NOTE:

Dear visitor (if there is any) please note the following: The blog "Broken Radius" is hosted at Google Blogger's server. I can therefore not guarantee that your visit to the blog or any comment you write wont be recorded by the NSA. If you have any worries about this, you can visit instead my alternative blog Letters-to-a-Persian-Cat. This one is hosted at a European server which hopefully acknowledges visitors privacy.

25.12.14

Waning Moon

On this December waning moon the mare and craters are nicely visible.

19.12.14

Upside Down Moon

This is the waning moon on December 19th. Because the telescope optics invertes everything, and because I was too lazy to invert it back with photoshop, it looks here like a waxing moon.


16.11.14

Leonides meteor shower 2014

In the night between Monday and Tuesday, in the early morning hours, this years peak in the Leonides meteor shower will cross the earth orbit.  It is expected that with a naked eye one will spot around 12 meteors per hour. Look out in Eastern direction. As the name suggests, the meteors seem to originate from the constellation Lion. In reality, however, they don't originate from any star, but from a former comet TEMPLE-TUTTLE, which a couple of million years ago exploded or was annihilated by spaceship Enterprise. 
 
In case somebody has an urgent wish to address to the Leonides, I have to warn that in astronomy we are counting not days, but millions or years. So whatever wish you silently send to the meteors these nights, be a bit patient for its delivery. I, for example received something extraordinary this summer, for what I asked for already 4 years ago.

15.9.14

Social Incompetence

The scientific community uses its own professional social networks, one of them is Research Gate.
It is intended to exchange opinions, news, find solutions for technical issues, and circulate career opportunities. Privat things are traditionally rarely a subject of debate - I guess for lab gossiping or emotional outcries about a failed experiment or a succesfully published study people use Facebook in parallel. 
But this seems to change, gradually.
At the end of last year we had formed a nice rock- and blues band with some colleagues from our research center, called "The Blue Knockouts". We were crazy enough to perform after 4 month rehearsal after the retreat of one of the band members institute. It was a big show, we made good noise, but since I did not knew anyone from the audience, I was reluctant to respond to any of the offers they made on their posters.



And obviously, many of the people on the dance floor thought that they should also express their opinion of the concert at Research Gate. Befor the concert, I had only about 60 people, mainly present and former colleagues, or international colaborators, who had me on the list of peers to follow on Research Gate. And they endorsed me for skills such as DNA sequencing, cloning, and teaching some survival tricks to laboratory mice. But after the concert, I noticed a lot of new people following my scientific activity at Research Gate, but none of them had any direct link with my projects, neither did I knew their names from before. When I saw, however, in which lab they wer working, I understoud the reason for their interest: They were all members of the institute that had invited our band for their retreat. Some of the people in the audience had really a great sense of humor, for they not only started to follow me on Research Gate, but the also endorsed me for the only skill they were able to judge at the concert:  Playing Guitar. I don't know if there are other people at Research Gate who are not only recogniced by the peers for their expertise in molecular biology or cancer genetics, but for playing a music instrument. I think it is a good sign of the moderators of Research Gate that they tolerate and appreciate extra-professional activities.
So it seems that with a one-night rock concert at a 100 people audience you can get almost more attention than doing biomedical research for 20 years and publishing 43 papers in international journals.


29.5.14

Thats for you, dad

Only recently, pediatric psychologists and sociologists start to appreciate the role fathers play for the mental and intellectual development of children. In the past, it was "good practise" to marginalize any role of the paternal half of the parents. Although classical genetics has shown without any doubt that the inherited DNA variants from both parents are equally important for the traits such as skin or eye colour, blood groups, body heights, facial shape and many more, features of personality, in particular mentality of a person was usually considered to be formed predominantly by a mother-child relationship. 
There was, however, on exception: psychatric problems such as depression, borderline syndromes or schizophrenia were frequently attributed to inappropriate behaviour of the father towards his children. Physical or mental violence against the mother or the chrildren themself, neglectance or even sexual abuse by fathers are "common sense" factors with a long lasting, detrimental effect on the mental health.
In 2013, the US National Organization for Woman still considered any positive effect of a fathers involvement of childcare "A myth". But also serious scientific studies used to ingnore any benefical influence of a joint mother and father eductaion of their children. Many psycho-social studies on children and adolescents used to classify the "Type of Maternal Behaviour" simply as “Baby given to father” , as if on a scale from careful to neglecting parental habit, a responsibility by the father must be the worst case.
Recently, an accomplished science journalist and father of five, Paul Raeburn has published a book that sheds a new look on this issue. "Do Fathers Matter?” is an odd reading experience. As you make your way through the scientific studies that Raeburn has assembled—the book touches on everything from prairie voles and Neanderthals to “the caudate, a deep brain structure associated with feelings of love”—you can’t help but notice the weirdness of the question it poses. Asking whether a father “matters” to a child verges on nonsense; it’s like asking whether the radius matters to the circle, or whether the root matters to the branch. Fathers matter to children in a simple way—without them, they wouldn’t exist—and in a way that is too complicated to explain. Like it or not, our families are part of who we are, in ways we can and cannot know. It’s the biology, though, that I find myself still thinking about. “Do Fathers Matter?” is a strange book, because it tries to answer a question about families in mainly statistical, biological terms. But the truth is that we inherit from our parents a mixture of the personal and the impersonal. It matters that our fathers were kind to us when we were children or teen-agers—that they loved us—and, on Father’s Day, we’re grateful for those kindnesses.

10.5.14

Cloudbuster for a Tehran Nightingale


Day after day 
I press my ear down to the earth, 
trying to hear the sound of your blue slippers,
while you walk along the pavements of Tehran.
And I realized how endless can be four days,
when you stay barefoot in this little room of your own.

