Prose and Passion

eight years on Mars

2012-01-25T02:24:00.000-08:00

Eight Earth-years ago today, NASA’s exploration rover Opportunity bounced down onto the surface of Mars, and I find it completely mindboggling that it is still operating there today. I don’t think I’ve known a CD player that has lasted as long in the relatively clement conditions here on Earth. As one rover team member told me, Oppy and the now defunct sister craft Spirit have outlasted several of the computers that were bought to steer them on their mission, which was originally scheduled to last three months.

Happy landing anniversary to Opportunity and to all who have made this amazing achievement possible. In celebration, here’s a snippet from my book Astrobiology: a brief introduction, describing Opportunity’s first (of many) day at work:

In early 2004, abiding by its Mars creed “follow the water,” NASA landed solar-powered rovers at two seemingly water-modified landscapes in Mars’s northern hemisphere. The first, called Spirit, touched down (bounced to a stop, actually, on airbags) on January 4 in the Guseve Crater. Located at the end of the 900-kilometer-long, 10-kilometer-wide Ma’adim Vallis (valley), Guseve appeared from orbit to have once been a lake. After extensive exploration, however, Spirit found little but the most indirect evidence that the crater was ever filled with water. Some three weeks later, Spirit’s sister craft, Opportunity, bounced to a stop on Meridiani Planum, a smooth, flat plain the size of the state of Colorado that had been selected because spectroscopic investigations from orbit indicated it was decorated with the mineral hematite. Hematite, an iron mineral, can be formed by several mechanisms, but on Earth it is most commonly deposited in aqueous environments. Cushioned by its airbags, Opportunity bounced a dozen times on the Martian surface before finally coming to rest in a small crater. When the rover shook off its landing and turned on its cameras, it found itself staring at thick, layered beds. The Opportunity rover, the fifth successful Mars lander, was the first to find bedrock.

On Earth, the majority of layered rock is sedimentary, laid down over successive seasons or successive floods by liquid water. But successive volcanic eruptions (either as lava flows or as successive layers of ash) can also form layered rock, as can shifting patterns of wind-blown dust. So which was it at Meridiani? The bedrock in Opportunity’s crater showed clear evidence of cross-bedding, layers formed at angles, as often formed in stream beds on Earth due to turbulent flow. Some of the rock surfaces also showed clear signs of polygonal cracks, reminiscent of the hexagons that sometimes form in drying mud. The layers were also filled with the type of small, round rocks that littered the ground at Meridiani. Termed “blueberries” after the fruit they seemed to resemble in shape and size, if not color (somehow “grayberries” just sounds wrong), the small spheres littering the crater are composed of hematite--again, most likely formed in situ in the rocks by the action of water.
Perhaps even more revealing than the gross structures of the strata are their chemical compositions. The rover’s α-particle and x-ray spectrometer (APXS), which can identify the elemental composition of rocks, indicated that the rocks at Meridiani contain large amounts of magnesium, calcium, and iron sulfates, along with traces of chlorine and bromine. On Earth such salts form preferentially by aqueous deposition, and on Mars are a near certain sign that liquid water was once present. Similarly, Opportunity’s Mossbauer spectrometer found evidence that some of the iron at Meridiani is tied up in the mineral jarosite, a hydrated form of potassium iron sulfate that, on Earth, is invariably formed by the aqueous leaching of iron minerals under acidic conditions. So it looks as if we have very firm evidence that at least parts of Mars were wet sometime in the distant past (albeit with rather acidic brine), but that Mars then took a very different environmental turn.

Opportunity looking back at its landing site (NASA).

folding helpers

2012-01-24T01:48:00.000-08:00

More than four decade have passed since protein folding was recognised as a "problem" inasmuch as nature can find the right conformation out of an astronomical number of possibilities in a split second using only the information contained in the sequence, while we mere mortals can look at the amino acid chain and have trouble to work out which bit goes where. During that time, a lot of effort has gone into clarifying some mechanistic principles, elucidating the role of helper proteins (molecular chaperones) in the cell, and creating algorithms that can predict structures of small proteins. For large proteins, however, folding prediction is still a hard problem.

I've written a feature covering some of the most original approaches that have in recent years been applied to the folding (prediction) problem, including the distributed computing network folding@home, the crowdsourcing project Foldit, and recent work on using the information included in evolutionary relatedness of protein families. The feature appears in Current Biology today and is freely accessible to all:

Folding research recruits unconventional help
Current Biology, Volume 22, Issue 2, R35-R38, 24 January 2012
HTML
PDF

PS In other news, my previous feature, We need to talk about nitrogen, is currently in 8th position in the Current Biology download chart.

year of the co-operatives

2012-01-12T06:55:00.001-08:00

The UK launch of the UN-supported International Year of the Co-operatives is today, so watch out for activities up and down the country. I've joined the Mid-counties Co-operative a couple of years ago - think it was after writing this piece about bees problems and their "Plan Bee" initiative, which drew my attention to their membership info, which has a nice honeycomb design (as has my membership card).

(our local co-op foodstore)

Last year I also switched my energy supply to the newly founded cooperative energy, and started moving my finances from a bailed-out bank to a cooperatively owned one. Still a few thing left to switch (such as insurances), but I find it hugely comforting in these scary times that we can actually stop feeding the fat cats and support the existing alternatives to predatory capitalism, including cooperative businesses and fairtrade products.

light up (the world)

2012-01-11T02:48:00.000-08:00

You can't have too many music videos filmed in Cuba, and I'm loving the latest one, by Yasmin ft. Shy FX & Ms Dynamite, Light up (the world):

we need to talk about nitrogen

2012-01-10T01:30:00.000-08:00

I have often mentioned in my various writings that the Haber-Bosch process produces as much reactive nitrogen as the natural nitrogen fixation, and that half of the world population's N content comes out of this synthesis. Yet I didn't really know anything about the ecological impact that doubling the global nitrogen turnover produces. I recently found out that it is a very complex biogeochemical network we're messing with, and we don't nearly understand what the consequences may be.

In an attempt to understand this issue a bit better, I have written a feature article about it, which is out in Current Biology today, and, I'm pleased to report, freely accessible to all:

We need to talk about nitrogen
Current Biology Vol 22, No 1, R1-R4

Photo: A 1921 vintage reactor from a Haber Bosch plant, now on display at the University of Karlsruhe. Source: Wikipedia

what the world doesn't look like

2012-01-05T08:40:00.000-08:00

I find the use of the Mercator projection to portray the world offensive in any context (as it hugely distorts the sizes of countries and continents, Greenland isn't really larger than South America, it's a lot smaller!), but in the context of trying to help developing countries (which all appear small and insignificant in this projection) it really drives me up the wall.

Apparently, applications that allow you to zoom in and out of maps, like Google maps routinely use the Mercator projection, as this is the easiest one to calculate (it’s all in squares), but that’s no excuse for displaying the world in a blatantly misleading way, as, for instance, Oxfam does here:

Food price volatility map

I am sure the clever people working at Google and other internet companies can come up with a way to program interactive maps without making tropical countries shrink to insignificance?

If one has to have a cylindrical projection (where all the longitudes and latitudes are straight lines), one could use the Gall-Peters projection:

(Wikipedia)

which with its very unfamiliar look reminds us how wrong the maps are that we see more often. Personally, I prefer the round or oval projections, as they also remind us that our planet isn't rectangular, e.g. the Lambert azimuthal equal-area projection.

PS checking up on Google I realised that even their satellite view is in Mercator projection. Surely the satellites don't observe a cylindrical planet from space?

new C&I

2012-01-04T08:48:00.001-08:00

The magazine Chemistry & Industry has been redesigned and relaunched as a monthly, so it now looks like this:

I have two pieces in the launch issue, namely a feature on the outlook for nanotechnology:

The future is ... nano! pp 38-41

and a review of Free Radicals by Michael Brooks:

The road to scientific success? p 47

SCI members can read the pieces here. Give me a shout if you want a copy.

shattered dreams

2011-12-28T05:07:00.000-08:00

There is a vibrant local rock scene around here, which I know far too little about. I used to know just one local band that I have a soft spot for (Borderville), but have now been able to double that figure with the discovery of female-fronted pop-punk outfit Shattered Dreams, who have just released their first video:

Apparently the video is playlisted on Kerrang Channel, which is great news for them, so I hope they are going to come out really big in 2012!

no trains going nowhere

2011-12-26T04:45:00.001-08:00

It’s Boxing Day, I hear the sales are on and Oxford United play at Wimbledon today, or somewhere, yet if anybody wants to go shopping or watching football by rail, they’ll have a hard time, as there are no trains going anywhere:

And there won’t be any trains London-bound tomorrow either, nor for the rest of the week, nor next Monday in fact.

I understand that Network Rail (the one part of the railways still controlled by the government) need to do some work on the tracks from time to time, but I seem to remember from elsewhere that between major cities there are often two or more tracks running in parallel, so you can still use one while you repair the other. I also have a vague memory that other places have power cables above the lines so they can run trains with electricity and don’t have to transport all that Diesel around, and they can also reuse the brake energy. I’m wondering whether these innovations will ever reach this area …

PS: The Guardian reports that only 5 of the 25 rail companies around the country are running any service at all today. Very depressing.

happy solstice

2011-12-22T01:44:00.000-08:00

I saved another tree this year by not writing any xmas cards, so here's my seasonal offering instead:

A few more seasonal pix are at the top of my flickr photostream right now.

