Friday, July 30, 2010

obscure search terms will find ... me!

My blog enjoys a reasonably good ranking in Google’s PageRank system, which decides which sources appear at the top of a list of search results. This means that from time to time, Google does actually send people my way. Naively, I might have thought that those googlonauts who touch down on my site would have started their voyage with search terms relating to the big issues that I write about, such as nanotechnology, genomics, autism, bioethics, etc. On second thoughts, however, one realises that such topics are also well-represented on sites that are still a few rungs higher up on the ranking ladder, including those of the BBC and major newspapers. The traffic that’s left for me is looking rather different and possibly more interesting.

When I realised that my visitors had typed in things like “philosophy of greed” or “think logarithmically” rather than biochemistry or nanotechnology, I started a month-long observation of the Google searches leading to my blog, of which I can now reveal the results. The only words I have excluded from the ranking are prose and passion – their presence in the title of my blog means that I get ranked highly in searches involving these words, even though people who look for prose pieces about cancer will not be very happy with the results my blog can offer. (I think the over-representation of “Prose of …” searches actually reveals a real flaw in Google’s algorithms; people setting up such things should realise that the title of a blog may be chosen in a roundabout way and may not literally specify the content of the site.)

So here comes the countdown:

In 6th place, Oxford – typically in combination with more unusual terms, including “Parson’s pleasure” which is the title of this blog entry. One customer’s search for “naked dons parson’s pleasure” led to the same entry, of course.

5th, an eternal favourite, and one that alerted me to the eccentric qualities of the search terms that lead people my way, is “greed philosophy” (or, more rarely, greed combined with other terms, such as “How is greed Neanderthal”). The relevant blog entry doesn’t really answer any deep philosophical questions about greed – it is in fact a short appreciation of a book by Naomi Klein.

4th, Sale el Sol – fair enough, that’s a video of a live appearance by Shakira which I embedded in my blog here. Oh, and there have been reports that this will also be the title of the album to be released later this year, so no wonder there are lots of searches.

3rd, another eccentric favourite, is “shark images” and other shark-related stuff. All I did was to write a blog entry about the Headington shark, an Oxford landmark somewhat off the beaten tourist track.

2nd, various members of the Strada family, including Katharina Strada (mistress of emperor Rudolph II), lumped together under Strada searches, and presented here.

And the unlikely winner is …

the Spanish painter Ana Medem, sister of film director and auteur Julio Medem. Ana died very young, and Julio used her paintings in the film “Caotica Ana,” which I reviewed here.

Obviously, having all these (relatively) popular search terms included in one blog entry will completely confuse the Google bots. So if you arrived at this entry hoping for insights regarding Ana Medem or one of the other five top topics, please follow the links provided.

For the future, what I really need to do to attract a larger audience via Google, is to cultivate more eccentric topics and to flag them up in my titles. Paradoxical but true. I should start a series about obscure composers right now.

Thursday, July 29, 2010

Henry Moore at Tate Britain

I enjoyed visiting the Henry Moore exhibition at the Tate Britain yesterday, just in the nick of time as it closes at the end of next week.



(one of his reclining figures in elm wood)
More photos from my visit to the Tate here.

I liked the early work especially, but also the reclining figures he did throughout his career. Should visit the Henry Moore Foundation at Perry Green, too.

PS As a former ribosome researcher, I tend to see the crude structures of the ribosome in Moore's abstracted "mother-and-child" pieces. I think one of them appeared on the cover of one of the ribosome books in the 90s. How amazingly prescient of Moore to sculpt the ribosome decades before scientists figured out its shape.

----------

In other arts news, I also visited the Howard Hodgkin exhibition at Modern Art Oxford, but didn't quite know what to make of it. The Guardian's Jonathan Jones managed to write an interesting article about it though: Howard Hodgkin - the last English romantic painter

Wednesday, July 28, 2010

How to circle the square

-- updated 13.1.2011 --

Some of the simplest geometric shapes are really difficult to recreate in organic molecules. Carbon loves the flat hexagon that we find in benzene and its numerous derivatives. It is also happy with the five-membered analogues (such as the cyclopentadienyl anion or the nitrogen-containing pyrrole), but when it comes down to building squares, things are getting complicated. Firstly, the angles are all wrong, as carbon with a double bond wants 120 degree angles between its binding partners, not 90. Secondly, theoretical organic chemistry predicts that a ring with 6 (or, more generally, 4n+2) free-floating electrons (on top of the ones involved in the direct bonds) will be stabilised by these electrons. A ring with 4 (or any other 4n) will be destabilised.

