oxford by night

As I am now learning to use my new digital camera, and as I spend a lot of time walking around with my son during weekends, I hereby announce that there will be more photos on this blog from now on. Emerging themes are "Oxford by night" (about the first thing that struck me about digital photography is that it is so much easier to make decent photos by night, and I'm planning to make use of that), urban wildlife, abandoned shopping trolleys and bicycles, and the writing on the wall.

Watch this space, and be very afraid. As a warning, here is one of my Oxford by night photos:



Locals will recognise this as The Plain, coming off Magdalen Bridge.

the art of biochemistry

Oxford's biochemistry department has a brand new building, and apparently there is a lot of science-related art to be admired inside it, as Georgina Ferry writes in Nature this week. Just over 1 % of the budget was spent on art.

I believe that in Germany, there is actually a legal requirement for public building projects of this scale to spend one percent of the budget on art, known as "Kunst am Bau". At the University of Regensburg, which was built from scratch in the late 1960s, there are so many works of art that there is a whole book about them:
Rund um die Kugel. The sphere of the book title is the most prominent of them all, a massive, maybe 5 m diameter metal ball that practically embodies the centre of gravity of the whole campus. My PhD supervisor was on the committee that commissioned these works, so he has a few stories to tell about the creative and selective processes.

Anyhow, I will have to have a look inside the new biochemistry here. In theory, there is a panorama to be viewed online, but it doesn't work on the computer I'm using right now. I definitely like the outside of the building, with the multicoloured panels sticking out of the facade. Nobody told the departmental website guys that they have a new building -- the website still shows an aerial view of the old ones they knocked down (next to the tower which they left standing for now).

sampling french fiction

One of the attractions of Oxford is, of course, that we have our very own island of French culture, the Maison Francaise d'Oxford (sorry, don't know how to do this accent in html), with a library and a busy events schedule. One of the freebies one can pick up from there is a collection of excerpts of recent French novels, in French and English, with details of the authors. Cultures France publishes this twice a year in the hope of attracting translation deals for these books.

Issue 3 of this publication (nominally out Sept. 08) has just shown up at the MFO, and if that's too far away, you can download the text samples here.

They also publish other magazines, including Cultures Sud which also looks interesting and covers the literature of Africa, the caribbean, and the Indian ocean area.

the wild rovers

I only realised yesterday that the rovers Spirit and Opportunity have been on Mars for over five years now and they are both still working and sending data! Considering the murderous radiation exposure and temperature swings, this achievement is absolutely mindboggling. I have never had a mobile phone that lasted so long in the relatively clement conditions on planet Earth. (While terrestrial goods are designed to break down after the end of the 6-month guarantee, the Mars rovers were anticipated to survive for just 90 days!)

Here's a NASA press release celebrating the occasion, and a recent feature from the Observer.

protein architecture

There is a very beautiful and cleverly designed artificial protein shown in the recent online release of Angewandte:



Essentially, the authors combined a peptide with helical tendency and one with beta sheet tendency in a closed loop and found that it forms an alpha/beta structure showing up as roundish particles in the electron microscope. Intriguingly, the open-chain version of this peptide doesn't work, it has to be cyclical.

In natural proteins, this resembles alpha-beta barrel proteins, of which Triosephosphate Isomerase is an example. Note, however, how the sheets and helixes in the natural protein are all twisted, while in the artificial one they are shown as straight and parallel features. If the protein really has this remarkably straight structure, it is most closely related to the architecture of Castel del Monte:



Isn't it amazing how these 13th century architects were ahead of their time ?

I have to point out, however, that the protein structure shown above is based only on the CD spectrum (showing alpha and beta structure) and the EM (showing roundish particles of the correct size for this structure). So far, there seems to be no crystallography or NMR evidence, but I'm hoping the authors will be able to fix that problem soon.

Reference: Y. Lim et al., Ang. Chem. Int. Ed. 48, DOI 10.1002/anie.200804665

elective affinities and reactions

Review of

Seduce me
By Megan Clark
Kensington Books 2008

In his short novel “Wahlverwandtschaften” (Elective affinities), Goethe conducted an almost chemical experiment, exposing the established bond of Charlotte and Eduard to the affinities of new arrivals Otto and Ottilie. The four people rearrange to form two new couples, but it all remains quite platonic and then ends in tragedy.