Have a good one, and see you on the other side.

the right diet for me

2011-12-20T01:25:00.000-08:00

review of:

The wine diet
Roger Corder
Sphere, 2007

I may be a bit biased, as I am very partial for a glass of Côtes du Rhone and a bit of dark (>70%) chocolate, so any book that tells me these two are good for me already has one bonus point. On the other hand, I’m not much of a foodie and wouldn’t normally dream of buying a book that has “diet” in the title, so I guess that cancels out.

My lifestyle choices and agreement with the author’s opinion apart, this is an interesting blend of popular science writing and nutrition advice including recipes, all informed by the author’s own research into the effects that one group of chemicals found in red wine and fruit has on the lining of our blood vessels and hence on the health of our heart and circulation.

The short message is that oligomeric procyanidins (and not the more widely known resveratrol) are the likely cause of the “French” paradox, namely the unusually long life expectancy of people in Southern France and other places where a Mediterranean lifestyle is cultivated (Sardinia is the place to be, apparently, if you want to live to 100!). These polyphenols are present in certain red wines (especially in those produced following more traditional procedures), as well as in fruit and berries including cranberries, pomegranate, and raspberries. As these molecules have an adstringent effect as well, modern food processing methods tend to do what they can to remove or destroy them.

The author is very eloquent at explaining what - according to recent research from his lab and others - is good for us, and manages to debunk some “voodoo science” along the way, including the excessive cult of antioxidants. Very interesting read – obviously even more satisfactory if you happen to like the kind of food he recommends.

ten fatal flaws of the financial markets

2011-12-17T08:52:00.000-08:00

The cover story of this week’s Spiegel (issue 50, page 40) is a lengthy but very enlightening report on the role of “the markets” in the whole mess we’re in, culminating in a list of ten things that are catastrophically flawed in the global financial system. As I didn’t find an English version I could link to, here’s my own summary:

1. The trillions circulating in the parallel universe of complex finance products (exceeding the turnover of the real world economy of goods and services by more than an order of magnitude) tend to multiply in ways that produce speculative bubbles.
2. These funds go looking for returns that would be unrealistic in the real world markets, thus sucking more and more money out of the real markets into the parallel world.
3. Banks keep inventing new finance products which tend to be opaque and often carry high risks.
4. Banks operate with insufficient levels of own (real world) funds.
5. Financial markets are intransparent and their risks unknown.
6. Concentration in these markets has produced mega banks that are too big to fail and thus a risk to the whole system.
7. Computerised trading encourages herding effects which lead to positive feedback loops, hence, disaster.
8. Interconnectedness of financial markets via derivatives synchronises them, another positive feedback loop that puts oil on the fire of any crisis in one market.
9. Financial markets resist attempts at regulation or supervision, evading into even more opaque systems.
10. Financial markets undermine conventional market economy and democracy.

The article concludes that of these 10 “monstrous” dangers, the G20 countries are currently addressing a grand total of 2, namely No. 5 transparency and No. 4 the minimum capital of banks. (Well done to our politicians – even I as a complete lay person in all things financial was aware of at least three of these! OK, only since I wrote the feature on food speculation this summer).

Now I’m really scared.

I’m beginning to realise that anything we do down here in the real world will have no effect whatsoever on this monster that’s probably going to eat us some time soon. Somebody should develop a clever algorithm that stops all these problems, for instance by introducing negative feedback and punishing herding behaviour. Trouble is, most of the people clever enough to do this are bound to be very busy making the problems worse.

The €ye of the storm ... European Central Bank in Frankfurt.

burning questions

2011-12-09T08:22:00.000-08:00

My three pieces published in German this month are aiming to address three burning questions:

* how many lab procedures can fit on one microchip?
* which type of pluripotent cells will enable regenerative medicine to take off?
* who needs an electronically controlled Bunsen burner with menus and joystick?

Specifically:

Organische Synthese: Alles auf einem Chip
Chemie in unserer Zeit 2011, 45, 370.

Blickpunkt Biowissenschaften: Drei Optionen für die Ersatzteilmedizin
Nachrichten aus der Chemie 2011, 59, 1160.

Ausgeforscht: Vom Bunsenbrenner zum iBrenn
Nachrichten aus der Chemie 2011, 59, 1138.

Image Source: Wikipedia

live from paris - review

2011-12-07T01:37:00.000-08:00

The Live from Paris DVD+CD arrived yesterday - ordered from Germany as Sony UK is being hopeless again. In the UK you can only get the DVD this week, the double pack is due to be released next week. And as track 2 says: "Why wait?" Here are my first thoughts on the new release:

This is Shakira’s fourth live DVD, so you may wonder whether she can add something new to the series, but as someone who knows the first three by heart I can reassure you that the new offering is a combination of the reassuringly familiar with the new and inventive.

Very familiar and mostly unchanged are the songs at the hard core of her repertoire from the 90s albums Pies descalzos and Donde estan los ladrones. As far as I can tell, she hasn’t changed a note in her own favourite, Inevitable, since the MTV unplugged concert, and Si te vas, and Ciega sordomuda are similarly steadfast reminders of the good old days.

A lovely new feature is the medley made of A'tini al-Nay (an Arabic song she used to sing as a child), the Metallica cover Nothing else matters, and her own Despedida from the Love in the times of cholera soundtrack. Travel around the world in just a few minutes. Within the same “acoustic” setting is a much-improved version of Gipsy.

Since I saw the show at Paris in December 2010, she added a lovely French song (Je l’aime a mourir by Francis Cabrel) and switched a few more of her announcements to French, which is a nice touch. My only moan about the programme is that none of the collaborators showed up (while Alejandro Sanz and Wyclef Jean did, the last time round).

The DVD with 99 minutes of concert footage and 20 mins “behind the scenes” extras is perfect as always. The CD contains as much of the concert as fits on a single audio CD (big improvement on the 5-track CD from last time!), which means all announcements and a couple of songs (Si te vas, Gordita) were dropped, and the A'tini al-Nay snippet was cut too. The sound editing on the CD is different from the DVD version; there were a couple of places where I think I heard things that weren’t so prominent in the DVD soundtrack.

Her last words on the concert recordings are “a la prochaine” (until the next time), so I’m very much looking forward to the next tour and the 5th DVD. After New York, Rotterdam, Miami, and Paris, maybe we'll hear her "live from Beirut" in four years time, complete with a full-length version of A'tini al-Nay?

(Cover of the DVD+CD pack, which comes in a CD case)
amazon.co.uk

mind your mouse brain

2011-12-06T02:45:00.000-08:00

Lots of neurosciences in today's issue of Current Biology. There's something on drosophila vision on the cover, a Q&A with Ann-Shyn Chiang, and a correction/clarification re. my earlier feature on optogenetics. Oh, and my new feature, which explores the rapid (and in some fields surprising) rise of the mouse as a model in neuroscience:

Small brain, big science

Current Biology, Volume 21, Issue 23, R935-R937, 6 December 2011

FREE access to PDF file

sticky stuff

2011-12-05T05:14:00.000-08:00

Earlier this year, I reviewed a book about biological adhesives and was intrigued by the large diversity of interesting materials that haven't been investigaten in much detail yet. I've further explored this field in a feature article which is out in this month's issue of Chemistry World:

Getting stuck in
Chemistry World 8, no. 12, pp 52-55

restricted access

inverted moons

2011-11-30T07:32:00.000-08:00

Love the story about the inverted moons on christmas cards: Your moons are rubbish, astronomer tells Christmas card artists

I should just add that one doesn't need to know about waning moons and what time they rise - it is completely sufficient to know that both Sun and Moon move from left to right in the sky (seen from the Northern hemisphere outside the tropics) and that the bright side of the moon points towards where the Sun is. So in the wrong xmas card, the bright side points to the left, so the Sun is trailing the Moon and will rise in a couple of hours, so it must be early morning. For an evening scene, you want a Sun that has recently set, so bright side of the Moon must point to the right. Simples.

Are these artists the same people who insist on putting inverted helices on the covers of books and magazines, I wonder ...

dancing about science

2011-11-22T05:57:00.000-08:00

My feature article about science-inspired dance, and Aesop's fable -inspired science is out in today's issue of Current Biology:

Dances with magpies
Current Biology, Volume 21, Issue 22, R905-R907, 22 November 2011
doi:10.1016/j.cub.2011.11.008

Summary and restricted access to PDF file

A European magpie (source)

Rambert Dance Company

water world

2011-11-10T06:29:00.000-08:00

My review of

Sex, drugs and seaslime: the oceans’ oddest creatures and why they matter
by Ellen Prager
University of Chicago Press 2011

has appeared in Chemistry & Industry, issue 21, page 27 (restricted access)

Here's a snippet:

[...] as a taster of the overwhelming biological diversity that is out there in the oceans, the book is certainly a stimulating read. Given the amount of slimy, shapeshifting, limb-regenerating, and deadly poisonous weirdness found in its pages, it is intriguing to think about what we may still be missing in those 91 % of marine species that remain to be discovered.