Both these considerations suggest that a ring of four carbons with two double bonds should not exist. Chemists have, however, with a whole arsenal of tricks, managed to make such a molecule, but it could only exist at temperatures near absolute zero and only trapped inside a cavity within larger molecules. No structural information about this elusive molecular prisoner could be obtained – until now.

The group of Mihail Barboiu at the University of Montpellier, France, has now developed a new kind of cage to trap and study the elusive carbon square in. They made a crystalline matrix out of hollow molecules (calixarenes), which enabled them to perform crystallographic structure determination on several compounds along the reaction path that leads to the desired product, thus also clarifying open questions regarding its mechanism of formation.

As for the final ring of four carbons, there are two structural options: a square with the four (rather unhappy, anti-aromatic) electrons smeared out around the ring – the structure one could write as a square with a circle inside, in analogy to the benzene structure; or a rectangle with two shorter (double-bonded) and two longer (single-bonded) sides. It is known that the equally anti-aromatic ring of 8 carbon atoms prefers the uneven solution, with localised double bonds. For the 4-ring, chemists had to await the study by Barbou’s group to learn that the answer is … Well, in fact, the crystal structure shows both versions, the rectangular and the square shape. Faced with two equally uncomfortable solutions to its structural problems, the molecule just can’t make up its mind.

Reference:
Y-M Legrand et al. Science 2010, 329, 299.

Fig. 4 from the paper shows the structures obtained:



PS (Oct.2010): I've also written a one-page piece about this in German, which is now out in Chemie in unserer Zeit

PPS (Jan. 2011): The results of this work have been disputed by researchers using computer simulations, but defended by the original authors. See the technical comments in Science online, and a detailed discussion here

Tuesday, July 27, 2010

oxford views

I added a few photos from around Oxford to my flickr photostream. Also helped the youngest photographer in our household to set up her own here which I think may have gone online the same day the Queen put some 600 photos on flickr. We've been more restrained and started with 6.

Monday, July 26, 2010

reflections on symmetry

My review of the book

Mirror-image asymmetry: An introduction to the origin and consequences of chirality
by James P Riehl


appears in today's issue (No 14) of Chemistry & Industry, pp28-29.

Here's a snippet:
I was intrigued to learn that the historic Dutch windmills, like so many other things, owe their unanimous chirality to the fact that they were designed for right-handers. Conversely, the plane of the Wright brothers is achiral, as it has two propellers that are mirror-images of each other.
All in all this is a laudable effort by a long-serving practitioner of science to popularise his field, and a book that can enlighten chemists and lay people alike.


The review should show up here soon.



A traditional Dutch windmill (1100 Roe) standing in a winter landscape on the outskirts of Amsterdam, the Netherlands.
Photo by Massimo Catarinella, from Wikimedia Commons.


PS solution to the windmill conundrum: operating the windmill involves climbing up the blades and unfolding the sails. All Dutch windmills are built such that you can do that with your right hand.

Friday, July 23, 2010

green reflections

I took a few photos at the weekly antiques market yesterday, coming soon to my flickr photostream. Here's some old mirrors:

Thursday, July 22, 2010

the feminine art

book review

The feminine art
Weam Namou
Hermiz Publishing 2004


The charming characters of this novel are all, like the author, Chaldean migrants (or at least would-be migrants) from Iraq, i.e. members of the Christian minority in the Middle East. According to the blurb, Namou is “the first […] Chaldean American novelist to portray the descendants of ancient Mesopotamia …,” so the book promises a new take on intercultural experiences.