 

Cloudbusting (by Kate Bush)

 



I still dream of Orgonon
I wake up crying
You’re making rain
And you’re just in reach
When you and sleep escape me

You’re like my yo-yo
That glowed in the dark
What made it special
Made it dangerous
So I bury it
And forget

But every time it rains
You’re here in my head
Like the sun coming out
Ooh, I just know that something good is going to happen
And I don’t know when
But just saying it could even make it happen

On top of the world
Looking over the edge
You could see them coming
You looked too small
In their big, black car
To be a threat to the men in power

I hid my yo-yo
In the garden
I can’t hide you
From the government
Oh, God, Daddy
I won’t forget

‘Cause every time it rains
You’re here in my head
Like the sun coming out
Ooh, I just know that something good is going to happen
And I don’t know when
But just saying it could even make it happen
The sun’s coming out.
Your son’s coming out

One of the most fascinating songs by Kate Bush, but probably also one with the most cryptic lyrics. “Orgonon” refers to the hypothetical energy field proposed by the psychoanalysist Wilhelm Reich. Reich, after fleeing Germany and settling in the US, also constructed a so-called cloudbuster machine, which in this video is operated by the scientist, played here by Donald Southerland. Whereas most people interpret the lyrics of this song by Kate Bush very much along the biographie of Wilhelm Reich, I have a different interpretation.

Kate Bush was not unfamiliar with unpredictable changes of mood, or emotional ups and downs and periods of depression. These are frequently described by patients as “Dark Clouds”, since they arise suddenly and scarry like the clouds of a thunderstorm. “Cloudbuster” might therefore refer to a person (a friend or a therapist) who helps to chase away these clouds of depressions. Many viewers of the video further think that Kate Bush here simply “plays” the part of Peter, i.e. Wilhelm Reichs son. Strange for me to believe that Kate Bush should play a male part here. I think she represents a girl who is regularily plagued by depressive episodes, and who looks for help from an elder friend (i.e. Donald Southerland).

W H Reich ‘discovered’ Orgone energy, and made a machine which he claimed he could collect this energy, an orgone accumulator. It was – I believe – to do with the sale and marketing claims of this machine that he came to grief with the law. Orgonon was also the name given to a body of Aristotle’s works by his followers. So dreams of Orgonon can be understood as an alluision to this new form of energy which Reich claimed to have discovered. It could also be viewed as a reference to Reich’s banned opus.

Reich also he tried to measure the male orgasm and believed this was a type of energy present in all life forms which he called “orgone.”. He built cloudbusters which he believed could manipulate streams of orgone energy to produce rain. His 280 acre estate in Maine was called Orgonon. He was banned from orgone-therapy equipment across a state line and was jailed for 2 years when he failed to do so. He died in prison.

Is there anything in Reich’s work? As a student of physics I have to say I am highly dubious of orgon energy. There are plenty of forms of electromagnetic energy, many of which are used in medicine (from X rays, to radiotherapy, even to those wrist bands people wear to stop car sickness) there are sure to be many ways in which known forms of energy can have as yet unknown effetcs on the body. There seems to me to be no independent evidence of organon energy. It seems to have little explanatory power except in some accounts of the positive effect of Reich’s machine, which are perhaps better explained by the placebo effect.
But it is a great song and does not need to be seen as an appraisal of Reich’s work by Bush, but rather a study in daughter’s love for a father.

1.5.14

Depression: The Individual Manifestation of a Social State

I don't know if this is just a chance observation, but of people I know personally or of which I heared of, and of people who write blogs I recognise more and more reports about phases of depression. And in biomedical research, this is also a big issue: Some colleagues in a neighboring institute of neuro-genetics have large projects on depression, including mouse models for this, but also large patient studies. There are big efforts, and some small results, about the importance of inherited factors (i.e. genes transmitted from one generation to the next) and about
the detrimental influences of a problematic childhood and adolescence (experiences of home violence, abuse, frequent change of partners, neglectance) for the development of depressive conditions. So the focus goes mainly to the patient himself (inherited factors) or to contributions from the surrounding family.
I think that the influence of the society (including social media) and of the working community by far underestimated ? I know of people who were really suffering from depression for long time, untill they change their job and became completely normal. And these were not people who used to complain about their former job. Nobody would have guessed that the job was somehow linked to their depressive state, maybe not even themself. But since their condition improved so much after changing job, it is obvious that parts of the problem must have been job related. And for younger patients in school age there is obviously the influence of school environment which can promote or prevent the development of depression.  Schools like in Germany or in some Asian tiger states, which are mainly to promote a high-power elite, teaching the students to follow the track of Ariana Huffington, Mark Zuckerman, Sheryl Sandberg and other role models who are unknown to have ever experienced a grey day in life, leave quite a large fraction of the young people left in a state of personal doubt. There are also several studies showing that an intensive consumption of social media steams, which are always biased to show happy people and success-stories, can contribute to depression. 
I'd be interested to know to which degree depression can be treated to focus on the patients themself, and how much the society must change the social condition that promote or cause depression.

22.4.14

This planet could become our future home

Since the first hominides climed down from the trees in the east-african savanna, they began to search around regularily for potential better places to live. So they first entered the Middle East, where they split in several groups, disagreeing whether the North-Western route towards Europe or the Eastern towards Asia should be taken. And the story continued, making mankind the most mobile species on earth, virtually driven in a restless move on the hunt for the even-better, even-cosier and even warmer home. Have they found it, this place where they feel finally perfectly at-home ?  Does not seem so. And even worth, currently many places on earth which for some centuries were quite habitable and convenient undergo changes related to the global warming that could soon make them again regions of massive emmigration. Rises of the sea level, landslides following alterations in the geo-hydrology, extension of steppes, droughts and devastating forest fires increase in frequency and in severity, making more and more people looking for a safer place. But where are these safer places, for an ever increasing world population ?

And we also have to seriously consider the future developement of the biomedical research and technology to overcome disease and death, virtually trying to extend human longevity further and further, heading for eternal life. So the natural question will be where shall all the people live in the furture, where could additional habitable space be conquered.  One is for sure:  Our earth' surface has a very limited size, and building more and more into the 3rd dimension as tried by the super-skyscrapers in Dubai, Abu-Dabi, Singapoor or Malaysia is no solution.