Neanderthals old and new

2011-11-08T02:16:00.000-08:00

Way back in the summer of 2003, Firstborn and I did some volunteer work helping to dig for Neanderthal remains in a cave in the Murcia district, Southern Spain. A single Neanderthal tooth that my daughter spotted was the most exciting thing that the hard work of 15 or so people produced during an entire week. There was also a femur head (the “ball” of the hip joint), but it was impossible to tell whether it was hominid or perhaps from a large mammal such as a deer. See my book The birds, the bees and the platypuses (pp77-80) for a more detailed account of our Neanderthal adventures.

I never went back to the cave and lost contact with the research team in the following years. Imagine my surprise then, as I researched an article on modern (genomic, imaging, etc.) methods of research into Neanderthals and found out that in the years 2005-2008, the very cutting where we had scraped around for a week had yielded skeletons with articulated parts of three Neanderthal individuals, found in an arrangement that suggests they may have been buried ritually (with their hands close to their heads, as has also been observed in other Neanderthal graves).

Given the slow progress of the excavation, which is carried out only during the summer months, we must have been less than a metre away from those skeletons. While there have been similar finds further north in Europe, this burial site is a first for the Mediterranean coast, and it may allow comparative studies re. how Neanderthals lived under different climate conditions. Sadly, however, attempts to retrieve DNA from the Spanish Neanderthals have remained fruitless. It appears that the genetic material doesn’t survive very well in the hot climate of southern Spain.

The discovery and excavation of the three skeletons is described in great detail in

M. J. Walker et al., Quaternary International 2011 (in press), doi:10.1016/j.quaint.2011.03.034

As the cleaning and detailed characterisation of each skeleton proceeds, individual studies will also become available. The first one appeared in September in PNAS:

M. J. Walker et al., Proc. Natl. Acad. Sci. USA 2011, 108, 10087

Oh, and my news feature on how genomics, imaging etc. is revolutionising palaeoanthropology is out in Current Biology today:

Virtual Neanderthals
Current Biology, Volume 21, Issue 21, R871-R873, 8 November 2011
doi:10.1016/j.cub.2011.10.031

Abstract and limited access to PDF file

Shakira live from Paris

2011-11-03T09:36:00.000-07:00

As I've seen Shakira's Sale el Sol tour only twice, I can't wait to get the DVD, which is out on December 6th, as has just been officially announced. Full details are here. As the title suggests, the show was filmed at the Bercy, Paris, but not during the December 2010 gig that I saw. There were an additional two shows at the Bercy in the summer of 2011 which were used for the DVD.

As the UK distribution is hopeless again (amazon.co.uk offers the DVD for an astronomical price of £ 26.75 and doesn't give a date when it might be available!), I've ordered my copy from amazon.de.

Oh, and there is a new live video out to promote the DVD, it's Antes de las seis from the Sale el Sol album. One of my favourite songs.

dying stars

2011-10-29T03:29:00.000-07:00

The current issue of Chemistry & Industry contains my review of the book:

From dying stars to the birth of life
by Jerry L. Cranford, Nottingham University Press

which is an attempt to popularise astrobiology. I can't really recommend the book, for the reasons outlined in my review, so I'll just politely fall silent here ...

tintin revisited

2011-10-26T06:26:00.000-07:00

Dear Mr Spielberg,

many thanks for offering your 3D, motion captured, animatronic, and everything else take on the Tintin stories, but I'm afraid I've decided to stick with the original:

This edition of "Le secret de la licorne" (the secret of the Unicorn) is even older than me, not dated, but from the list of other Tintin adventures on the back, it must have been printed between 1960 and 1963.

For some deeper insights into the Tintin oeuvre, see the brilliant book Tintin and the secret of literature by Tom McCarthy, which I reviewed here.

PS: Further reasons not to watch the film:

why the CGI doesn't work and only produces zombie impressions (interesting in that it tells us how our brains process people images differently from everything else!)

Tom McCarthy on how Spielberg missed all the interesting bits in Tintin

Peter Bradshaw's review of the film

Nicholas Lezard trying to cope with the trauma the film inflicted on him

PPS Art critic Jonathan Jones tries to mediate between Tintin fans and those who appear to like the movie.

illuminating brain function

2011-10-25T04:24:00.000-07:00

As I have followed the story of bacteriorhodopsin - the biological computer that never happened - for many years now, I was very pleased to learn that somebody found something very clever to do with this and similar microbial opsins. Specifically, the recently developed methodology of "optogenetics" involves expressing microbial light-responsive ion channels or pumps in neurons, meaning that one can activate or inactivate these neurons by shining light of a certain wavelength onto them.

Stanford researcher and practicing psychiatrist Karl Deisseroth, who invented the method and pioneered its use, is keen to apply it directly to psychiatric questions. Others think a few fundamental things need to be sorted out first. Read more about all this in my feature, which is out in today's issue of Current Biology:

Shining new light on the brain
Current Biology, Volume 21, Issue 20, R831-R833, 25 October 2011
doi:10.1016/j.cub.2011.10.007
Summary and restricted access to PDF file

walking with molecules

2011-10-13T03:20:00.000-07:00

Among the molecular motors of the cell, there are quite a few that appear to walk on two legs like we do. However, the rules in the nanoworld are very different from our world. Walkers there can't rely on gravity to keep them connected with the track, and they have to muddle through the chaos that is Brownian motion.

Researchers have been able to build synthetic walkers from DNA for a few years now, and recently have also introduced the first small molecule walker that matches the key criteria of the walking molecules in the cell.

I wrote a feature about all this which is out in Chemistry & Industry this week:

Walking in the nanoworld
Chemistry & Industry issue 19, pp 20-22

free access to full text (html)

A couple of macroscale walkers appear on the cover of the issue by coincidence.

don't play with food

2011-10-11T06:27:00.001-07:00

Following the deregulation of the finance markets in the early 00s (whose bright idea was that?), finance people have discovered food commodities as a new toy to play with, and the prices have become unpredictable and decoupled from the real world parameters such as supply and demand. While the guilty parties deny that their gambling has any impact on the real world, experts increasingly believe that speculation does drive real people into real hunger.

For more info about this scandalous situation (and some of the science behind it, including, again, herding), read my feature in today's issue of Current Biology:

Don't play with food
Current Biology, Volume 21, Issue 19, pages R795-R798, 11 October 2011
doi:10.1016/j.cub.2011.09.037

summary and restricted access to pdf file

On the same issue, the World Development Movement (also mentioned in my feature) have today issued a press release:

450 economists call on G20 finance ministers to stop speculation fuelling hunger

October crop

2011-10-06T08:52:00.000-07:00

the roundup of German pieces in October has philosophical insights gained in mitochondrial research, RNA scaffolding in synthetic biology, crop protection, and an appreciation of the conical flask / Erlenmeyer flask on its 150th birthday.

Die Energie der Mitochondrien und ein bewegtes Forscherleben, Spektrum der Wissenschaft 2011, Nr 10, 100. (review of "Feuersucher" by Gottfried Schatz)

RNA-Gerüst bringt Ordnung in die Zelle, Chemie in unserer Zeit 2011, 45, 351
restricted access to PDF file

Ungestörtes Wachstum erwünscht, Nachrichten aus der Chemie 2011, 59,966

Eine schräge Geschichte, Nachrichten aus der Chemie 2011, 59, 936

Erlenmeyer's original design drawing, apparently. Source: wikipedia

when, where, and why people riot

2011-09-27T01:40:00.000-07:00

I've rounded up some experts to explain the science behind the "English riots" that happened in London, Birmingham, Manchester, and some other cities at the beginning of August. Geography, social issues, crowd psychology, network science all have something to say about it, though detailed research, such as the Guardian's collaborative effort with the LSE, Reading the Riots, is only just beginning.

My feature about all this is out in Current Biology today:

Why do people riot?

Current Biology, Volume 21, Issue 18, R673-R676, 27 September 2011
doi:10.1016/j.cub.2011.09.015

abstract and restricted access to pdf file

broken britain 2011

food fight

2011-09-13T04:59:00.000-07:00

I don't often write about food and agriculture, but hey, it's harvest time, and world population is going to pass the 7 billion mark soon, so naturally our thoughts turn to how to feed all those people.

Chemical crop protection is under attack from all sides, as GM crops push some of it out of the global market (though not the European one, where people mistrust GM), resistance to established herbicides is spreading, and the fears of side effects (most recently: on bees) aren't going away either.

So I've looked into what direction the industry may take to get out of this trouble, and found a few interesting new approaches.

Read my feature in today's issue of Current Biology:

New directions in crop protection
Current Biology, Volume 21, Issue 17, R641-R643, 13 September 2011
doi:10.1016/j.cub.2011.08.055
Summary and limited access to PDF file

Don't know what they fed this quince tree (not mine)!

book projects

2011-09-12T02:26:00.000-07:00

It turns out that I have two new books to complete by the end of January, so there won't be much time left for random blog entries until then. For the first time in nearly 12 years of self-exploitation, I've had to make a weekly timetable to allocate ringfenced time slots to both projects. Will keep plugging my feature articles though (one coming up tomorrow, in fact) and gradually reveal more about the upcoming books.

