Science Surf , accessed 02.04.2026
Genetics

Convert external maps to OziExplorer

Many map software vendors like German TOP 50 do not include export functions. Printing, however, is usually not a problem.

I therefore suggest to use the print function for exporting map data. Just print your desired map area into a PDF file (TOP 50 nicely allows to set anchor points for that).

A PDF printer driver will be already installed on many systems (if not, please go to sourceforge and download pdfcreator). Write down the upper left and lower right GPS coordinates of your rectangle as you will need them later in OziExplorer.

You will need to download also two graphics packages: netpbm and xpdf.

Move your PDF print export and all downloaded executables into one directory. After running the following script you will see a bmp file that can be imported and calibrated in OziExplorer. Happy navigating!

ozi.cmd
|wj_ozi.cmd|

 

CC-BY-NC Science Surf , accessed 02.04.2026
Philosophy

How many human diseases do we have?

… asked my daughter this morning. I can´t renember having heard any figure before – my rough estimate is about 10,000. It depends very much how you count each viral/bacterial disease and how you are dealing with the ageing process (the recent German invention of IGEL services in medical practice may have doubled disease numbers).
Nevertheless there are only 379 chapters in the renowned Harrisons textbook with the most frequent diseases are about 15. This was the result of a projection already 10 years ago in Nature Medicine. Yea, yea.

 

CC-BY-NC Science Surf , accessed 02.04.2026