However, the idea to move away from our flat Earth' surface goes into the right direction, but we have to extend our vision from global to universal. During the last few years a new branch in astronomy and astrophysics evolved that by using highly sophisticated instruments is able to identifiy and study extra-solar plants. The spectroscopic techniques are so sensitive that even the atmospheric conditions at these "Exo-Planets" can be estimated. Together with the planets size and mass this allows to evaluate the "habitability" of the candidate planets, virtually meaning not only how likely it is to find primitive or higher forms of extra-terrestrial life there, but also how could would be chances to settle a permanent outpost of our human civilization there. The latest and most promising candidate for a habitable planet is Kepler186f. 
The discovery, announced on Thursday, is the closest scientists have come so far to finding a true Earth twin. The central star around which Kepler 186f rotates is located about 500 light years away in the constellation Cygnus, is smaller and redder than the sun.
Kepler 186f is the star’s outermost planet and receives about one-third the radiation from its parent star as Earth gets from the sun, meaning that high noon on this world would be roughly akin to Earth an hour before sunset, said astronomer Thomas Barclay, with NASA’s Ames Research Centre in Moffett Field, California.
The planet is at the right distance from its host star for water – if any exists – to be liquid on the surface, a condition that scientists suspect is necessary for life.  “This planet is an Earth cousin, not an Earth twin,” said Barclay, who is among a team of scientists reporting on the discovery in the journal Science this week.
I am happy that I have not applied yet for the no-return journey to our neighbour planet Mars, considering that the living conditions there seem to be much worse. So I better wait for the first available space-ship heading for Kepler 186f.  According to the phantom artists impression of its surface as shown on the above picture , it must be a quite nice place. With its autumn leaves, the lake and snow covered mountains in the background it reminds me of the alpine landscape south of Munich or the alpine lakes in Swizzerland. But I hope that once human arrives at this pictoresque scenery at Kepler 186f, they are wise enough not to implement the stringent system of laws and legal constrictions as on earth, but at the same time are intelligent enough not to damage the planets eco-system.


17.4.14

Are the social media really social ??

Since the advent of the internet 2.0, the way we can exchange information in virtually real time and with every point on earth and with everybody in almost every country revolutionized the knowledge about our global world. Whereas in the past only a few large sources of comprehensive information dominated the world (like the Encyclopaedia Brittanica or the Big Brockhaus or the Encyclopedia Iranica and of course big publishing houses for fiction and non-fiction literature), each of which representing the general, expert approved opinion about our universe and our life and human history, this situation changed dramatically about 10 years ago. Nowadays, virtually everybody can write down and publish his very individual view about the state of the world, and appart from some funny conspiracy theoretics and creationists and health food vegans, this wealth of information contributed a lot to the real picture of our world. Whereas in the past, we could only read essays, articles, opinions by established authors, who made it onto the payroll of the Washington Post or the New Yorker and the like, the appearance of social media make sit easy now to follow the stories, the daily blogs, the political statements by complete unknowns.  Without this, we would have probably never heard of Marina Keegans "The opposite of Loneliness". Even books which later became bestsellers started as social media texts, "Axolotl Roadkill (aka Strobo)", "Work and Structure" byW.Herrndorf, "Super Sad True Love Story" by Gary Shteyngart or the notorious "Shades of Grey" novels.
But I'd like to understand to which degree the social media really fulfill a new social function. Are these social media really social ??

Since a couple of years I was following some interesting blogs, which I always enjoyed reading, even so they were updated only in a very irregular fashion, with some of them suddenly ending altogether. Since I was always dissatisfied, sometime even sad if a formerly active and inspiring blog writer suddenly abandoned its web diary, I tried to understand what are the motivations to write or what are the reasons to stop a blog. for this I did a sort of statistic analysis which shows, that there is a peak activity of postings in many blogs, usually at the 2nd and 3rd year, and than it slows down, gradually, and most of the blogs completely “dry-out” after 5 or 6 years.



I also try to understand what is the reason for this ? is it that people changed their life situation such that too many new and “serious” commitments don't alowe them to write posts to their blog anymore ? In my eyes, that would be really sad and virtually indicating that their life situation has not changed for the better. But maybe it is that after many years writing a blog, and feeling too little response from readers, the writer decides to go back to the old fashioned way and write a paper diary ?

Detailed activitiy plots of individual internet blogs over the years beginning from the first year of their set-up. Single curves and absolute numbers of their posted posts can be found here.
Please note that the values for the current year 2014 might underestimate the real activity of the blogs owner, since this number is based only on the activities of the first 3 month and is therefore not as representative as those calculated for fully completed years.

 
The list of blogs analyzed above contains classical types of web logs, diary stiles, daily observations and considerations about what the authors regarded as important from their very personal point of view. None of the blogs are of semi-commercial type, none are maintained by an editorial office on a paid base and none of them attempt to attract web-traffic to make money with banner ads. So in essence, these 18 blogs were set up and maintained by people who wanted to share their daily thoughts and opinion, without a commercial intention. And since all of them at one day or the other  appeared quite interesting to me as reader, I continued to follow them over several years. They were worth this, and I learned a lot about peoples life in other countries and other cultural backgrounds. But always, after a certain time, the frequency of their postings declined, not in terms of length, or quality or content, but simply in terms of the number of posts per month. After a while, several blogs became inactive at all, what I regret. On the other hand, there are many blogs around which are really boring, like endless rows of food pictures, travel pictures, celebrity news and so on. I just summarized my top-8 list of blogs I would ban from the internet, in case I would ever become the WWW-Inquisitor. You can have a look here:   http://brokenradius.com/2014/03/03/blogs-i-recommend-to-de-follow-immediately/

But I like to understand what makes people, who over some years wrote interesting and relevant articles in their blog, slow down their activity or stop sooner or later at all. There are some trivial possibilities:  It could be that somebody died (I hope that it does not happened to any of the authors of the above list of blogs).  It could be that people usually start writing blogs at a particular period of life or age, for instance when they leave their parents home and enter college or university, therefore spending many evenings alone in a students dorm or a privat appartment. If this is a motivation to start writing a blog, than it would be logical that after about 5 to 6 years they are about to finish this period of life, they are about to find a fix partner or even marry and live together. Maybe this is a critical time for the long-term survival of a blog. Maybe spending most of the time in a domestic environment with a fixed partner makes the blog of a person recieving lower priority. So this would imply that the near-field social interaction (i.e. with one or several persons in physical vicinity) suppresses the social activities via the electronic social networks.
But there is one aspect that I found most variable among the blogs listed above: the degree of social interaction between the blog owner (or the main author of the blog posts) and his followers or commenters.  In general, each of the blogs allowed the readers to submit comments. Some of the blogs publish all comments. Some of the blogs publish only comments selected for relevance. The really active and socially responsible bloggers even reply to readers comments, sometimes with a lenghty answer, sometimes with a short "Thanks for the valuable remark". 
Some bloggers have the comment function by default set to "Show comments without approval by blog owner", but they actively delete comments later on, based on an unclear selection policy (nationality, language, religious or political statements in the comments). 