Meanwhile, the completely revised and updated second edition of Astrobiology: a brief introduction is available around the world now, so get your copy to find out everything you always wanted to know about Life and the Universe. (Note that the hardback is made for library use and therefore doesn't have a dustjacket, so it's just plain black and you don't get the lovely cover design.)

budapest globalised

2011-09-01T02:04:00.000-07:00

The next thing I noticed about Budapest (after the red trolleybuses) was how thoroughly Western brands have taken over the place. It's not just the fast food outlets and coffee shops that you find everywhere in the world. The supermarkets are called Tesco and Spar, the banks are German, the phone booths (rusty and red, like the trolleybuses) were decorated in the livery of German Telekom (of T mobile fame) and had their trademark pinky-purple receivers:

Add to that the German-built cars that block the roads (traffic is a bit of a nightmare on the main routes through the city, but amazingly, drivers very willingly stop to let pedestrians cross), and you'll come to the conclusion that the profits of virtually every economic activity that goes on around there (with the possible exception of haircuts) will be skimmed off by somebody in the west. Oh well.

Funny that after 18 years in the UK, finding the German logos in Hungary is just mildly amusing. It's the Tesco branches, ranging from "expressz" to "hipermarket" that really annoyed me. From our experience here we know that these spread like Japanese knotweed.

budapest's red trolleybuses

2011-08-27T05:23:00.000-07:00

Third stop on the recent trip, Budapest. I soon realised I love the city to bits, all the crumbling splendour (as in Havana, Venice), plus you can walk along the Danube for miles (easier on the Pest side than on the other one, but also nice on the island). Love the falling plaster and the art nouveau villas, and the red and rusting trolleybuses (electrical buses with overhead cables):

They kept reminding me of a lovely song by Bulat Okudzhava (1924-1997):

I actually saw Okudzhava playing live many years ago, when we lived in Regensburg. I knew his work as I was learning Russian at the time. There was a cultural centre on the opposite side of the square where we lived and one day I just walked past the door of that centre and spotted a plain A4 sheet of paper taped to the door, saying Bulat Okudzhava will be playing here on (date, time), which happened to be the day after I saw the notice. That was the only announcement there was, and accordingly it was a very intimate event. I seem to remember there was a translator who read out German versions of the lyrics before each song.

Well, anyhow, more about Budapest to follow.

Almodóvar’s Frankenstein

2011-08-26T02:00:00.000-07:00

The skin I live in / la piel que habito

I guess the quickest way to define this film is “Almodóvar’s take on Frankenstein,” although it is loosely based on a different book, a novel by Thierry Jonquet. As I’ve seen a dozen of Almodóvar’s movies, most of them more than once, but zero Frankenstein movies, I’m coming to this junction from a different angle than most people in the English speaking world. So here are some thoughts on how the film fits in with the work of San Pedro (I unilaterally elevated him to sainthood in a previous blog entry, these catholics are sometimes too slow in recognising achievement).

The movie is in fact, Almodóvar through and through, in every part of it there are aspects that are familiar, from the medical / bioethical issues through to he (trans)gender, rape, and sexual identity themes. As these are natural parts of the story, they don’t feel like the auteur is quoting himself – it just amazes me every time that he can assemble a completely different story from what at first glance might appear to be the same building blocks. (Which strikes me especially as I don’t necessarily share his obsession with these recurring themes, and yet they win me over every time.)

There is one interlude where Almodóvar is in fact shamelessly citing himself and contrasting the shrill style of his early work with the mellower style he has adopted since “All about my mother.” It’s the sequence that features a man in a tiger carnival costume and references Kika among other early works. The tiger aside, the rest is all in very mature taste - just savour the interior decorations, worlds away from the women on the verge of a nervous breakdown, although everybody in this movie has good reasons to be on the verge of that or worse.

For fans of the early work it is, of course, a major occasion to welcome back Antonio Banderas, who last appeared in Women on the verge and in Tie me up, tie me down! I prefer not to think of what he did in those 21 years in between (am very busy erasing those spy kids movies from my memory), but it is good to have him back, even if he looks ten times older than the last time. He looks a bit like Sean Connery from some angles, maybe Almodóvar and Banderas should do a Bond movie together, now that would be interesting!

Another familiar face (for the aficionados of Spanish cinema, at least) is the female lead Elena Anaya, who had a supporting role in Julio Medem’s Sex and Lucia and a lead role in Room in Rome (and a small role in Talk to her, apparently, will have to watch that one again to find her). And we welcome back Marisa Paredes who starred in All about my mother and Flower of my secret.

The Frankenstein-esque story is interesting too, of course, not least because of all the bioethical dilemmas that we also have to confront here in the real world, but that wouldn’t necessarily have convinced me to watch the movie if it had arrived from somewhere else. It’s the way San Pedro does it. He could make a movie out of the phone directory of Madrid and I’m sure it would still be fascinating.

The skin I live in is on general UK-wide release from today (I was lucky to catch a preview last night). Full details at IMDB.

Peter Bradshaw's review in the Guardian (his second take, as he already reviewed it when it was shown at Cannes).

walking in Vienna

2011-08-25T08:53:00.000-07:00

Second stop on our Main/Danube tour was Vienna – though it turns out that the Danube only touches the city rather peripherally. From the hotel near the Westbahnhof we had to walk across the entire city to find the river, taking in an interesting cross section from the Parisian style boulevard Mariahilfer Str. that leads from the station down to the historic city centre, through the Burggarten, past the disneyfied tourist spots with their horse-drawn carriages and people in Mozart costumes trying to sell concert tickets, and then through some outer districts with crumbling industrial sites between the Danube canal and the Danube river itself.

Clearly, the city turned its back on the river, and the idea that anyone might walk down to the river never occurred to anybody involved with its planning. Parallel to the river on the city side there is a little used railway line, but to cross it there are only the motorway bridges crossing over the river as well. Walking along the rail line, we eventually found an old station with a level crossing where we could sneak through and on to the river bank. Which was, of course, blocked up entirely with several Titanic-sized cruise ships.

The city’s other river, the Wien, is also disappointing, as it is completely walled in (see photo, left) and over long stretches even covered up.

A bit of a history lesson, we saw the spectacular Flakturm in the Augarten, and the one in Esterhazy Park, which hosts an aquarium/terrarium. These WWII upright bunkers with walls 5 metres thick are apparently so strong that it wasn’t economically feasible to demolish them, so they are still sitting around. The Lonely Planet guide of Vienna offers a half-page explanation of these monstrosities, while the German Baedeker chooses to ignore them, a case of “Don’t mention the war”?

On the Northeast side of the Burggarten there is a tropical greenhouse specially for exotic butterflies, the Schmetterlingshaus:

More photos

synthesising life

2011-08-23T07:27:00.000-07:00

I've always been puzzled by the field of synthetic biology. Every now and again, I write a piece about it in a bid to understand what it really is about. My latest attempt at understanding is out today in Current Biology:

What exactly is synthetic biology?
Current Biology, Volume 21, Issue 16, R611-R614, 23 August 2011
doi:10.1016/j.cub.2011.08.002
abstract and restricted access to pdf file

As always, I have used examples of recent research to try and define the field, but surely, I will need a few more articles to sort this out.

Image source: wikimedia commons

Frankfurt

2011-08-19T09:29:00.000-07:00

Just came back from a rail trip to Budapest, visiting a few cities on the Danube and Frankfurt which happens to be on the wrong river (Main) but is as far as you can safely travel in a day starting from Oxford at a sensible time.

We stayed at a hotel close to the European Central Bank, so were close to one of the epicentres of world events when the markets took a nosedive on Monday 8.8. Didn't notice any suspicious activity in the banking quarter of the city, but then again we were busy dodging the torrential showers that swept by in half-hour intervals.

Only in the evening, watching CNN in the hotel room with the Dow Jones shown in a corner of the screen and losing dozens of points every few seconds, did we find out there was trouble.

So here's the peaceful scene outside the ECB after the markets closed:

Banks aside, Frankfurt also has a very lovely promenade where you can walk (or jog, cycle, rollerskate) along the river Main for miles. Such an obvious boost to quality of life, but not all cities get it right.

Additional photos from F. in my flickr set Germany, and further riverside adventures to follow ...

autistic genomes

2011-08-18T02:14:00.000-07:00

Much like everywhere else in the application of genomics to medicine, the hunt for the genetic origins of autism has proven harder than expected, and the genetic variants detected still only explain a minute fraction of the cases. Recent research suggests that copy number variations, many of them occurring spontaneously in the person affected, play a much bigger role than anticipated. While de novo changes are still genetic in that they reside in the genes, they also rhyme with recent suggestions that the heritability of the disorder isn't quite as high as believed.

I've written a feature article about all this which is in the latest issue of Current Biology:

Copy numbers count for autism
Current Biology, Volume 21, Issue 15, R571-R573, 9 August 2011
doi:10.1016/j.cub.2011.07.031
abstract and restricted access to pdf file

rocks falling from the sky

2011-08-17T08:54:00.000-07:00

My review of the book

Chemistry of the solar system
Katharina Lodders and Bruce Fegley, Jr.
RSC Publishing 2011
ISBN 978-0-85404-128-2

is out in Chemistry & Industry issue 15, p26

I'm afraid it's premium content but do let me know if you need a copy.

I've been rather critical of the book, I'm afraid, but here's a snippet from my review about the chapter on meteorites, which was the part of the book I liked best:

"Meteorites also cast an interesting light on the history of the scientific revolution. Many of the first scientists in the modern sense rejected the idea of rocks falling from the sky as a medieval superstition. Enlightened modernists at the end of the 18th century evicted meteorites from museum collection. Only in 1794 did a brave soul start building the case for their extraterrestrial origin, which gradually won the day."

phages and pili

2011-08-06T03:39:00.000-07:00

the roundup of German pieces in August is all about bacteria, namely first the phages that infect them, and then the hairs that enable them to infect us.