That promise is kept very nicely in the first part (2/5) of the book, while the characters live their ordinary lives in suburban Michigan, and their very oriental values are shown in sharp contrast to the American way of life. For instance, the thorough preparation and consumption of food seems to pervade people’s thoughts so comprehensively that practically every metaphor used comes from cooking, and every relationship is defined in terms of who cooks what for whom. In a way, this is a celebration of “slow food” and as such preferable to the American culture of junk food, but one can’t help feeling that it also stops people from achieving anything else in their lives, as food and family networking seem to take up 100% of their time. Similarly, the quest for an arranged marriage, which drives the plot of the story, contrasts with the sexual freedom that the potential groom has enjoyed in the US so far.

Not knowing (or caring) much about religions, I got the impression that the value system on display here seems to resemble those of Islamic communities from the Middle East more closely than those of European Christians. I only mention this because it suggests, interestingly, that geography and history may have had a stronger influence in shaping it than the actual religion.

Intriguingly, the characters (and their real life models?) don’t seem to appreciate the value of their heritage languages (Arabic and Aramaic) for their cultural identity, as it is mentioned that they randomly speak English, Arabic, or Aramaic to each other throughout the day, and often it appears to be English with Arabic words thrown in, as it is in the novel. As a former agony aunt in all things bilingualism I believe that if one wants to maintain one’s cultural heritage, the first and most obvious thing to do is to speak the heritage language consistently (and unmixed) whenever it is possible without offending outsiders.

To me, the novel lost interest a little bit after the action moved to Amman, the capital of Jordan, where the groom is to meet his prospective bride from Baghdad, and a wedding is to take place, or maybe not. With the geographical side of the culture clash removed from the equation, only the clash between the mildly Americanised Chaldeans and those fresh from Iraq remains. We are left with a claustrophobic circle of people panicking over wedding arrangements, while the underlying emotional conflicts remain veiled (or maybe one needs the "feminine art" to figure out what’s really going on, but I’m afraid as a man I need to have it explained in plain English). Although the beginning of the novel played the contrast of Michigan vs. Baghdad really well, I got absolutely no sense of place from the parts set in Amman.

Also galling the experience is a complete lack of editing – there are homophones and other spelling errors throughout the book (e.g. people waive for taxis and message their legs!), which has clearly never passed the hands of a competent copy-editor. These moans aside, it has been a very interesting insight into a culture that doesn’t get all that much media attention.

Wednesday, July 21, 2010

bumblebee on thistle

Did I mention there are lots of bumblebees around here? I'm especially fond of those with the red backside, which are a bit rarer than those with yellow / white barcodes. It's also worth learning to find flowers that are attractive to both bumblebees and human viewers. (Not sure whether the thing below counts as a thistle, actually, the flower looks like one, but the leaves aren't prickly.)




I've uploaded this and a few other (even nicer) new photos to my flickr photostream.

For a selection of my favourite photos, visit fotocommunity where I am only allowed one upload per week, so have to be very selective.

Tuesday, July 20, 2010

how to be always on time

Considering that Oxford is the birth place of Alice in Wonderland, it is perhaps not that surprising to see crazy things all over the place, like trains being listed as "on time" 16 minutes after they should have departed:



I spotted this magically punctual train to Bicester Town last Sunday in passing, but I've seen similar cases lots of times before, and it's not because someone forgot to delete the train from the list after it has left the station. Typically, the train hasn't even arrived yet, is long overdue, and still listed as "on time." So when the local radio people do their usual line at the end of the traffic news: "a quick look at the departure board at Oxford Station - all trains are running on time," you know what to think of it. Mad laughter would be the appropriate response, I think.

Monday, July 19, 2010

lop-sided bird compass

More than 40 years ago, Wolfgang Wiltschko discovered that migrating birds use the Earth’s magnetic field for orientation. Further research has shown that the bird compass responds to the inclination of the magnetic field (i.e. its angle against the horizontal) rather than the north-south direction as such, and that it is likely based on chemical reactions involving molecules with unpaired electrons, i.e. radicals. This chemical compass is believed to reside in the eyes. In 2002, Wiltschko and coworkers have shown that the birds need the right eye but not the left eye for orientation – suggesting that the left hemisphere of the brain does the calculations on the magnetic measurements coming in from the right eye. Careful with the conclusion that the compass is located in the right eye only -- my guess would be that the left eye has the same compass but the right hemisphere of the brain just doesn’t know what to do with the signals.