My initial assumption that blogs "dry out" over the years if the blog-author does not feel any response from readers appeared not to be true. I know of blogs which publish very witty and long posts continously over a long time, without ever receiving much response from readers. On the other hand, there are blogs which had a very vivid discussion from readers following each post, usually with very interested and polite readers, but still the author decided after some years to stop maintaining and updating the blog.

So I have to admit that I did not find a conceivable explanation as to why some blogs are maintained for a long time, and why some are doomed to die too early. As in epidemiology there are always two possible factors causing a blurry observation:  Either unknown individual differences (maybe not genetically, but in terms of mentality) or several external factors that act together (i.e. change in living situation + change in personal status + inadequate response from readers).
The good thing is, however, that usally blogs stay in the internet, even if the author has abandoned it for a long time (unless the blog is on a paid server space). So the wealth of information which tells us and maybe later readers about peoples observations, experiences and opinions from all over the world remain available.  We should not underestimate the value of the social media correspondences, all these splinters of informations from ordinary peoples brains for later generations.  The sumer of ancient Mesopotamia would have never predicted that the cuniform account lists they once wrote on clay tablets help the historicians in the 20th century to learn about these 3 000 year old civilization.



16.4.14

One day out of 32872 days

  • Woke up at 6:50
  • Prepared avocado-egg-salad, half of it eat on black bread, half I left for Marischa
  • Watched 15 minutes morning news, about the dreadful stupid fights between Ukrainian military and Russian separatist
  • Went out with Ivo for a 15 minutes morning walk, realized that it is pretty cold but sunny
  • Gave food to Ivo
  • Jumped on the bike heading for work, taking with me the damaged rear wheel of Marischas bike
  • Cycling through the North of Munich, across the Isar river and through the English Garden
  • At the junction of Leopoldstreet and Neuherbergstreet, meet Mr. Osenberg, head of our Research Centers financial control department. He is a really small, slim and non-typical sport shape man. But on his bike, he is like a racer, like a grease lightning. Three minutes after we both start at the green traffic light, he is already about 500 m in front of me. I calculate he is about 20km/h faster than me.
  • Arrive at the institue, and take a shower (poor Mr.Osenberg once told me that they don't have a shower over there at the administrative department. I'm proud to feel privileged as a researcher in this instance.
  • At my desk I check my e-mail. Two students, one from the Netherlands and one from Bulgaria confirm their participation on my lecture series. A professor Martazavi from Tehran also wants to participate, but needs a letter from me to apply for a German visa.
  • Went to the cell culture to check the mesenchymal stem cell cultures. Three out of 10 from last weeks explantations are bacterial infected. Have to sterilise those and discard. But the remaining 7 cultures are clean and grow well.
  • Yashodhara comes to the cell culture room to tell me that Life Technologies have problems to continue supplying us with Stem Cell approved serum.  I explain her to request from other suppliers ordinary bovine serum test samples, check them for growth potential on our cells, and just order a large badge of the best charge. As usual, Yasho expresses deep dissatisfaction, as if over there in her Indian home everything would be just perfect. Never had somebody in my group who is so unwilling to improvise or solve problems.
  • When I pass along the coffee room, I realize that Bahar has birthday today, and she is already arranging her cake.  I feel ashamed, it happened what I was afraid of: that I might forget the birthday of my most reliable, most pleasant and most witty technician. I try her really delicious (and hallal) cake, and tell her that the present will arrive after lunch only.
  • Back to my office, I close the door behind me and start to write to Fatemeh, my friend so far in Tehran. I send her back one of the pictures showing the Afgani girl, after I added the IPCT tags according to Mrs. Tieth from Ullstein. I know I could write endless letters to Fatemeh, but have to stop here and wait for the evening, because
  • Costanca enters. Once again, she is very nervous and plagued with doubts about the deadline for her master-project. I tell her that she shall focus the presentation of next week on the novel findings in telomerase regulation in mesenchymal stem cells, but not on the problems with low protein concentration of her samples. I tell that with all these worries she reminds me of Sherly Bassie (when Bassie was 50 years younger, of course). She starts to smile a bit, and again asks me why I address her with the polite German "Sie", rather than with the familial form "Du". I tell her that with all others we communicate in English, and there is no difference between a formal and this privat form of addressing a person. But in German, I use instinctively the official polite form for colleagues much younger or students. I promise to organize some of the much-sought-after Amicon protein filtration tubes from another institute. Indeed, Ines from the Pathology institute gives me her entire storage of 14 tubes, which should make Costanza happy for tne next few days, untill our order from Merck is delivered. Next problem with Costanzas experiments is the missing master-mix for the Eliza assay. I call Roche Incs customer service to explain them our problem with master mix shortage. They promise to send some extra tubes free of charge.
  • Back from phone, I check the status of my submitted manuscript at the editorials office website. It is still of "under review" status (since 4 weeks).
  • I do the first outline for the manuscript on osteosarcoma, telomere alterations and the Rb1 gene and PML protein status. While reading through the recent publication from Sanger Centers ICGC group and what they called as Kataechis mutation spectrum I suddenly understand that this looks very similar to the AID hypermutations in B-cell lymphoma. I go to Jan to tell him about this possibility. As usual, he has never heard about this molecular process, and me (a physicist) have to explain to him (a biologist) all the basics of this essential process of immune development. As usual, he seems completely drowned in this mass of genome data, but is unable to bringe some sense in. I tell him that I will talk to Jean-Marie, who is a specialist in somatic hypermutation and kicked out from the research center 4 years ago, to find a way to determine if the cytosin point mutations in osteosarcoma are from dysregulated AID somatic hypermutation. I doubt that Jan understands the relevance of this possibility. But the head of his research unit is of similar weak scientific vision.