In her 21st century update on the subject, US author and former exotic dancer Megan Clark explores the area where Goethe didn’t dare to venture. She investigates the chemical rearrangement reaction (her version could even be described as a redox reaction, as a lot of fiery oxidation potential is transferred from one participant to another) in full carnal detail. As in chemistry, stability and reactivity are mutually exclusive but can be traded. One of her characters (but not the woman in the initially stable couple) is called Charlotte, too, but that was the only nod to the old master that I spotted.

The book makes good on the promise on the cover (“an erotic novel”), but it becomes clear that the eros serves to illustrate the issues of liberty and commitment and is neither the main issue nor the driving force. As in Goethe’s novel, the structure and the momentum of the story is provided by the chemical rearrangement between the four characters.

Clark records this experiment with verve and a fast pace. What lets her down is the lack of words in the English language to describe erotic experiences, due to the long established taboos surrounding this area. Where Spanish has hundreds of words, English writers can use about 5. I think they should be more audacious in making up new ones. Go on, don’t be shy! Also, there should be awards for erotic novels in English, like the “sonrisa vertical” award in Spain. So far, there is only a negative award for bad writing on this matter, which I believe is in itself very revealing.

return to Titan

Apparently, there is going to be only one major mission to the outer solar system in the next 30 years or so, and NASA are deciding this month whether to visit Jupiter's moon Europa, or Saturn's Titan.

Of course we all want both, and as soon as possible, but looking at the prospects laid out in a special report in this week's Nature (p366), the choice is clear. Europa would get an orbiter, possibly combined with an ESA-sponsored Ganymede orbiter, which is exciting for the physical investigation of the subsurface ocean, but if there is life in that ocean, we won't see it from the orbiter. Plus, can you get the general public excited about orbiters? Earth has hundreds of them! While the Titan proposals include an orbiter along with ESA's contributions, a splasher (i.e. a lander targeted at the hydrocarbon lakes) and a "hot" air balloon that could sail around Titan's atmosphere for six months or longer. (Considering the temperatures on Titan, the air in the balloon would still be way below freezing.)

Now these two elements would be completely new and at least as cool as the Mars Rovers, so, if we have to choose, it's got to be Titan. Mind you, I'll be a pensioner by the time that balloon sails around Titan in 2030.

But can't we have the Europa mission a couple of years after that ? I know it costs three billion dollars, but hey, that's only a week or so operation in Iraq (I'm guessing, so don't start nitpicking over the number), so if the US managed to avoid foreign policy disasters for a while, the money saved could pay for the exploration of the entire outer solar system in our lifetimes. Alternatively, it's 10 bucks a head for the US population(similar calculation holds for the European contribution and the EU population), that's surely affordable if we as a civilisation decide we want to afford it ? It's surely a lot less than people spend on entertainment involving space-travelling civilisations ...

Siepmann family

updated 7.8.2010 - see PS My daughter and I recently saved a pile of over 100 old books from ending up in landfill, and in one of them, a 1916 edition of George Meredith, we found the name Doris M. Siepmann stamped and signed, with the additional information "from Dad". As I also have distant ancestors by the name of Siepmann, I pricked up my ears and consulted the 1901 UK census re. who these people were and where they came from. Sure enough, the whole family is there, and "Dad" turns out to be Otto Siepmann (1861-1947), a pioneer of foreign language teaching in the UK (I'm sure it's not his fault that this field is still in less than perfect condition!). He taught at a private school near Bristol, sat on various boards, and wrote and edited numerous language teaching books including a whole series that bears his name (search his name at amazon.co.uk, you'll be surprised). He has a quite detailed entry in the Oxford Dictionary of National Biography. This entry tells us that Otto Siepmann was born at Waldbröl, near Cologne, and that he "was the eldest of the nine surviving children of August Siepmann (1835–1908), insurance broker, and his wife, Wilhelmine Henriette Hasenbach (1836–1891). The Lutheran Siepmann family came from a long line of wealthy landowning Rhineland farmers." While the name Siepmann is quite widespread today, its geographic distribution clearly points to a single origin in the Ruhr area, around Dortmund. That is precisely the area where my ancestor of that name, Anna Siepmann, resided in the 18th century. Her son, Georg Wilhelm Düselmann, was born there in 1757. I am hoping that by following back the "long line" of Siepmann ancestors of Otto, I may find out something of interest to Anna. (They must be related, they're both palindromic!) So if anybody out there knows anything about any Siepmann family in the 19th or 18th century, I'd be interested to hear from them. And isn't it amazing what an inscription in a random old book from a rubbish skip can teach us ? PS (7.8.2010): Reading an article about the elusive founders of the Aldi empire, Karl and Theo Albrecht (the latter died a week or two ago), I found out that their mother was called Anna Siepmann as well, before she married Karl Albrecht senior, and she's from the right kind of area too, just some 170 years younger than my eponymous ancestor. However, as the Albrechts are famous for keeping their lives extremely private, this isn't going to help much, unless one of their descendants is into family history and finds this ...

higher ground

watch the obama family clapping along to Shakira (and Stevie Wonder and Usher):

bacteria stick together

... just one German piece published in January, and it's about bacterial "swarming", i.e. the phenomenon that groups of individuals of the same bacterial species may stick together and form visible boundaries to other groups. Just like humans really.

