Category Archives: 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.

 

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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.

 

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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.

 

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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.

 

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Is religion a natural phenomenon?

I do not want to discuss the rather polemic view of Daniel Dennetts “Breaking the spell” or promote other books of the new secularism. The Guardian digital edition writes on 29th Oct 2006

Secularism is suddenly hip, at least in the publishing world. A glut of popular science books making a trenchant case against religion have soared up the bestseller lists both here and in America. The phenomenon represents a backlash against a perceived rise in religious fundamentalism and recent crazes for ‘spirituality’ by way of books such as The Da Vinci Code. Secularists are now eager to show that the empiricism of science can debunk the claims of believers.

More interesting is the question if human morality is an inborn trait or not. Nicholas Wade has a nice essay in the NYT:

Marc D. Hauser, a Harvard biologist, has built on this idea to propose that people are born with a moral grammar wired into their neural circuits by evolution. In a new book, “Moral Minds” (HarperCollins 2006), he argues that the grammar generates instant moral judgments which, in part because of the quick decisions that must be made in life-or-death situations, are inaccessible to the conscious mind. People are generally unaware of this process because the mind is adept at coming up with plausible rationalizations for why it arrived at a decision generated subconsciously. Dr. Hauser presents his argument as a hypothesis to be proved, not as an established fact. But it is an idea that he roots in solid ground, including his own and others’ work with primates and in empirical results derived by moral philosophers.

I renember also an article by Roger Higfield in the Washington Times (24th March 2003) than unfortunately vanished from the internet:

Scientists are hunting for a “God gene” that underpins our ability to believe. The idea of genes linked with beliefs does not look far-fetched, given the influence of genetics on the developeing brain.

Higfield is refering to an empirical twin study:

To investigate the heritability of religiousness and possible age changes in this estimate, both current and retrospective religiousness were assessed by self-report in a sample of adult male twins (169 MZ pairs and 104 DZ pairs, mean age of 33 years). Retrospective reports of religiousness showed little correlation difference between MZ (r=.69) and DZ (r=.59) twins. Reports of current religiousness, however, did show larger MZ (r=.62) than DZ (r=.42) similarity. Biometric analysis of the two religiousness ratings revealed that genetic factors were significantly weaker (12% vs. 44%) and shared environmental factors were significantly stronger (56% vs. 18%) in adolescence compared to adulthood. Analysis of internal and external religiousness subscales of the total score revealed similar results. These findings support the hypothesis that the heritability of religiousness increases from adolescence to adulthood.

Time on Oct 17, 2004 referred to a book of Dean Hamer “The God Gene”

Chief of gene structure at the National Cancer Institute, Hamer not only claims that human spirituality is an adaptive trait, but he also says he has located one of the genes responsible, a gene that just happens to also code for production of the neurotransmitters that regulate our moods. Our most profound feelings of spirituality, according to a literal reading of Hamer’s work, may be due to little more than an occasional shot of intoxicating brain chemicals governed by our DNA. “I’m a believer that every thought we think and every feeling we feel is the result of activity in the brain,” Hamer says.

This looks very much like a completely physical view of spiritual affairs (Hamer became famous for his failure of the “gay gene” before abandoning science).

So we may better turn to the question if there is any theological background? I renember a famous guest lecture in Marburg 1980 about the Epistle to the Romans by Herbert Braun (Braun is a Bultmann scholar. Ernst Fuchs was in Marburg too; together with Ernst Käsemann and Günther Bornkamm they are all famous scholars of Rudolf Bultmann. Käsemann and Fuchs both wrote a “Commentary on Romans”).

Fuchs highlighted Rom 2:14 in King James translation saying:

13 For not the hearers of the law are just before God, but the doers of the law shall be justified.
14 For when the Gentiles, which have not the law, do by nature the things contained in the law, these, having not the law, are a law unto themselves:
15 Which shew the work of the law written in their hearts, their conscience also bearing witness, and their thoughts the mean while accusing or else excusing one another;

Science and theology are not far away here. Maybe it is even common sense that most humans have an inherited deep feeling of religiousness.

 

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Genetic code and God’s language -cont’d-

There is a new book by Francis Collins “The language of God“, one of the leading persons in human genome sequencing. As the commentary says:
Continue reading Genetic code and God’s language -cont’d-

 

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Who goes first?

A recent example of self-experimentation is the famous trial where Dr. Barry Marshall swallowed a tube full with Helicobacter pylori which led him to develop gastritis. Lawrence K. Altman, M.D. has written the story of self-experimentation in medicine covering the many facets of these heroic experiments. Published already in 1987, I discovered this book only now. Highly recommended, yea, yea.

 

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For some, the system is working well

Just received an email – the fall 2006 desk-to-desk message from Dr. Zerhouni, “Making it Work for our Emerging Scientists”
http://www.nih.gov/about/director/newsletter/Fall2006.htm. It says “For some, the system is working well. The best and brightest are reaching their full potential in solid, research careers. We have the evidence in the number of competitive grant applications being submitted. For others, the queue is backing up… Between 1980 and 2004 the average age of Ph.D. scientists earning their first R01 award went from 37 to 42 years… The problem appears to be largely the result of the ever-increasing age at which a researcher receives his or her appointment as an assistant professor.”
I would like to add that the average life expectancy also increased between 1980 and 2004, so the relative age remains the same. Yea, yea.

Addendum

Science magazine has different data on salaries of postdocs: academic salaries rose from $74,000 to $78,000 and industry salaries of $106,000 to $116,000 between 2005 and 2006.

Addendum

German salaries in biotech lab, research and marketing increased at the same time by 3.7% to €99,000 (for leading positions) and 3.3% to €74.000 (for specialists) according Laborwelt 1/2006 page 45.

 

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Truth in science (and religion)

A recent interview of Jane Glitschier in PLoS genetics with Tom Cech nicely shows the relationship of truth and research: “There is a search for absolute truth in research. You never get there—but there are criteria by which you judge how close you are. You’re always criticizing yourself and criticizing your colleagues, and they’re criticizing you. And there is a test, very often, that you can do to decide who’s right.”

Addendum

Here is a difference between science and religion — Jesus told his disciples, “I am the way and the truth and the life” (John 14:6). Yea, yea.

 

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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

 

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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.

 

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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.

 

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