Category Archives: Philosophy

Philosophy

Da steh’ ich nun, ich armer Tor!

[sorry in German, one of my favorite poems, Goethe – Faust you are right]

Habe nun, ach! Philosophie,
Juristerei und Medizin,
Und leider auch Theologie!
Durchaus studiert, mit heißem Bemühn.
Da steh’ ich nun, ich armer Tor!
Und bin so klug als wie zuvor;
Heiße Magister, heiße Doktor gar,
Und ziehe schon and ei zehn Jahr
Herauf, herab und quer und krumm
Meine Schüler an der Nase herum –
Und sehe, dass wir nichts wissen können!
Das will mir schier das Herz verbrennen.
Zwar bin ich gescheiter als alle die Laffen,
Doktoren, Magister, Schreiber und Pfaffen;
Mich plagen keine Skrupel noch Zweifel,
Fürchte mich weder vor Hölle noch Teufel –
Dafür ist mir auch alle Freud’ entrissen,
Bilde mir nicht ein, was Rechts zu wissen,
Bilde mir nicht ein, ich könnte was lehren,
Die Menschen zu bessern und zu bekehren.
Auch hab’ ich weder Gut noch Geld,
Noch Ehr’ und Herrlichkeit der Welt.
Es möchte kein Hund so länger leben!

 

CC-BY-NC Science Surf accessed 18.02.2026
Genetics, Philosophy

Peer production

firstmonday has an interesting article about the limits of self-organization and “laws of quality”. Given 52 million tracks in the Gracenote database, 1 million entries in Wikipedia and 17,000 books in project Gutenberg, Paul Duguid throughly examines the two laws of quality

  • Linus law: “given enough eyeballs, all bugs are shallow” which means that almost every error will be discovered and ultimately fixed
  • Graham law: “people just produce whatever they want; the good stuff spreads, and the bad gets ignored”

Although more professionalized, similar principles operate in science. With these large genetic studies, I have the feeling that most errors occur at the interfaces, during hand-shaking of disciplines. There are certainly only a few people that can design a study, examine a patient, go to the laboratory, analyze and annotate the data and publish them. This means that even many eyeballs can not look around the corner and that it will take many years for the “good stuff to spread”. Yea, yea.

 

CC-BY-NC Science Surf accessed 18.02.2026
Philosophy

Blog together

Just read the entry of Janet D. Stemwedel about the 2007 North Carolina Science Blogging Conference, a “free, open and public event for scientists, educators, students, journalists, bloggers and anyone interested in discussing science communication, education and literacy on the Web.” Do not miss her tag “Shameless self-promotion” ;-) Three editors from The Lancet will take up to 49 registrants. Who can give me a free ride from Munich (bonus miles welcome)?

 

CC-BY-NC Science Surf accessed 18.02.2026
Philosophy

The journey is the reward

The analysis of a large dataset can be done in many different ways. At least in my experience documentation is getting confusing after many weeks of work – what has been done at which time? Can I reproduce my earlier findings? Where are the latest figures? What remains to be done? …

This is an ever increasing problem. Some information is documented in lab books, other in clinical journals, or even sitting on a server database where it may change over time. I have therefore described my own documentation procedure in a PDF paper that is online at this site.

With a quick view at the figure you will see that I am (mis-)using spreadsheets for documentation Please note (1) the drop down arrows at date and task that can be used for selecting lines even of long lists and (2) that tabs can used for fast switching between results (3) one tab contains all analysis scripts (4) and one tab all links.

spread.png

 

CC-BY-NC Science Surf accessed 18.02.2026
Philosophy

Not just a face-lift

The redesign of the PLoS journals today is not just a facelift. They continue to have fresh ideas and unconventional approaches. A recent email said that

we encourage authors who are fluent in languages other than English to submit translated versions of an article summary … in other languages. Translations should be submitted as Supporting Information files labeled “Translation of the article summary (or entire article) into language XXX by author YYY”.

That is a nice idea, showing another benefit of online journals, yea, yea.

plosone.png

 

CC-BY-NC Science Surf accessed 18.02.2026
Philosophy

Born to be write

A decade ago Karen Hunter (at that time Senior Vice President of Elsevier) did a brilliant analysis why scientists publish:

For academic scientists, the research paradigm is the experiment and the publication output is a journal article. Academic science researchers publish to establish their claim at a specific time to a specific result. They publish to gain other forms of recognition (such as promotion and tenure) that require publication. They publish in order to have independent certification of the results and to have those certified (refereed) results archived in perpetuity. Finally, they publish to communicate with those who may be interested in their works today …

She continues with another important aspect

… not the circle of cognoscenti (who do not need publication to be informed) but researchers in related fields, researchers in less well-connected institutions and students working their way into the inner ring.

In my opinion, the “claim at a specific time to a specific result” is probably the most relevant motivation for a scientist. Nevertheless having claims on ideas presented in a printed paper seems to be still a habit of the pre 1995 stone age of scientific publishing. Databases will be certainly as reliable in the future as printed paper. I guess that in 50 years the access to current electronic documents will be even better than to any printed paper. Yea, yea.

 

CC-BY-NC Science Surf accessed 18.02.2026
Philosophy

Can anybody become a Nobel Prize winner?

Anders Sandberg attended a seminar in Stockholm and has written an interesting report. I have doubts if we have so much need for heroes. There are so many prizes that you can apply for – an impressive list of prizes and honours that you can find at the CVs of some laureates: Albert Lasker Award, Paul Ehrlich Prize, and many, many more. Google returns 60.100.000 hits if you search for “science prize” and there is now even the European database of science prizes that will find a prize for every scientist. Yea, yea.

 

CC-BY-NC Science Surf accessed 18.02.2026
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 18.02.2026
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 18.02.2026
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 18.02.2026
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 18.02.2026
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 18.02.2026