Planet der Phagen
Spektrum der Wissenschaft August 2011, page

Wie die Haare der Bakterien wachsen
Chemie in unserer Zeit 45, No. 4, page 234
DOI: 10.1002/ciuz.201190057
abstract and limited access to PDF file

a chestnut tree, as featured in the phages work reported

a poisonous surprise

2011-08-03T05:32:00.000-07:00

Oxford Zoologist Fritz Vollrath is famous for his work on spiders, but sometimes his team also gets involved in finding out amazing things about larger animals, such as rats storing poison in their fur. They have a paper out today, here's an excerpt from the press info:

For many years mystery has surrounded the sudden collapse, sometimes followed by death, usually at night, of dogs in north-eastern Africa. Typically, if the dogs do not die at once, they lose co-ordination, froth at the mouth and show symptoms of acute distress. In some rural areas elders or hunters might identify a wooly grey rodent as the culprit and warn that the rat is extremely poisonous. New research has confirmed that warning.

The Crested Rat, Lophiomys imhausi, 40-50 cm. long, looks quite innocuous as it clambers about in rocky, wooded valleys in Kenya and the Horn of Africa. If disturbed the long fur on its flanks parts to expose a vivid black and white pattern around a leaf-shaped tract of peculiarly specialized hair. Just how specialized the hair is and how well designed each hair is to hold and dispense poison has been revealed by a group of East African and Oxford scientists.

The group have identified the toxin, which comes from Poison-arrow trees of the genus Acokanthera, long celebrated for an extract from their bark and roots which, when applied to an arrow-head, can fell an elephant.

The scientists have observed the rat gnaw Poison-arrow tree bark directly from the plant, chew it and then deliberately slather the resulting colloid onto the flank hairs. These hairs are designed to rapidly absorb the colloid, acting like a lamp wick. The poison,Ouabain, is well-known as a heart-stopping cardiac glycoside and for centuries doctors have used minute doses of Ouabain to stimulate weak hearts.

The Crested Rat is the only mammal known to sequester plant toxins in this way. When more is known about the chemistry and genetics of the Crested Rat’s immunity to and use of Ouabain there may well be applications for human medical therapies.

In 1974 the senior author, East African Jonathan Kingdon, first advertised the mystery of a poisonous rat and invited further study. It has taken nearly 40 years for the mystery to begin to be solved.

A poisonous surprise under the coat of the African Crested Rat.
Jonathan Kingdon, Bernard Agwanda, Margaret Kinnaird, Timothy O’Brien, Christopher Holland, Thomas Gheysens, Maxime Boulet-Audet and Fritz Vollrath

Proc. R. Soc. B published online before print August 3, 2011, doi:10.1098/rspb.2011.1169

full text (open access)

anarchy in the proteome

2011-08-01T09:57:00.000-07:00

My feature article on intrinsically disordered proteins, based on the Barcelona conference I attended last year, is out in Chemistry World this month:

Anarchy in the proteome
15 years ago, the idea that proteins might be functional without a well-ordered 3D structure was heretical. But Michael Gross discovers, a little flexibility can go a long way

Chemistry World August 2011, pp 42-45

limited access to PDF file (drop me a line if you can't access it)

The field has certainly grown amazingly in the 14 years since I first wrote about it ...

Among other illustrations, the article features a photo from Stacey Raven, which I accidentally discovered on flickr:

inspirational diatoms

2011-07-27T02:24:00.000-07:00

Diatoms are among my favourite examples of "Nature's nanotechnology" from which we still have so much to learn. I wrote quite a few pieces about them in the late 90s / early 00s, but then lost track of them a bit. Now I've caught up with the field and have written a feature article which is out in this week's issue of Chemistry & Industry (issue 14, page 21-23).

It appears to be freely accessible here - you just have to click on the sub-headings to get the next part of the text.

Photo: Wipeter, Wikimedia Commons

nature's value

2011-07-26T02:37:00.000-07:00

At the end of June, I had the opportunity to take part in this year’s “World Forum for Enterprise and the Environment” at Merton College, organised by Oxford’s Smith School.

It was all about how we may still be able to avoid blowing up our planet if we get businesses to recognise the value of the natural resources they are using, polluting, or destroying with their activities.

Personally, I would prefer if people could just do the right thing because it is the right thing to do, and wouldn’t need price tags and bribes to steer them in the right direction. But as we do live in a society where money talks, and which isn’t going to change any time soon, I guess the ecosystem services idea may well be our best chance for saving what's left of our natural environment.

As this is all very topical and important, I wrote a feature about what I learned at the Forum, which is out in Current Biology today:

Valuing Nature
Current Biology, Volume 21, Issue 14, R525-R527, 26 July 2011
doi:10.1016/j.cub.2011.07.003
summary and limited access to pdf file

Oh, and I especially enjoyed Sandra Bessudo's talk (in Spanish) on the natural wealth of Colombia, and what should be done to protect it, so here's a picture of her:

This is my own photo, but there are lots of official photos from the event at the Smith School of Enterprise and the Environment's photostream.

Common Hogweed (Heracleum sphondylium)?

2011-07-23T02:21:00.000-07:00

As I'm not much of a botanist, I am struggling to identify this plant which grows in abundance along the river Cherwell in Oxford:

Young leaves look like this:

I now think it's Common Hogweed - also see the German Wikipedia entry which has better pictures - according to those, all details seem to match. But all expert botanist advice welcome.

Oh, and I'm also clueless about the insects that often crawl around on it, as in the photo above, but the plant is more important as my son is obsessed with it and I was worried that it might be poisonous (I found half a dozen similar looking plants that are poisonous, in fact).

sustainable chemistry

2011-07-13T02:24:00.000-07:00

My short essay review of the book

Chemistry for sustainable technologies: A foundation
by Neil Winterton

is out in this week's Chemistry & Industry, i.e. issue 13, page 28.

Here's a snippet:

Winterton developed an optional module course covering the chemical foundations of sustainable development, out of which this book evolved. The somewhat unconnected chapters still feel a bit like coming into a lecture theatre and hearing: “This week we’re going to…” And the over-used parentheses sound like professorial asides.

Each lecture / chapter covers a significant aspect of sustainable development, up to and including the importance of science for society. Each comes with full scientific detail and an extensive bibliography. This book clearly means business. It wants to be worked with and doesn’t take kindly to being read for pleasure.

we're all Africa

2011-07-12T03:16:00.000-07:00

It doesn't happen that often that I get the chance to use a quote from Shakira in my writing, so I jumped at the opportunity to open my article about African genomics with a reference to last year's Fifa World Cup and its official tune, which includes the spoken words at the end: "We're all Africa."

Because, you see, considering the facts that we all came from Africa at one point, sooner or later, that most of human genetic diversity is found between African populations, not between "races", and that a large part of the global disease load weighs down on Africa, it really is quite weird that the new investigation of personal genomes so blatantly followed the money rather than the scientific interest in sequencing lots of males of European descent before even beginning to include some token people of different origin (or even gender).

Obviously, I have phrased this sentiment much more diplomatically in my feature and I also report on several initiatives which aim to empower Africans to take part in the genome revolution and also to reap the medical and economic benefits from it.

My feature is out today in Current Biology:

African genomes
Current Biology, Volume 21, Issue 13, R481-R484, 12 July 2011
doi:10.1016/j.cub.2011.06.047

Summary and limited access to PDF file

Shakira performing "Waka waka: This time for Africa" at the closing ceremony of the 2010 World Cup.

not the end of the world

2011-07-08T09:12:00.000-07:00

I'm loving the front pages of the UK newspapers today, after the coyote had to bite off its paw to get out of the trap ... Loving them so much I made a little collage:

(I tried a couple of news agents to see whether I could get a proper photo of the papers nicely arranged, but they all had them in very unphotogenic places and arrangements.)

I have to disagree with the headline writers who seemed relish the idea that the NOTW is "the world." I think the world at large will be a lot better off without that paper, thank you very much, and rather than the end, it is hopefully going to be the beginning of a new, better world. I think this is a historic opportunity for the UK to rebuild a democracy where elections are decided by the electorate, not by Rupert M.

PS I'm also blogging and reblogging on tumblr these days - more pics, less text than here, check it out.

astrobiology - second edition

2011-06-27T07:46:00.000-07:00

Back in 2006, Johns Hopkins University Press published Astrobiology: a brief introduction, which I had co-authored with Kevin Plaxco. Since then, the field has become quite popular. (I would love to take credit for it, but maybe it’s just dumb luck.) The quest for life or at least habitable planets in the rest of the Universe is now a universally supported endeavour to the extent that NASA now justifies much of its research and exploration work with that goal.

The discovery of extremophiles in the most unlikely locations here on Earth has played a large part in propping up our hopes that life may also exist elsewhere. Add to that the discovery of more than 500 extrasolar planets in just 16 years since the first one was reported, and you get a proper scientific gold rush.

Thus, our 2006 book was beginning to look out of date and there was a strong case for a new, revised and expanded edition, which we prepared over the last year or so. We have revised the entire text, added a glossary and lots of new illustrations. New discoveries are included up to and including last December’s arsenic eating bacteria. With all this, the book will be around 90 pages thicker than the first edition, but hopefully just as readable.