You can read part of the text here, and subscribers can download the pdf from that site.

Spektrum der Wissenschaft No 1, p. 16
Bakterielle Vereinsmeierei

quite a tale, but I'm kind of detached from it

Daughter of the river
By Hong Ying
Bloomsbury 1998

Having read K-the art of love recently, I became very curious about its author and decided to read her autobiography next. It didn’t exactly tell me how she came to write K, nor how she came to write at all, but it turned out interesting nonetheless.

Hong Ying was born at Chongquing in 1962, at the end of a major famine that hit China as a result of population growth and mismanagement of the agricultural production. Thus, her novelized recollection of her childhood, culminating in discoveries about herself that she makes on her 18th birthday, could have easily produced one of those misery memoirs that have been so epidemic in recent years.

What saves it from descending that road is the curiously detached voice of the author who never seems to pity herself or the other protagonists. She describes hunger, violence and the regular sight of dead bodies floating down the river with equal emotional detachment, making the reader wonder whether this is a natural defence that children develop when they grow up in horrific circumstances, or whether there is an Asperger gene or two at play. For a teenage girl, our heroine cares remarkably little about what other people think. She sometimes even muses about her own detachment and aloofness.

Driven by her quest to solve the mysteries of her past, this story is quite gripping, even though the signposting often gives the events away beforehand. Most of all, it makes readers born at around the same time in a different place (like me, for example), consider ourselves very lucky indeed. What we now need from her is a sequel telling us how she escaped from the life of misery that could have become her destiny, and how she became a writer recognized around the world.

a word turns 50

I was intrigued to find that 50 years ago, one could get a "letter to Nature" published just on the grounds of having invented a new word. Though I have to admit that the word suggested by Karlson and Lüscher in January 1959 was indeed very useful, and today we really wouldn't know what to do without it. The word was "pheromone." The key element of their new definition, setting it apart from the previous attempt, ectohormone, was that it referred to substances secreted by an individual to be sensed by another individual of the same species. 50 years after this definition, we know a lot about animal pheromones, but the human variant and its perception has remained elusive.

The 1959 paper, just a page long, is online here.

There is also an essay (2 pages!) commemorationg the anniversary in this week's issue.

PS: To German biochemists, Peter Karlson is known as the author of a highly successful biochemistry textbook, possibly the first one to be written in German.

reasons to be symmetrical

Given that proteins are fundamentally asymmetric (their chain has a unique directionality, and most of the chain links have a handedness), it may seem surprising that a majority of natural proteins forms highly symmetrical complexes involving two or more protein subunits.

In a "dispatch" in the current issue of Current Biology, Kevin Plaxco and I have commented on recent work that manages to explain this natural tendency towards symmetry at least for dimers:

Protein Complexes: The Evolution of Symmetry
Current Biology, Volume 19, Issue 1, R25-R26, 13 January 2009
(summary is free, access to pdf requires subscription or institutional access)

expensive error correction

Protein biosynthesis is a field that keeps coming up with new surprises. In the current issue of Nature researchers report that incorporation of a wrong amino-acid (carried by a wrong tRNA) increases the probability that the synthesis will be aborted after the next step, and also the probability that further errors are made which may then lead to termination.

This strikes me as a very expensive quality control system that indiscriminately weeds out significant errors and insignificant ones. Many amino acids can in fact be exchanged without endangering the folding or the function of the protein. Somebody should do a calculation of how economical this kind of error correction is, where the whole polypeptide chain synthesized so far is discarded because of one error that may or may not have an effect.

Reference:
H. S. Zaher, R. Green, Nature 2008, 457, 161

silly questions

Review of
Can cows walk down stairs? By Paul Heiney (ed.) Sutton Paperback 2006
and Do cats have bellybuttons? By Paul Heiney (ed.) Paperback 2008

These two books came out of a remarkable institution that lived only for a few years. London-based ScienceLine (not related to the current project scienceline.org) offered scientific answers to any question that ordinary citizens chose to fire at it via phone or email. After a few years and 16,000 questions answered by 8 gurus (teachers? scientists?), government funding for the project ceased and it closed down in September 2003.