  • It is almost lunch time, and I remember that I have to buy a birthday buket for Bahar and bring Marishas bike wheel to the repair shop. So I jump on the bike and drive over the field towards Euro-Industrial-Center, the last 5 min through the abandoned military camp, which is now the camp for the asylum seekers. The security guards are liberal today and allow me to drive through this by-pass-road. At the bike shop, I buy a new rear wheel and the service guy changes the gear set from the old to the new one. Great, seems to have worked out.
  • On the way back, I feel that the pneu on my own bike is flat: I must have perforated it while drove over a sharp stone at the asylum-serkers camp. Walk back to the bike-shop, to exchange the pneu. This costs me another 20 min and my hands look dirty as pig. But finally, I can drive back to the institut. Stoping over at the the flowers shop, I find a beautiful buket of long, red-yellow roses.
  • Back to the instute, I can finally congratulate Bahar, and she is honestly amazed by the buket. I understand that it is a stupid stereotype that muslims don't acknowledge flowers. Muslim or not, Bahar is really happy about the roses, and she askes all other peoples in the lab who has ever been given such flowers from the boss (I complain with her again about her addressing me her boss). I know that at the age of 32, Bahar is not completely free of worries regarding age. I tell that know, 12 years after she started working with me, she still looks the same, and this is a big compliment for her, considering that she got 2 kids meanwhile. And she says that indeed she still feels like an18 years old, but that she also  never believed that I am 20 years her senior, in particular after we went recently to a couple of rock-concerts together. So we are a good team at work, we know how much we can trust each other and although so different educational and cultural background (muslim versus bloody atheist), we usually stick together like "tar and sulphur". The only thing I disliked was that 8 years ago she stoped wearing a hijab. So after another piece of her birthday cake, and with the buket, I told her to take the afternoon off to celebrate with her family.
  • The afternoon I went back to work on tne manuscript on the osteosarcoma hypermutation and our genome profiling. I found an older paper that claimed that osteosarcomas mutational spectrum indeed resembles somatic hypermutation, but for some unclear reason they suspect the gene APOBEC to be the underlying cause, rather than my hypothesis favoring AID. But AID would be more logical, since it is a DNA editing enzyme, rather than the RNA editing activity of APOBEC. But APOBEC is ubiqiously expressed in many tissues, whereas AID is restricted to lymphoid immune cells. But it could be that AID becomes ectopically expressed in the process of osteoblast transformation, and hence exerts its DNA editing activity to the entire genome, causing wide-spread hypermutation.
  • Suddenly Anna from Michas iPS stem cell group calls and says that tomorrow she will have differentiated cells from her ES and iPS models to give us for assaying telomerase activity. I tell Costanza that next day she should expect additional cell samples for her experiments. As expected, she wrinkles her brows showing her unease with this extra work.
  • At 4:30 p.m. I decide I had enough fullfilled my professional duties, and now want to go to the cinema to watch "Her", a movie by Spike Jonze, featuring Joaquin Phoenix as a young man who falls in love with a computer OS. Since it is a love which mainly manifests itself as dialogues by computer chat, I thought it could explain a bit why I feel so much confidence with Fatemeh. But the movie is a sad story, and Theodore, the main character of the movie, is a poor victim of his fears and LA typical undecisiveness in terms of partnerships. So Samantha, the computer OS who he falls in love with, is programmed such that it behaves as the ideal girl of his dreams. So this virtual relationship is rediculous, whereas my attraction to Fatemeh is to a very real person, and objectively, we are very different, she a very creative artist, religious, and very open and positive about meeting and learning about new people every other day. Me, scientist, atheist or pantheist, and readily bored or pissed off as soon as I meet stereotypic people. But anyhow, there is a deep emitional and spiritual link between the two of us, and nothing in the world is currently so important for me as Fatemehs opinion about me. Since I lack any religious higher instance to judge my deeds and my person, I have choosen Fatemeh, whos words I rely so much. The movie "Her" has nothing of this mutual trust. In the movie, Theodore simply needs a projection for his unfulfilled phantasies, but he does not really expects Samantha to challenge his concept of life.
  • After the movie is over, I drop in at Lehmkuhls bookstore to buy Wäis Kiani's "Behind the Moon", to give it to Nineliah for Eastern. On the way along the University Hospital I meet Birgit Luber, to hand her over the exam protocol and review of Sebastians master project. We chat a bit, and I remember the box of white chocolate pralines in my suit-case. And she is suprised to receive an Eastern present from me. But it feels nice to make unexpected gifts.
  • Arriving home, I realized that Ljowas has a friend visiting him at school holidays, and they are in his room, with the sun blinds completely turned down, and all lights inside switched on. This pisses me off, and I sneak silently into the house and down to the basement to pull the fuse to Ljowas room. After the two sit for a few seconds incomplete darkness, Ljowas comes down to check the fuse box in the basement. This is a good chance for me to scare him off, explain again my dissatisfaction with turning on the ekectric lights at daytime. Ljova says he met a mouse in his room. What has this to do with leaving on the electric light throughout the day?
  • Rest of the evening is as usuall: watching some international TV news, laughing about the ridiculous stupid Western comments and helpless attitudes of NATO officials with Marisha, having some simple sandwiches for dinner and going out for a walk with Ivo.
I hope that tonight the sky will be clear enough to make a photo of the full moon, as I wanted to send to Fatemeh. It was a good day, with some ups and some downs, but the best moments where when I wrote the e-mail to Fatemeh. Maybe she has answered already.
Summary: It took me more than 3 hours to write this 4 page summary of today, what I did over an period of about 14 hours. It is nothing I will do on a regular base: 3 hours to write down what happend within 14 hours: thats not very efficient.