Now Wiltschko’s group at the university of Frankfurt has reported that getting light into the right eye is necessary but not sufficient for the compass function (1). The right eye, the researchers find, actually has to be able to see properly. The experiment involves goggles that let through the same amount of light on both sides but blur the vision on one side. If the birds have a blurred view on the right eye, they lose the orientation, if it’s on the left, they orient just fine.

Wiltschko et al. discuss two possible explanations:

1) compass orientation may rely on computational connections between compass data and visual input. The case against this interpretation is that, in the 2002 experiment that first showed the dominance of the right eye in orientation, there was practically no visual input that could have served such a role. Still, the authors seem to prefer this version, as they go to great length to defend it.

2) the normal process of shutting down the input from the eye with the blurred vision may shut out the compass data as well. To me this is the more plausible interpretation (if only because it’s easier to understand).

Some fairly elementary questions remain, however, for instance, if one tests a reasonable number of birds, will there be a small population of “lefthanders” that has the compass processing on the other side ? Also, if a young bird lost the right eye in a fight, would the brain find a way to process compass data from the left eye? And lest we forget, the precise molecular details of the molecular compass also remain to be uncovered, see my pieces on the bird compass from last year, in Oxford Today (as a sidebar to the ESR feature) and, in German, in Chemie in unserer Zeit. A significant 2009 paper that I missed when I researched those articles comes from Stefan Weber's group at Freiburg and reports the observation that light can stimulate the formation of radical pairs in the most promising candidate molecules believed to host the chemical compass, namely cryptochromes (2). This adds to the growing body of evidence suggesting that the bird compass really is a radical pair mechanism residing in cryptochrome proteins.

Reference:
1. K. Stapput et al., Curr. Biol. 2010, doi:10.1016/j.cub.2010.05.070
2. T. Biskup et al, Angew. Chem. Int. Ed. 2009, 48, 404.

Sunday, July 18, 2010

a cap on addiction

I’ve often said that I am lacking the “gene for addiction,” as I can, for instance smoke or drink without risking excessive use. New research suggests that, at least in rats, the “I’ve had enough” factor is not a protein gene but a micro-RNA, i.e. a short piece of RNA that plays a role in gene regulation. As J. A. Hollander et al. report in last week’s issue of Nature (vol 466, page 197), expression of the micro-RNA miR-212 puts a cap on cocaine-seeking behaviour in rats that have free access to the drug.

So, rather than terrorising and criminalising people who get addicted to drugs, policy-makers should fund more research to find the equivalent mechanisms in humans that protect those like myself from addiction and work out a way to provide this protection to those people who don’t have it naturally. Shouldn’t be so terribly complicated, and the research would be a lot cheaper than current spendings on the “war on drugs” and all that. If somebody wants to check my genes for this research, I’ll be happy to provide a sample.

Thursday, July 15, 2010

twitter 102

After nearly a full year on twitter (and 2180 tweets unleashed on up to 450 followers), I may have lost some of that gushing enthusiasm expressed in my twitter 101, but I’m still sticking with it.

Since my last post on this topic, I noticed a few changes in the general atmosphere in twitter, which, I think, are all going into the direction of bringing the new medium, which was amazingly democratic in its early days, into line with the rest of society (which, as someone once remarked, is partitioned into celebrities who appear on TV, yuppies who produce TV, and morons who watch TV – you may replace “TV” with any other established medium, of course).

I definitely noticed that my offerings, as those of a non-celebrity, are now finding less attention than they got last year. There was a time when any link I posted would get at least seven clicks within a few minutes (this was when I had only some 100-150 followers, so it meant that at any given time 5% of them were paying attention, which I found quite intriguing, and which may mean that some of the attentive followers were robots). This response rate fell away steeply; soon I could count myself lucky if there were two clicks, which is why I stopped checking. From following the traffic on my blog I can also confirm that I hardly ever have incoming traffic from twitter these days.