The cover design, which we all love, has been kept. Only the colour of the title will now be green instead of orange, so you can easily tell the second from the first edition. The new version should be available by September in the US, maybe a few weeks later in the rest of the world.

In preparation for the release, I’m also updating the astrobiology web pages, but that’s work in progress still. (At the moment the ISBN numbers and the cover are there, but the exact page number and amazon links are still missing.)

hidden treasures

2011-06-25T03:00:00.000-07:00

After the most-viewed flickr pix, here now a selection of the least-viewed and underappreciated. There are quite a few flowers, such as this tulip with dew drops:

water fountains, like this one at Barcelona:

pedestrian bridges, like this one in Amiens:

and our local bumblebees, such as this one:

Some of the other bumblebee pictures are in double figure views only because I posted specific links on twitter - this adds 10-15 views in a minute.

But maybe I just haven't found the right flickr groups yet to promote these types of photos ? Some of the highly specific groups I'm in, specialising on windows, pedestrian bridges, fountains, etc. seem to have little effect.

Anyhow, a set of my hidden treasures is here.

suerte

2011-06-24T06:46:00.000-07:00

Spanish/English mixed version of Jason Mraz' song Lucky, featuring the Mexican singer/songwriter Ximena Sariñana:

As luck would have it, I just found out that Ximena has an English album in the pipeline, due to be released in August. There is already a video for the first single, Different, and I love both the song and the video (and the cuddly yellow monster, too), so even though I only meant to post the Suerte video, here comes another one ,enjoy:

so, mucha suerte to Ximena, at least in the UK she will need it.

flickr winner

2011-06-22T02:12:00.000-07:00

So, after one year on flickr, I'll now reveal what is by far and away the most-viewed of my pictures. Strangely, it's not one of my wonderful bumblebees, even though they are nice and fluffy, very colourful, and have six legs. Instead, it turns out to be a Homo sapiens female with only two legs and very short shorts. Who would have thunk.

I do like the picture, of course, partially because of the composition with the female figure cutting across the white table cloth, also because I have managed to disguise the face quite cleverly. But I wouldn't have picked it for the top spot. Oh well. Some of the underappreciated gems from my photostream to follow soon.

For the complete chart countdown, click the "flickr" tag below. Alternatively, visit my flickr set more than 100 views.

neuroscience in China

2011-06-21T02:19:00.000-07:00

In a rare departure from my comfort zone, I wrote a big feature article about neuroscience in China, which (like much of Chinese science) has seen a massive boost in the last 12 years, to the extent that new institutes can now attract both Chinese researchers returning from the US and international experts willing to try a new experience.

From the epic list of addresses at the top of my thank-you email I gather that it took at least 12 kind and helpful people to help me find my way in this big topic, and during the four weeks when I kicked this around, I certainly learned a lot.

So, the result of all this is out today:

Boom time for neuroscience in China
Current Biology, Volume 21, Issue 12, R441-R444, 21 June 2011
doi:10.1016/j.cub.2011.06.001

and as it is part of some bigger event across the Cell Press journals, it is on open access here:

summary page / PDF file.

It is accompanied by a Q&A piece featuring Fang Fang (not mine, this interview was set up by the editors separately), which is also on open access.

I'm blue

2011-06-20T01:50:00.000-07:00

The silver medal in my flickr countdown goes to an abstract architecture photo. This is a bit odd, as these pix, much as I love them myself, normally don't get more than the median number of views. My guess is that the group "Photography is not a crime" is mainly responsible for this. I mentioned in the caption that I got told off by a security guard, and people responded to that, so I guess some people will have clicked on the photo to read the story, rather than to appreciate the photo. But it's all good, they get a nice photo as a bonus:

This is in London, between Paddington station and Little Venice.

summer legs (No. 3)

2011-06-19T13:39:00.000-07:00

No. 3 in my flickr charts is one of my lucky ones, and one of my very first candid shots. The stripes caught my attention and I just hit the button. Only when I got home and looked at it on the screen I noticed that the legs are looking nice too, especially the way they seem to be forming arrows pointing downwards:

jogger on the fast track

2011-06-18T05:58:00.000-07:00

This candid snap of a jogger who just sped past me is no. 4 in my flickr charts, and still gaining views and faves, so may make it to a higher position. While I have no particular interest in athletics or in athlete's legs, I like the way the jogger's shadow is enclosed in the triangle between the legs and the ground.

(click photo to see larger versions in flickr / click the "flickr" tag below to find other photos in my countdown)

Lady Gaga and philosophy

2011-06-17T02:12:00.000-07:00

To my utter shock and bewilderment, I have just found out that neither of the two publishers that run book series on popular culture and philosophy has yet published a book about Lady Gaga and philosophy. In fact, searching the exact phrase “Lady Gaga and philosophy” I got only two hits, one to the twitter profile of someone who lists her interests and ends the list with these two items (as you would), and the other to a philosophy blog which also notes the lamentable absence of this title.

So, while we are all waiting with baited breath to find out what the serial philosophers will have to offer once they have woken up to the semiotic treasure trove that is the work of Gaga, I’ll start compiling a few suggestions of topics they may want to consider:

Is it music? Why Mozart might have written “Bad Romance” if he were alive today (for more about this, see here)

Is it art? The school of gagaism and its position in the development of occidental art

Baby you were born this way: The quest for sexual identity in the 21st century.

I’m in love with Judas: Gaga vs. God

Scheiße Scheiße be mine: the language and languages of gagaism

P-p-p-pokerface: The semiotics of make-up and masks

I am my hair: Hair style as a cipher for personality in postmodern society

I’m on the edge of glory: Feeding the reward system in the age of individualism

Papa paparazzi: Iconography and perceptions of fame

Monster ball: Identification and motivation of fans and followers

Gossip girl: The education of a cultural icon

All suggestions for additional chapters, and indeed authors, welcome.

I notice that Open Court have among their forthcoming titles "Rolling Stones and philosophy" (due to join a male-only club of artists like Bruce Springsteen and U2), so they are clearly catching up and might get round to the Gaga title in a few decades. My favourite title on their list of 59 books is "Woody Allen and Philosophy: You Mean My Whole Fallacy is Wrong?" (2004). The competitors at Wiley-Blackwell have Metallica as their only musical entry. Gaga apart, I really do think one of them should have covered the philosophy of Alanis Morissette by now.

Oh, and as bonus material, here are my random thoughts on the new album, jotted down a bit hastily after the first two or three times playing it:

Would I still enjoy this album if it had arrived in a brown cardboard sleeve and I knew nothing about the artist?
Actually, I think I would. Not all tracks are great, but there is an interesting variety and I sense the genuine artist's urge to express herself in many details. I'm not wildly excited by the first three tracks including the title track, but love the middle section starting with Judas (which I read as an attempt to recapture the glory of Bad Romance).

As someone familiar with several European languages, I find Scheiße interestingly disturbing - it mangles fragments of half a dozen languages into a meaningless but attention-catching pidgin pudding. Gets me every time. My attention tends to wander off after Bloody Mary, and come back for You and I, strangely.

Surely it's not to everybody's taste and will irritate many, but that's what art is supposed to be like. So please ignore the hype and try it with an open mind.

cyclist, abstracted

2011-06-16T01:23:00.000-07:00

No. 5 in my flickr chart countdown is a cyclist. There's no shortage of these in Oxford, and I've snapped a few that were unfortunate enough to cycle past my camera, but most of these snaps are a bit boring. In fact this one is the only one I posted on flickr, and I love it because the backlight, the perspective, the stripes, and the crop all work together to make it a bit more abstract and artsy. It also helps that the face and legs are out of sight so viewers (and even men) can focus on the photographic qualities.

Needless to say that none of the qualities described are down to my planning. This cyclist just brushed past me on the footpath and I instinctively pushed the button.

Greens on course for federal government

2011-06-15T03:16:00.000-07:00

I've just realised, somewhat belatedly, that Germany's Greens have become the second strongest party in the wake of the Fukushima accident and have stayed in second place quite firmly since then.

Today's Forsa poll indicates that in response to the "Sonntagsfrage" (what would you vote if federal elections were held next Sunday?), the votes were distributed as follows:

31% CDU/CSU (conservatives)
26% Green
23% SPD (labour)
9% Linke (left)
4% FDP (liberal)

source, and additional polls from previous weeks

This would give a putative green-red coalition a solid majority, as the FDP (currently Merkel's junior partner) would fail to get into parliament, staying below the 5% threshold.

For someone who first voted in 1983, these figures just look crazy. Having been a member of the Greens from the early 80s to 2001, I never thought I'd live to see this happen.

Mind you, it's only a partially due to voters becoming greener, and a large part due to the party becoming more mainstream and normal since the days that I witnessed.

candid portrait

2011-06-14T06:03:00.000-07:00

No. 6 in my flickr charts is again untypical, as it is a candid portrait - this person stood right in front of my camera at a pedestrian crossing and I couldn't resist the early morning sun playing with her hair:

Most of my candid shots do not contain a recognisable face though - if only because we tend to have strong opinions on human faces and it is difficult to appreciate the qualities of a photo when we're busy responding to the face.

Although it has attracted more than 100 views, this photo hasn't done particularly well considering that it is in more than 25 groups, so there have been only 4 clicks per group. Anyhow, I do like it, still.