9.4.14

Norouz - The ultimate formular

Two weeks ago Norouz was celebrated, the traditional feast of the New Year that goes back to the Iranian Achaemenidian empire. It is still the one of the most important traditional events of the seasonal cycle for people in Iran, Afghanistan, Tadshikistan and Kurdistan. But in fact, it is highly regarded by everybody who likes mathematics, celestrial mechanics or astronomy. 
In contrast to the christian new year which is very ill-defined (just think about the arbitrary adjustment by inserted lap-years or pope Gregors order to cancel 11 days of the year 1582. The reason for this highly imprecise calculations of the beginning of each New Year is the complete asynchronity between the earth' revolution around the sun (determining the seasons and in particular the points of spring and fall equinox) and the earth' rotation around its own axis. And since christian New Year always starts at 0:00 am on January 1st, all these artifical and highly unscientific adjustments have to be made.

It has a certain irony that although the United Nations a few years ago adopted the tradition of Iranian New Year at the spring equinox and included it into their official list of word-wide days to celebrate, they fall back into the very primitive and un-scientific approach by setting a fixed the date for the "International Day of Norouz", which is statically commemorated each your on March 21st, irrespectively if the the people in Iran, Afghanistan and so on celebrate "real" Norouz at 20th or 21st of March.

Quite different is the precise approach which the Achaemenidian astronomers used to define Norouz: The Achaemenidian emperors (the Shahs) were simply obsessed by understanding precisely the regular movement of stars and planets, including our earth. And they employed excellent scientists like Ibn-Sina and Omar Khayyam to make precise observations, find the general laws of the celestrial mechanics and allow precise predictions of astronomical events.
And for them, the most important was the moment of spring equinox, the beginning of their new year. This is roughly equivalent to the beginning of spring in the western world, which there always happen on March 21.
Iranian Norouz took place this year on March 20th, at precisely 17:57:07 GMT. And here starts a bit of confusion, of course, if you consider the common definition of Norouz as the spring equinox, or moment of the year when day and night have exactly the same duration. So how can day and night have the same duration at 17:57:07 GMT ???  In fact, it will happen very very rarely that any day-and-night pair at around the 20th or 21st March will be of equal length. The best one could do with measurement of day and night duration would be to say that a particular pair of night-and-day or day-and-night have the smallest difference in their length. But then, how can a precise time as this years 17:57:07 GMT can be related to a measurement of day or night length ??

So in fact, by measuring the length of day and night would not have satisfied nor the Achaemenidian rulers neither their skilled astronomers. It would not have been much different than the error prone definition of christian New Year, also linked to the midnight point of the earth rotation around its own axis. The Achaemenidians wanted to know precisely when the earth passes a definite position on its way around the sun, and they understoud that the clock time on earth is absolutely irrelevant for this and should be introduced only at a very late stage of calculation.

What is really relevant, though, is the orientation of the axis of earth rotation relativ to the direction of the link between earth and sun. And this direction is of course adequately described by a vector. 

So we have to vectors here, the earth own angular momentum A and the radius between sun and earth. direction R. The absolute length of both A and R is irrelevant for the later calculation, the only thing that matters is their direction.

A, the earth angular momentum is in first instance (for a period of several thousand years) fixed in space and as we all know orientated to the Polar star. For convenience, we can shift A from the earth to the center of the sun and still have it pointing to the Polar star.

Assuming that coordinate origin for all our calculations is at the center of the sun, than this point O has the  coordinates                               O:   [Xo=0; Yo=0; Zo=0].
The position of the polar star is   P: [Xp; Yp; Zp] 
and hence the unit vector of A will be defined as

                                         A  : [Xa; Ya; Za) = (Xp;Yp; Zp) / Sqrt(Xp*Xp+Yp*Yp+Zp*Zp)

                                               abs(A) = 1    angel(A)=23.4 degrees  (obliquity of the ecliptic)

The second vector that defines the trajectory point of Norouz is the earth radius around the sun. 
                                         R :  [Xr(t); Yr(t); Zr=0]
Here the bracketted t denotes that X and Y of the radius tip move during one year on a quasi-eliptical path around the sun (not taking into account disturbances by other planets).
Therefore, X and Y of the radius vector are interrelated by the formular
                                                                      
http://upload.wikimedia.org/math/a/d/d/add7be4b380e1f42c44809a08d18f1e3.png

                                                                                          (I)


with a and b being the smaller and the larger radius of the ellipse. Conveniently, we also set this vectors at unit length.

And now the precise definition of Norouz is very simple. It is the point on the earth trajectory at which the vector A is orthogonal with vector R, i.e. when the rotational axis of the earth stands orthogonal on the radius between sun and earth. At precisely this position the rays from the sun illuminate the southern and the northern hemisphere at exactly the same degree, and the Northern and the Southern pole are at an equal distance from the sun, and the radius between sun and earth stands also orthogonalon the equator.

Although the scheme is still using the Ptolaemaus model (with the earth resting in the center and the sun revolving around it), the conditions and the mutual positions of earth and sun are equivalent to the Galilaean model. In the scheme above, the earth is conviniently not only place at a resting point in the eliptical path of the sun, but the earth own rotational axis is set exactly verticaly.

The algebraic formular for two orthogonal vectors can be expressed as the scalar (or point) product and should be zero:
                                              A o R = 0

And the scalar products A o R is the sum of the single components products
                                   A o R = (Xp*Xr(t) + Yp*Yr(t) + Zp*Zr)  /  Sqrt(Xp*Xp+Yp*Yp+Zp*Zp) 

since Zr=0, we can reduce further to
  
                                  A o R = (Xp*Xr(t) + Yp*Yr(t)  /  Sqrt(Xp*Xp+Yp*Yp+Zp*Zp)  

and after on the condition that the scalar product should be zero
                                  A o R = (Xp*Xr(t) + Yp*Yr(t)  /  Sqrt(Xp*Xp+Yp*Yp+Zp*Zp)  =  0
                   -->          (Xp*Xr(t) + Yp*Yr(t))  = 0
                   -->          Xp*Xr(t)  =  - Yp*Yr(t)                                                              (II)

With equations (I) and (II) we have now a system of one linear and one quadratic equation for Xr(t) and Yr(t)
                                 
              Xp*Xr(t) + Yp*Yr(t)  = 0
                                        
                                          http://upload.wikimedia.org/math/a/d/d/add7be4b380e1f42c44809a08d18f1e3.png
                                                                  
With x and y in the lower equation should in fact be Xr(t) and Yr(t) as in the formular above, and Xp, Yp, a and b are fixed tabulated values.  
Using a formular solver program like from Wofram Research' Mathematica this system of equations will straightforward give you a value for t (or in fact two values, one for spring and another one for autumn equinox). Be aware that t is note the a time, but the trajectory parameter. It is, however unequivocally related to the celestian time on earth and hence can be directly converted to a day and time.

 But this is the point where the whole fuzz of the precise beginning of Norouz, or Sal Tahvil gets in. But in fact, the confusion is not caused by any of the above equations to calculate Noruoz, but the fuzz is due to the
astronomical unprecise definition of the normal, global calender and its weak association with the celestrial calender. So the Sal Tahvil can vary between afternoon of the 20th of march till midday of 21st of march (according to the global calender and global time), but in relation to the fix stars and to the sun, Nowrouz is always precisely at the same position.