These two books are its legacy – two colourful bouquets of vaguely science-related questions plucked from the ScienceLine archives and arranged by non-science author Paul Heiney.

I came across them because the youngest member of my family picked the first of these books and enjoyed it. With the style of the questions very much along the lines of children’s questions (we are told nothing about the age or demographic profile of the people who asked them! They may be mostly children, for all I know.), the short(ish) answers and the funny cartoons, it’s no wonder the books appeal to children, and probably also to grown-ups whose scientific education got stuck at that level.

For the scientist, they are a mixed blessing. Reading most of the questions but only a selection of the answers, I found equal measures of interesting and trivial stuff on both sides. Some of the answers contained silly errors that should have been eliminated at proof reading, e.g. mix-ups of the effect of convex mirrors (in book 2, the answer suggests wrongly that it makes things appear closer). Some answers didn’t match the question (one question was about the limits of the galaxy, and the answer was about the limits of the universe), and some left me unsatisfied, including the answer to the title question regarding cows and stairs. Now I know that they can walk upstairs but not downstairs and that it has something to do with their knees, but I still don’t understand why they can’t walk down. I’m sure cows in the Swiss Alps can walk down the mountainside!

The questions are a reminder of how difficult it is to ask a good scientific question. If these are the 500 best ones, I feel for the people who had to answer the 15,500 questions that were not selected.

Still, the kind of dialogue established by ScienceLine is a good idea in principle and it’s a shame it was discontinued. If I were to establish something like this, I would probably avoid promising to answer every question. If, say, only the 5 best questions get answered every day, and one of them is syndicated out to be printed in a few newspapers for a fee, maybe ScienceLine could even be commercially viable without that government grant that proved so short-lived. At least the number of questions sent in and the popularity of the books suggests that there is a demand for this kind of dialogue.


PS: A nitpicker’s guide to some of the other errors:
Asked whether one is more likely to win the lottery twice in a row or twice in a lifetime, the gurus say “it would be easier if” and go on to answer a completely different question. In fact the question is very straightforward, as the outcomes representing two wins in a row are a subset of those for two in a lifetime. Thus, anybody playing the same lottery more than twice in their lifetime is more likely to achieve the latter result than the former.
Asked how many prime numbers exist, the gurus give the right answer (infinitely many) and proceed with a wrong explanation, saying it must be infinite because the whole numbers are infinite as well. In fact, there is a very simple proof that would have enlightened the readership:
Imagine the opposite were true, and there were only a certain number of primes. Write them all down, multiply all, and add 1. Call the result P. Try dividing P by all known primes. It is not divisible by 2, as there will be a residue of 1. Same situation for 3, 5, 7, and all primes on our original list. Hence P is a prime that was not on our original list, proving our initial assumption wrong.

go forth and be creative

In case you didn't realise, 2009 is the European Year of Creativity and Innovation. So go forth and be creative, this is an order!

Well ok, even though I don't believe that creativity can be produced by bureaucratic devices (dear old Tony Blair would have set targets and benchmarks for this, as in: we are going to increase creativity by 35 % this year and cut boredom by 80% by the year 2020!), it may be worth keeping an eye on create 2009 in case they come up with any interesting events.

The official launch of the year of creativity is happening at Brussels on the 20th of this month.

So let's all have a very creative year ...

deutschsprachige Informationen

a new beginning

After the 50th anniversary of the Cuban revolution, and the much-anticipated change at the White House, will it be too much to hope for an end to a US policy that has created most of the problems that it pretends to solve ?

Nature magazine, which normally supports scientific revolutions, not political ones, praises Cuban biotech and calls for an end to the blockade of scientific collaboration with Cuban scientists:

Cuba's biotech boom
The United States would do well to end restrictions on collaborations with the island nation's scientists.

That's in today's editorial, page 130.

why music doesn't add up

review of

How equal temperament ruined harmony (and why you should care)
By Ross W. Duffin

Norton paperback 2008

Music, I was led to believe, is a supremely elegant manifestation of pure mathematics. The intervals we know as fifths (think “Twinkle - twinkle”), fourths, and octaves correspond to simple fractional relations between the sound frequencies, of 2/3, 3/4, and 1/2, respectively. And as an illustration, one gets shown the corresponding keys on a piano keyboard.