Medem medley

2011-06-13T06:03:00.000-07:00

All seven of Julio Medem's feature films are mashed up in this six-minute clip, highlighting recurring themes. Must-see for all fans:

flickr charts no.7

2011-06-11T01:58:00.000-07:00

According to the stats I recorded in the first week of June (there has been a fast riser since then) No. 7 of my most-viewed photos is my Escheresque self-portrait. As will become clear in due course, this picture is rather untypical of the top 8, but still my self portraits have generally attracted more viewers than most of my pix.

Click the image to see larger versions in flickr.

I'm counting down from 8 to 1 - use the "flickr" label below to find the other entries.

rabiosa

2011-06-10T01:51:00.000-07:00

One wouldn't be able to tell from the UK media, but Shakira has a new video out from the Sale el Sol album, called Rabiosa. The Spanish version features El Cata, the English one PitBull. Here's the Spanish one:

Oh, and the Sale el Sol tour is still going strong too, sadly I can't attend at the moment ...

top 8 flickr pix: No. 8

2011-06-09T01:57:00.000-07:00

As I'm approaching the first anniversary of my flickr photostream, I'm going to post some of the best-clicking pictures here, and also some of my favourites that may not have been appreciated by that many flickr visitors so far.

Counting down the top 8 most-viewed pix, we start with No. 8, taken on a rainy evening at Lyon:

(click image to see larger versions in flickr)

This has done reasonably well thanks to the award-driven group "Photography in the Rain".

sticky stuff

2011-06-08T08:19:00.000-07:00

My long essay review of the monograph

Biological Adhesive Systems: From nature to technical applications
By Janek von Byern, Ingo Grunwald (eds.)

is in this week's issue of Chemistry & Industry (No. 11), page 27. It's premium content, I'm afraid, so only the lucky few with a subscription or institutional access can read it online here. For the rest of us, here's a snippet describing the most entertaining part of the book:

The prize for the most accessible chapter goes to the Australian frogs of the genus Notaden. Apparently these creatures are so well-rounded that they can’t cling on to each other with their short limbs during mating. Which is why they need glue, literally, in order to stick together while they are exchanging body liquids. The author tested the adhesive power of the frog secretions by sticking two full, cold and humid beer cans together, lengthwise in one experiment and bottom to top in another.

bees, ETs, ACGTs, and old samples

2011-06-07T01:27:00.000-07:00

Among the German articles published in June we have bees, ETs, re-evaluation of Stanley Miller's samples, and third generation genome sequencing:

Rückkehr zum Ursprung des Lebens
Chemie in unserer Zeit Vol 45, No 3, page 158
Article first published online: 6 JUN 2011 | DOI: 10.1002/ciuz.201190041
limited access to PDF file

Genomsequenzierer. Die dritte Generation
Chemie in unserer Zeit Vol 45, No 3, pages 184–187
Article first published online: 6 JUN 2011 | DOI: 10.1002/ciuz.201100553
limited access to PDF file
most recent English article on this topic

Ausgeforscht: Und täglich grüßt E.T.
Nachrichten aus der Chemie Vol 59, No 6, page 605

Biowissenschaften: Keine Ernte ohne Bestäuber
Nachrichten aus der Chemie Vol 59, No 6, pages 629-631
most recent English article on this topic

Summary: Das Sterben ganzer Bienenvölker und der Artenschwund bei Hummeln bedrohen die Landwirtschaft in Europa und Nordamerika. Daran sind vermutlich mehrere Faktoren beteiligt, auch Pflanzenschutzmittel stehen unter Verdacht.

PS: The bees article also features my photo of a Bombus hypnorum (tree bumblebee):

(click image to see larger version in flickr)

protein portal

2011-06-01T15:09:00.000-07:00

Gabriel Waksman's group at the Institute for Structural and Molecular Biology (shared between Birkbeck College and University College London) has an exciting article out in tomorrow's issue of Nature, on the molecular machine which builds pili, i.e. the "hairs" that pathogenic bacteria use to attach themselves to their host. I wrote the following summary for the ISMB website:

The ability of bacteria to cause diseases in humans or animals depends, among other things, on their ability to stick to their host in order to be able to establish an infection. Many kinds of bacteria do this with the help of very thin protein hairs, known as pili. Like our hair, these pili grow from the root. With a detailed structural analysis of how this growth happens, ISMB researchers have now laid the foundations for medical applications.

E. coli strains causing urinary tract infections are one of many examples of bacteria depending on pili, as they would otherwise get washed away with the urine. The outermost end of their type I pili is a sticky protein that attaches itself to the surface of the urinary tract, using the host’s carbohydrate receptors.

Following the pilus from the tip inward, we first find two linker units FimG and FimF and then a large number of copies of the main hair builder, FimA, which is anchored in the outer membrane. In 1999 and 2002, the team of Gabriel Waksmann (then at Washington University Medical School in St Louis, USA and now at the ISMB) showed that these subunits fit together like pieces of a linear jigsaw puzzle. Each protein subunit has a well known structural pattern (the same that is also found in antibodies), but one bit of this structure is missing. The following subunit brings along the missing bit that latches into the hole and completes the structure.

This structural incompleteness of each single subunit means that each of them on its own is unstable in the periplasm, the space between the outer and the inner membrane of certain bacteria (only Gram-negative bacteria have this feature), where pili are manufactured. Therefore, they are being looked after by molecular chaperones, i.e. proteins that can protect these contact points from aggregation.

Now Waksman’s group has elucidated the detailed structure of a complex involving the outermost, “sticky” FimH subunit of an E. coli pilus, as it is being exported through the outer membrane by a specialised protein export machine (the FimD usher) and still being guarded by such a chaperone, FimC. The structure, which shows the pilus tip protein lined up inside a hollow cylindrical channel of the usher protein, is unique in that it is the first such structure of a complete protein export machine including the proper protein to be exported.

Previous biochemical studies had implicated the front end of the usher protein, the N-terminal domain, as a binding site for the pilus proteins to be exported. The new crystal structure, however, shows this site to be idle, while a second site, near the other end of the usher protein, the C terminus, binds the FimH-FimC complex. The authors conclude that the usher has two binding sites such that the growing pilus can remain anchored to one, while the next subunit to be added to it docks to the other.

The authors also conducted a crystallographic analysis of the empty FimD usher for comparison (although the structure of a similar, empty usher, PapC, had been solved before). They found that the binding of the substrate proteins induces a major structural rearrangement. The empty usher has an oval pore sealed by a specific part of the protein, the plug domain, while in the presence of FimH-FimC, the protein adopts a perfectly cylindrical shape, and the plug domain moves out of the way to open the channel for the substrate proteins.

Because this highly complex mechanism by which E.coli and similar bacteria assemble their pili has no equivalent in higher organisms, it appears to be a very promising drug target for new antibacterial therapies. Researchers hope that structural details of this mechanism, such as those revealed in this study, will help them find a way of stopping bacterial hair growth. This may offer a fundamentally new way out of the current crisis caused by drug resistant bacteria, which seem to be spreading ever faster.

The crucial difference is that drugs targeting a non-vital virulence factor such as the assembly of pili, will not kill the bacteria, which has two significant advantages. Firstly, there is less evolutionary pressure in favour of resistance genes, and the evolutionary pressure only applies in the location where the pili would normally anchor the bacteria, e.g. the urinary tract. For the survival of bacteria outside this location, the pili aren’t necessary, so any drugs leaked into the environment don’t breed resistance – in marked contrast to leaked antibiotics.

Secondly, the “disarmed” bacteria may remain present in the organism for long enough to allow our immune system to learn how to fight them most efficiently, such that they act as an immunization against the disease.

Some substances targeted at pilus formation are already under investigation as potential drugs, but the detailed molecular understanding of the process will certainly help to address this target more systematically.

Reference:

G. Phan et al, Nature 2011, 474, 49–53 doi:10.1038/nature10109

Background:

Gross M:
Education in Chemistry 2008, 45 No 4, 141-143
Better than antibiotics?

Groß M:
Nachrichten aus der Chemie 2008, 56, Nr 2, 148
Blickpunkt Biowissenschaften: Bakterien am Schopf gepackt

our living earth

2011-05-30T04:19:00.000-07:00

Review of

Our living earth
Yann Arthus-Bertrand, Isabelle Delannoy
Thames & Hudson 2008

Yann Arthus-Bertrand is famous for his aerial photographs of our planet and its inhabitants. I understand the photographer typically works from hovering hot-air balloons, so his vantage points are distant enough to reveal patterns that we don’t see from the ground, but close enough to still see the humans and their vehicles that create these patterns.

He has very successfully marketed these photos in coffee-table books with titles like “The Earth from above” and in exhibitions. In this book, his photos are hooked up with facts and figures about the current threats to our environment, and with pleas to save the Earth, which puts the photos to a good use and also gives the reader the warm feeling of doing something useful rather than just looking at pretty pictures.

The text, aimed at young readers, doesn’t delve into scientific depths, and doesn’t cite sources for the numbers given, which is a bit of a shame. If the photos and alarming facts manage to stir readers up to the extent that they want to find out more, they will have to go googling to find more comprehensive accounts.