Simultaneously, the follow-back rate has worsened as well, turning twitter into a one-way medium much like the old media. An increasing number of people who aren’t actually famous in any meaningful sense of the word seem to be using twitter mainly as a way to broadcast to their fans without following back or paying any attention to those unfortunate tweeps who may be slightly lower in the pecking order than they are. Using friendorfollow.com I have discovered that a shocking number of fellow science writers have never followed back, even if I have retweeted some of their tweets or helped them in some way. As I started building up an unhealthy excess of followees over followers, I have had to unfollow some of those who didn’t follow back.

These moans aside, though, twitter still comes up with stimulating insights every day, and the number of two-way connections is also growing slowly but steadily, so all is not lost. There’s always the hope that one makes it into the ranks of those whose posts are actually read and retweeted.

PS my twitter ID is: @michaelgrr


PPS (20.7.) Just came across this nice blog entry by Jonah Lehrer, on why it makes sense to follow random strangers. Couldn't agree more - and am in fact following quite a large number of people from very different backgrounds, who only have one thing in common: they all use twitter.

Wednesday, July 14, 2010

messy bumblebee

I had a lucky click on Monday, watching this bumblebee disappear in a flower I couldn't see into (as it was pointing away from me, and behind a fence) and just reaching over to point the camera at the flower blindly. This is what the camera saw but I didn't:



I've uploaded this and a few other new pix to my flickr photostream.

For a selection of my best (or at least favourite) photos, visit fotocommunity where I am only allowed one upload per week, so have to be very selective.

Oh, and I've also got pix on View but not sure it's worth the trouble as I don't get that many clicks there. Any views re. what's the best site for sharing photos?

Tuesday, July 13, 2010

how whales combat climate change

I had huge fun writing the story about whale poo which is out in Current Biology today. According to recent research, the net effect of sperm whales is that they help to remove carbon dioxide from the atmosphere. They do this by picking up iron rich food in the deep, and defecating most of the iron near the surface. This encourages the growth of (iron-limited) diatoms, which after their death sink to the sea floor and take their carbon with them.

Which means, of course, that reducing sperm whale populations by 90 % in the era of industrial whaling may well have had a significant effect on greenhouse gas concentrations.

Iron findings
Current Biology, Volume 20, Issue 13, R541, 13 July 2010
doi:10.1016/j.cub.2010.06.042

summary and limited access to pdf file

Sunday, July 11, 2010

still life with giant lemon

For some reason which I never quite understood, TV chef Jamie Oliver owns (runs? inspires?) an Italian restaurant in George St, Oxford. As far as I know he's neither Italian nor Oxonian, but at least his name is above the door. The restaurant is easy to spot, as there is usually a queue outside. I've tried to ignore this, but today Jamie very kindly arranged this still life in the window, and it would have been rude not to take a picture:

Friday, July 09, 2010

Dvořák Humoresque Op 101 No 7

The young cellist in my family is currently studying a version of Dvořák's humoresque No 7, so I looked it up on youtube and found this arrangement for violin and cello, which I find quite amazing:



Oooops, sorry, video has been removed, try this version instead.

Love the very talkative eye contact between the musicians.

targeting the right ion channel

Back in 2000, Oxford researcher Frances Ashcroft published a popular science book that is kind of complementary to my "Life on the Edge", in that it deals with the effect of extreme physical conditions on human physiology, which I had left out of my account of life under extreme conditions. Her book "Life at the extremes" is still in print as a paperback.

Unlike me, however, she's very successfully carried on with her research since then, which addresses ion channels, i.e. the "doors" in the cell membrane that specifically let through certain kinds of charged particles, under certain conditions. Her group has a paper out in science express this month which shows how important it is to address the right kind of channel. To treat a muscle weakness that is often seen in children with neonatal diabetes, the research shows, one needs to target not the muscle version of the mutated ion channel but the brain version. Which has direct implications on how the drugs need to be designed, including the fact that they need to be able to pass the blood-brain barrier.