What nobody told me in the first 44 years of my life is that the intervals you play on the piano do not correspond to the simple fractions cited above. I only started hitting on this problem when my daughter’s cello teacher dropped a hint that the piano was out of tune by default. The piano is actually tuned not in pure intervals but in a system called “equal temperament” for the simple reason that the fractions don’t add up. If you add up 12 fifths, all around the circle of fifths (C - G - D - A - E - B - F+ - C+ - Ab - Eb - Bb - F - C) you get 3/2 ^12 = 129.746. Theoretically, the first and the last C in this series should be seven octaves apart, so their frequency relation should be 2^7 = 128. And not 129.746. And there are even worse clashes with other intervals. So in fact it would be impossible to tune a piano according to the pure intervals defined by simple fractions. This is why we as a civilisation have settled for equal temperament, which means the octave is split into 12 equal semitones.

Equal temperament (ET) is so widespread today that knowledge of the alternatives has gone missing, and even many musicians are unaware of the problems that this compromise solution causes. Duffin argues that some of the “unequal” solutions favoured in renaissance music and through to the end of the 19th century (he dates the total victory of ET to 1917) would still be useful today and that the question of temperament should be considered afresh for each piece of music, taking into consideration the likely intentions of the composer, the context of its creation, and what’s best for its harmonies. This will all be self-evident for practitioners of early music who use historic instruments and temperaments already, but it may be new to many people dealing with the classical repertoire from Bach to Beethoven (who, the author argues, cannot have become used to hearing ET by the time he went deaf).

This argument is all very well and convincing, but it would fill only around 30 pages, so to bulk his pamphlet up to a marketable 196 pages, the author has included lots of repetition (as you tend to do in music!) and biographical profiles of everybody who has ever voiced an opinion on temperament, from Mozart’s father, via the flautist Quantz, through to the cellist Pablo Casals. And cartoons. And diagrams. But all this is redundant in principle, so if you’re just after the meat of the matter, you can probably read the relevant pages within an hour, at a bookshop cafe.

What remains is the impression that music is in fact a lot less mathematically elegant than it is often claimed to be, and that it is a rather messy compromise between pure mathematical beauty and practicability. The good news is that a messy system leaves you free to mess with it, giving performers more freedom. When I play out of tune, I can always claim I am experimenting with different temperaments.

seven of the best

www.litprom.de, the website of an organisation supporting literature from Africa, Asia, and Latin America, has picked the 7 best titles from these areas published in German translation in 2008.

In 7th position we find my mother's latest translation work:

Sefi Atta. Sag allen, es wird gut
Übersetzt von Sigrid Groß.
Peter Hammer Verlag

Oh, and the book at the top of the list also won last year's Booker
prize.

protein in the womb

Scientists at Birkbeck College, London, have obtained the first images of a new-born protein in the “womb” of an enclosure that helps it find the proper structure.

Most of our genes serve the production of different proteins, which first emerge as a long string of building blocks, the amino acids. This string has to arrange itself into a well-defined pattern of coils, twists, and turns, so the protein can proceed to fulfill its biological function in the cell. For this process, known as folding, many proteins need helper proteins known as molecular chaperones. An important group of these helpers comes in the shape of a molecular barrel, which accommodates the new-born protein and releases it when it has attained its properly folded structure.

As the newborn moves and wriggles around in this barrel, researchers have so far been unable to get a clear picture of it. The group of Helen Saibil at the department of crystallography, at London’s Birkbeck College, in collaboration with the group of Saskia van der Vies at the Free University, Amsterdam, has now succeeded in imaging such a “newborn protein in the womb” by using a particularly large protein baby. The researchers studied the case of a virus that infects bacteria (a bacteriophage) and uses the bacterial barrel to help fold its own shell protein. This protein is too large for the barrel, such that the virus brings its own lid along so its protein can be securely locked up in the folding chamber.

This hijacking by a virus is rather unfortunate and fatal for the bacterium concerned, but it is a lucky break for structural biologists, as the bulky virus protein can’t move around as much as other proteins do. In fact, its position inside the barrel was sufficiently well defined such that Saibil’s team succeeded in taking its picture using low temperature electron microscopy to image the proteins in their natural state, and computer image processing to distinguish between complexes captured at different stages of binding and assembly.

Comparing their images to the existing pictures of the empty barrel, the researchers could gain valuable insights into how a protein is bound and released during the assisted folding process. They could also observe that the enclosure, like a womb, has to stretch to accommodate this relatively large protein baby.

------------------

This is a draft press release I wrote, regarding a paper that appeared in the current issue of Nature (1.1.), vol. 457, p. 107