4.4.14

Pantheism could be a cool alternative

Today a new colleague asked what she should fill in the field of "employers religion" on her tax from. I warned her that if she admits to be catholic or protestant, 8% church tax will automatically be deduced from her salary. This, apparently brought her into a mind conflict between her christian faith, as she was raised in a traditional Italian families with catholic values, and her wish to spend this extra tax other things. As an alternative I recommended her to write "Pantheism" on the form, so nobody could deduce tax for this.
I remembered this very sophisticated faith, which fascinated me after reading Baruch Spinoza for an essay I once did at University. Funny enough, I first learned about this great philosopher through Karl Marx, whos works were obligatory part of the University curriculum. Spinoza, of jewish descendants and therefor trained to discover Gods will and identity came to the conclusion, that the whole world is an emanation of God, but that humans are not his preferential creature, without any dedicated mission. With such revolutionary concepts, Spinoza soon found himself in the center of mis-credit not only by his own Jewish community, but strangly by a joint oppresion of the Jewish leaders and the political authorities of his country (than the Spanish Netherlands). The Jewish religious authorities issue against Spinoza an excommunication (Cherem, expelation from the Jewish community). About 30 years after Spinozas early death, the english freethinker and rationalist John Toland became influenced by both Spinozas "Ethics"  and the ideas of Guirdano Bruno, the astronomer and researcher who a centrury before insisted that the entire universe of the stars and planets move without any devine will or power. For these thesis the Vatican sentenced him to death on the autodafe.
Toland used the terms 'pantheist' and 'Spinozist' interchangeably and in 1720 wrote a book "Pantheisticon: or The Form of Celebrating the Socratic-Society in Latin, envisioning a pantheist society which believed, "all things in the world are one, and one is all in all things ... what is all in all things is God, eternal and immense, neither born nor ever to perish. 

After pope Pius declared Patheism as an erroneous beliefe in 1862, in the 20th century it was often declared to be the underlying theology of Neopaganism. The dogmatic and conservative pope Bendict renewed the official catholic condemnation of Pantheism for its denial of human superiority over nature and "seeing the source of man's salvation in nature" (Papal encyclia 2009 and New Years address 2010).
Since Pantheism considers the entire physical world, both the living and the not-living as filled with devine spirit, it repeatedly attracted philosophers and scientist. Among others, Walt Whitmann, Ralph W. Emmerson, Coleridge, J.W.Goethe, Abraham Lincoln, H.D.Thoreau and Albert Einstein became pantheists. Einstein, in a letter to friend wrote in 1954 "We followers of Spinoza see our God in the wonderful order and lawfulness of all that exists and in its soul ["Beseeltheit"] as it reveals itself in man and animal..."
Scientist are very often undecided about the question of faith or pure materialism/rationalism. Sure, the vast majority of scientists have an issue with any organized religion, and usually consider their rules and rites as primitive, useless and rediculous. But on the same time they feel a deep devotion to the imense beauty of nature, and fascination by the perfection of the natural laws. Although they never see any requirements for a divine creator in the logic and relationships of the universe, they always miss a satisfactory explanation of who and why the world exists and what is their purpose. 
Pantheism, therefor should have much more followers today, not only as an easy way to avoid church tax.

  

3.4.14

Dimensions

Sitting in a meeting room, by invitation of our administration to an event they call " science meets management". The three dimensions of the hall are filled with empty speeches, hot air and with one-dimensional thought. What a waste of space, I have to think, when here three dimensions could easily collapse to a single one. Suddenly I begin to estimate the potential of new technologies: A flat tablet computer in front of me allows to escape from the hollow mesh of opperational support, business modules, administrational interfaces into the many dimensions of real people talking about real life in the real world of the global blogosphere.


31.3.14

Legal Immigrants

The smell of harvested wheat can be tantalizing. When the golden straw is cut and the bulging grains are harvested they produce a parfume like odor, not less breath-taking than that of roses or lime-trees. I am always happy if I see in spring that the farmers have choosen to grow wheat, instead of the odor-less, but more profitable corn.

And than at a late summer day, usually at the end of August or early September, all the golden wheat is harvested, leaving behind only the short stubbles. This always makes me melancholic, since it signals that the summer time will soon end.

This,  in fact is not wheat, but barley. But it also has this tentalizing smell in later summer

But thanks god, a close relative of wheat, namely rye, is already seeded out in late autumn, with its fresh green shots staying throughout the winter time and bearing the promise of a next years golden grains.
This years the farming cooperative, obviously driven by a similar challenge as myself of testing to grow plants from more southern, oriental regions of the world, chose a range of wheat variants from countries as far as Tunesia, Nepal or Korea.
Iranian Variant, Maybe we do some Bagels from it
Greek variant, Good to bake Pita Bread


Variant from Chile, Do they bake pan-cake there ?

Wheat from Tunesia: Arab spring role

Wheat from the roof of the world:  Nepal

Wheat from Korea: Must be an old sort, since the label still mentions DVR ("democratic peopels republic", now simply North Korea)


I am sure the farmers are well aware that wheat is pollinated by wind, and the close vicinity of these6 variants from different European, Asian, North-African, Middle-Eastern and South-American variants will produce an interesting hybrid of intercultural mixtures next year. But first I hope that all these immigrants will flourish here at the tempered European climate and give us later in summer interesting novel variants of their tantalizing smell.

Three weeks later, the wheat strains from different parts of the world all started to grow. But they exhibit different growth rate. Currently, Greece and North-Korea are leading the ranks, Tunesia, Nepal and Chile are in the middle, and Iran is slightly lagging behind. Don't be misled by the green on the photo below:  Most of it is weed, the wheat sprouts in between are still pretty small.


Wheat three weeks after sowing. From left to right wheat sorts from North-Korea (K); Nepal (N); Tunesia (T); Chile (C); Greece (G) and Iran (I). The wheat shots are visible at closer inpsection, but most of the green is in fact weed.

21.3.14

Quantum Mechanics according to Fatemeh

It is well known in quantum mechanics that from a pure vacuum state discrete points of pairwise existing particles-antiparticles can arise by shear fluctuations of the zero energy. But as measured on the macroscopic time scale, these particle pairs have a relatively short existence: only a few Nanoseconds. But who knows maybe in their own time scale these nanoseconds have the duration of an entire life. Whereas these particle-antiparticle pairs arise "out of the blue", seemingly from nowhere, when they disappear by anihilation they emit a defined amount of energy in the form of electromagnetic radiation.
These vacuum fluctuations of particles and energy are believed to be the reason for dark matter and dark energy, two essential components to hold together the inflating universe.
Because of their opposite charge and the very short distance between them, the particle-antiparticle pairs exert an intense interaction (best studied in the case of electron-positron pairs).