Reference:

Muscle Dysfunction Caused by a KATP Channel Mutation in Neonatal Diabetes Is Neuronal in Origin
Rebecca H. Clark, James S. McTaggart, Richard Webster, Roope Mannikko, Michaela Iberl, Xiuli Sim, Patrik Rorsman, Maike Glitsch, David Beeson, and Frances M. Ashcroft
Published online July 1 2010; 10.1126/science.1186146 (Science Express Reports)

Wednesday, July 07, 2010

ghost forest

An art installation of gigantic tree trunks from African rainforests, meant to highlight the alarming depletion of the world's natural resources, and in particular the continued deforestation, has just turned up outside Oxford's University Museum:







More about the project: Ghost Forest Art Project.

For other events lined up in the year of the University Museum's 150th anniversary, click here

Update (30.7.2012): The Ghost Forest has now moved on to its final resting place, at the National Botanic Gardens of Wales in Carmarthenshire (ITV news coverage).

Tuesday, July 06, 2010

Juan Gabriel Vásquez

A fascinating profile of young(ish) Colombian novelist Juan Gabriel Vásquez appeared in the Guardian recently, written by Maya Jaggi. About his latest book to be translated into English, Jaggi writes:

The Secret History of Costaguana (2007), published this month by Bloomsbury in McLean's translation, is a humorous, picaresque novel of adventure and a knowing take on a family saga. Set in 19th- and early 20th-century Colombia and London, it probes the political intrigue that mired the building of the Panama canal, complete with financial crash and US intervention.


Vásquez, 37, is from Bogotá, so his experience of Colombia (he emigrated to Europe in 1993) is bound to be different from that of the country's most famous writer, Gabriel Garcia Marquez, who hails from the tropical climes of the northern coast. I'll definitely chase up his books (not trivial getting the original versions around here).



It is also around the 100th time that I spot something really interesting with the byline of Maya Jaggi - she definitely reads the same kind of literature that I like to read. Yet I have been unable to find out what her background is. By now, there is a profile with a photo of her on the Guardian website, but the CV starts in 2000, so no indication of how she came to report about world literature. Which of course needs explaining as I sometimes feel that in the UK she's the only person who knows about this sort of things. So, dear Guardian Review, I want a double page spread about Maya next week, can you arrange that?

PS even though the English version of the book is out now, getting reviews, publicity etc., the original version is not available at Blackwell's main bookshop, and costs more than 30 pounds at amazon.co.uk. Time to revive my account at El corte ingles ...

Monday, July 05, 2010

a racemate of giant lollies

This blog needs an infusion of colour, so I took a snap of the sweets on display at Mr. Simm's Olde Sweet Shoppe on the high street:



Scientists may enjoy spotting the chirality of the helical lollies in the back row - there are actually a few right-handed helices among a majority of left-handed ones. Which is kind of surprising as one would expect that the machine that makes these things would always turn in the same direction.

Friday, July 02, 2010

my double life at amazon.com

Just updated my profile pages at amazon.com and am still intrigued that I have separate identities as a reader / customer and as an author. I use the same username and password for both profiles, but the site doesn't make a connection, and the customer site regularly asks me to review my own books (based on the fact that I bought a few copies to be dispatched to friends directly from amazon).

Similarly, they haven't managed to get their head round the fact that I use amazon in four different countries (US, UK, D, F) both as an amazon associate and as a buyer, and in the UK also as a marketplace seller. (At one point they closed down my marketplace account in Germany, as it had the same password as the UK account, and apparently, the system no longer supported that. I would have had to sign up from scratch again with a new ID but didn't bother.)

Anyhow, I find it quite reassuring that I am still too complicated to be understood by the world's most successful online retailers, and long may it last ...


PS: I have to acknowledge, however, that the changes I made to my author profile on the US page today were swiftly passed on to the UK profile. So their computers do talk to each other ...

Thursday, July 01, 2010

neanderthals and twins

the usual round-up of German pieces published this month includes a detailed look at the scientific challenge behind the Neanderthal genome, and an appreciation of twins research in the times of epigenetics, plus some fun with chemical fingerprints:


Spektrum der Wissenschaft No. 7, pp 12-14
Neandertaler-Erbgut entschlüsselt

Nachrichten aus der Chemie No 7/8, pp769-771
Identische Gene, verschiedene Schicksale
(plus a box with a brief Neanderthal update - have covered the N. genome project in this magazine before)

Nachrichten aus der Chemie No 7/8, p 733
Chemischer Fingerabdruck
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