Mrs. Fatemeh now gave rise to the hypothesis that a pair of a man and woman can also arise from virtually nowhere, out of the blue, to develop a strong intellectual and emotional interaction, a force that suggests a very small distance between the two. In her blog Mrs Fatemeh cited a short poem by Emily Dickinson as the inspiration for her new model:

     I'm nobody! 
     Who are you?
     Are you nobody, too? 
     Then there's a pair of us — don't tell!
     They'd banish us, you know. 
     How dreary to be somebody! 
     How public, like a frog 
     To tell your name the livelong day To an admiring bog! 


What is unique in Mrs. Fatemehs model and distinguishes it from the well accepted vaccum fluctuations of quantum particles is that the small distance between the two partners (responsible for the strong exchange force between the two) is not related to the ordinary spatial distance (as measured in terms of nanometers or thousands of kilometers). The two interacting partners can be quite far apart, thousands of kilometers in our 3 dimensional world, in different countries or continents. But in a yet to be proven 4th dimension, lets call it the dream scale because it is usually hidden from us, the two can be extremely close together, like entangled particles. 
And she proposes, that when they disappear like the electron-positron pair in vaccum fluctuations disappeares, it is only a collapse of the 3 ordinary dimensions, but the 4th dimension remains intact and the two will always stay bound together.       

19.3.14

Books of the week: Crimea change sides

In 2010 I had the pleasure to visit Crimea, on the occasion of a genetics conference in Alushta. What a magical landscape, I thought, and I met Russians there and some Ukrainians and many Tartars. The Tartars invited me to a after-wedding brunch in their own restaurant at the beach, when the shops and cafes run by Russians or Ukrainians were clossed at this out-of-season time of late October. Later I visited Bakhchisaray, the old palace of the Crimean Khans. Aside of the muslim study rooms and the paradise and rose gardens and the turkish bath, Alexander Pushkin was commemorated there where a dripping spring inspired him for his poem "The Fountain of Bakchisaray".
Who could have imagine, that now, just three years later, another kind of books might become useful again to understand what is going on there at this beautiful peninsula, that was once the melting pot of Russian, Greek, Jewish, Tartar and other people. 


4.3.14

The Systems Biology Hoax

I know I'm supposed to give a talk at this meeting, called something with Systems Biology, and I have only 16 hours left to sort out my slides. Sixteen hours is not so much time, if you are still jetlagged from the long flight to Japan, and you know the tiredness will come in 5 hours from now.
So what shall I do ?  I already gave a talk yesterday at another institute near Tokyo, but this was o.k., this was not about the Hoax "Systems Biology", but this was about something real biological, some molecular processes of stem-cell stability and long-term cancer risk. But tomorrow, everybody will talk about Systems Biology, and most of them have no clue what a System means, what modules are, what interactions or feedback means, and how this can only be understand with highly sophisticated mathematics: differential equations, topology, non-linear algebra and the like. But tomorrow a bunch of mediocre biologists are going to meet, to mask their limitted biology knowledge behind the Title:  Systems Biology. 
I just can not take them seriously.
The view out of my hotel room at the 14th floor is amazing:  An ocean of lights and illuminated bill-boards, despite the pledge by the Japanese gouvernment to reduce all unneccessary consumption of electricity after the 2011 Fukushima disaster ripped the country of a larger part of its nuclear energy supply. In daily life, you feel little committment to switch off electricity: At least every toilet seat in the country has an electric heater that is always on. Funny to see, that even the toilets could not be used if there is a black-out. In the Kimi-Ryokan in Tokyo, the service personal used to install huge hot-air blowers each time they change the blankets in the rooms.They explained me that the blankets are still wet, when they get them from the laundry, and by blowing hot air through the newly covered beds, they make sure the guest can sleep under a dry cover.
I forgot what this has to do with Systems Biology ? Only as much as at tomorrows conference some people from Fukushima will talk about the long term health consequences of the 2011 accident. Hot air, blown everywhere around.

21.2.14

The Golden Dust of the Sahara

Half a year ago I sold my old Toyota Corolla, which I drove for about 8 years, including long holiday trips to the Cote de Azur, Venize and the Dalmatian coast. But I also experienced a couple of accidents, one at night on the Autobahn when I fall asleep at 95 miles/hour and only woke up by the shouting of my family and the care crashing into the side rail. 
The most tender memories that I associated with the Toyota were multiple rides around Munich with Ghazal, a student who did her master project with me. Anyhow, last year I decided that a car should not be the subject of romantic emotions, and its declining technical state simply caused me more and more headache than could be compensated by any romantic memories. So when I finally decided to get rid of it, I remembered some guys from Africa here in Munich, who already approached me on a public car-park to express their interest in the Corolla. They told me it is a much sought after model, to be transferred to Africa where people like to use it as a taxi cab. So indeed, the guy was ready to pay me 500 € for it, even though I told him frankly that the air-conditioning was not working any more, but that the stand-alone gas-driven heating was still perfect. 
As a last farewell, before I handed the car over to a specialized over-sea export company for used cars, I wrote with a permanent marker behind the sun screen some "Greetings to Africa, Bone Voyage". Of course I never expected to receive any message back, and till yesterday I had almost forgotten about my old Toyota.
  But obviously, some message indeed came back. First I was a bit annoyed, when in the morning I found my new car completely covered with a layer of yellow dust. I suspected a nearby construction site to have polluted the road side and the cars parking along with their debris. And I also recognized a strange smell in the air, like laim or clay dust, and even a rough feeling in my troat.
Then I was worried why almost all cars that I saw in Munich and even vehicles from colleagues which  came from outside the city to work, they all showed the same pattern of dirt on the outer surfaces. But is was also obvious that the stuff was not spread up from dirty streets, but it had fallen down from the air, since it covered almost exclusively the roofs, windows and the engine covers.
 
The solution to this mystery was found by scientists working at the atmospheric observatory on the Zugspitze mountains in the nearby Alp mountains. They detected a jet stream from the far south, virtually from the African Sahara desert, loaded with masses of desert dust that blow North up to middle Europe and for some reason deposited most of the yellow dust over Bavaria.

Now I am wondering, that if mineral dust can be easily transported by the jet stream over thousands of kilometers, what else might be carried over here ?  Gold dust, diamonds, oriental spices, seeds of funny plants, bacteria or viruses for not so funny diseases ? 
But maybe it is simply the dust that the new owner of my Toyota somewhere in Nigeria brushed out of the cars chairs.