I found copies of the book at The Works for 99 pence, which is outrageous – but grab one if you can.

go wild

2011-05-27T02:23:00.000-07:00

Wild swimming
By Daniel Start
Punk Publishing Ltd. 2008

On my map of Oxford, which dates from the year 2000, but probably hasn’t been updated all that thoroughly for the 2000 printing, there are five places by the rivers marked as “bathing place,” including Parson’s Pleasure and Sunnymead by the river Cherwell, and three others by the river Thames (or Isis, as it is called in Oxford).

In the real world, however, if I walk down to the river Cherwell, I find big signs saying “no swimming or diving” or something to this effect, and hardly anybody dares to swim there these days. There is a simple reason for these signs cropping up just about everywhere – land owners are scared of being sued if somebody comes to harm, so they stay on the safe side and put up the signs:

Yet there are many places around Oxford and indeed around the UK where swimming in the wild is at least as safe as crossing a road, for those who can swim and are willing to behave with the necessary caution. Thus it is very welcome that Daniel Start’s book lists around 150 such places around the country, complete with practical tips regarding how to get there and how to stay safe, and with as many gorgeous photos of surprisingly large numbers of people engaged in the forgotten pleasures of wild swimming.

Our local spot, Parson’s Pleasure, is only mentioned in a historical anecdote in the text and not officially included in the list – presumably due to those signs that the university put up after someone drowned a few years ago. But I might one day check out the place at Stonesfield, which, as I learned from this book, is the village where the first fossil was found that came to be recognised as a dinosaur. There is, actually, although the book fails to mention this, a local bus service from Oxford to Stonesfield.

The trouble with a guidebook that covers the whole country when you only need to know about your nearest place, is that it doesn’t appear to be very good value for money and you may be tempted to look up the info in the library or bookshop. I’d recommend to buy the book regardless, though, firstly to enjoy the wonderful photos, and secondly, to support the severely threatened art of wild swimming.

A picture taken at Parson's Pleasure - click to view full size on flickr.

PS: The site "dereliction in the shires" has a nice appreciation of Tumbling Bay bathing place by the Thames.

Germany's nuclear exit strategy

2011-05-24T01:43:00.000-07:00

Immediately after the Fukushima disaster, the German government performed a spectacular U-turn on nuclear energy. Just six months after drawing up a plan to slow down the planned closure of its remaining nuclear power stations, Germany now looks likely to speed it up, and may well do so by 2020. This would make Germany the first country to abandon nuclear energy after using it for decades, so it would set an interesting example for others to study and possibly to follow.

Read my news feature which is out in Current Biology today:

Energy U-turn in Germany
Current Biology, Volume 21, Issue 10, R379-R381, 24 May 2011
doi:10.1016/j.cub.2011.05.003
Summary and open access to pdf file.

This is also one of the rare articles to be printed with one of my own photos, namely this one:

(click image to see larger versions in my flickr photostream)

-------
Updates:

31.5. German government gives detailed plan for 2022 exit: Guardian report.

25.5. Pleased to note that the Swiss government is now moving in the direction I anticipated and taking steps towards a phase-out of nuclear energy (see this Guardian report. It would have been slightly embarrassing if they had changed their mind in the weeks between my writing the article and its publication.

The UK, meanwhile, has decided to dump radioactive waste in an ordinary landfill site. What a brilliant idea. I wonder whether nuclear energy expert Homer Simpson was involved with the planning? And seeing that the company involved is called Augean, will they divert a river to wash the waste into the sea?

seven days in Havana

2011-05-23T05:55:00.000-07:00

I hear that my all time favourite film director, Julio Medem, has started filming a short feature which will be 1/7th of a movie called "Seven days in Havana" (7 dias en La Habana). His contribution is called 'La tentación de Cecilia' (The temptation of Cecilia), and it stars German actor Daniel Brühl. The other 6 parts are from colleagues including Benicio del Toro and Gaspar Noe.

There is preliminary information available from IMDB and spanish cinema blogs (such as this one), hoping to find out more soon, watch this space!

Picture from official website: www.juliomedem.org

flickr stats

2011-05-21T01:39:00.000-07:00

After 11 months on flickr, I have now accumulated enough clicks to do statistics with them, so I'll look into that for the first birthday of my photostream. What's beginning to emerge is that the audience isn't terribly interested in cute bumblebees like this one:

Instead, they seem to have an inexplicable fondness for Homo sapiens females with short shorts and implausibly long legs (beats me). Luckily, Oxford provides plenty of those as well ...

emanuela de paula

2011-05-19T02:28:00.000-07:00

I took this photo of a large NEXT ad ages ago in London (see reflected balconies for scale), but didn't know who the model was:

Following a chance encounter with a NEXT catalogue, I have now figured out she's called Emanuela de Paula, and she has a blogspot blog too, so go visit her.

eleven minutes late

2011-05-11T02:26:00.000-07:00

review of:

Eleven minutes late
Matthew Engel
Macmillan 2009 / Pan paperback 2010

This month it’s 18 years since I moved to the UK, so I’m coming of age as a UK resident, but one of the things that still puzzle me to this day is why the railways aren’t working. The symptoms are familiar to anyone who’s ever tried to travel by train here – half an hour after the start of your journey, the train may stop because of a “signal failure” or something similarly unconvincing, sit on the same spot for any time between ten minutes and two hours, and then crawl onward to your destination. Or you try travelling on a Sunday, and find that all trains have been replaced by buses, due to scheduled engineering work. And as most of the network (including the lines out of Oxford) isn’t even electrified, the trains aren’t much better than buses anyway, and not much better for the environment, as they burn diesel like the buses do.

But why? With my anti-corporate instincts, I might have put the blame on privatisation, which happened soon after I arrived here, so I don’t have as many bad memories of British Rail as I have of the privatised mess that came after its demise. Engel’s book, part travelogue, part amateur history of the railways in the UK, reassures me that privatisation isn’t where things started going wrong. Apparently, they have been going wrong from the start, or at least from the point when speculative building of railways in random places led to a bubble and the inevitable implosion.

Since then, the railways have always been under the control of people who didn’t care about their passengers or services, and who made every conceivable error and a few inconceivable ones on top of that. All this makes for a fascinating read and would be really funny if it was fiction, but sadly it happens to be history and current affairs, and it continues to bring real misery to real people.

I like to spend my holidays in continental Europe and typically travel by train, so I get regular reminders of the fact that it is actually physically possible to run a rail network that gets people from A to B at the advertised time, in comfort, and at a fraction of the price one would pay in the UK (see my praise of ICE and TGV). However, Engel suffocates any nationalist pride I might develop when thinking of the German railways too much by reminding me that the efficiency of their infrastructure is largely due to the fact that it was planned strategically by the Prussian rulers. They didn’t care about the travelling public either, but they did care a lot about moving troops across the country as efficiently as possible.

Amazingly, their warmongering motivation has produced an invaluable asset for peaceful travellers using the network more than 1.5 centuries later. Come to think of it, the Bundesbahn network is strongest in north-south directions, transporting holiday makers to the Alps or the North Sea, while military aggression was typically directed in eastern or western direction, so maybe somebody secretly did think of the travelling public after all.

Engel starts out by describing his own exploration of Britain’s rail network with the benefit of a rover card, then slips into chronological history mode, and only returns to his exploits at the end. Given the sheer mindboggling madness of his subject matter, however, even the chronological core of the book is never at risk of becoming tedious. It reads like Alice in Wonderland, you fully expect to see the Mad Hatter turning up any time.

The title of the book refers to one of the many symptoms of systemic madness. Up to and including ten minutes after the advertised arrival time, a long-distance train is still recorded as “on time.” (In fact, I have seen trains listed as on time on departure boards half an hour after their scheduled departure time had gone by.) Thus, the author hoped on his exploratory travels to catch a train that was more than ten minutes late. In a freak coincidence, none of his trains was.

Engel also offers explanations for the trials and tribulations we suffer locally. I knew that the absence of a line linking Oxford to Cambridge is because this line was closed down in the 60s. What I didn’t know was that this happened within months of the same government’s decision to build a new city adjacent to this doomed line: Milton Keynes. Britain’s largest new town was actually built on land belonging to the village of Bletchley, which had a station on the so-called Varsity line. Oxford-MK-Cambridge would have been a valuable link saving thousands of unnecessary rail travels through London and road trips through the Chilterns every year. The author’s comment, concise and to the point: “Crazy.”

As for the line leading north from Oxford, to Worcester and Hereford, Engel says “much of the route was single-tracked to save money.” They actually paid people to rip out tracks from an operating double track railway line to convert it back to single track? Why don’t we single-track a couple of A roads as well? That would save money on fixing those potholes. And does the M40 really need four lanes between Oxford and London, in these cash-strapped times?

Engel also examines the political short-termism that is partially to blame for all this. Obviously, people who only think as far as the next election won’t be spending much time planning a railway system for the next decades. Maybe France has the TGV because its presidents served for seven years at the time when that kicked off? I’m not quite convinced yet, but it might be an explanation.

For all his brilliant (yet amateur, thus accessible) analysis, Engel can’t offer any remedies to fix this mess. Personally, when the pain gets too strong, I take a coach to London, and the Eurostar from there.

A freight carriage rotting away at Oxford station - I presume it is being used as a storage shed.

third generation sequencing

2011-05-10T03:47:00.000-07:00

I recently posted a blog about third generation genome sequencing, so this is just to add that my latest feature on this topic is out in today's issue of Current Biology:

Genomics in permanent revolution
Current Biology, Volume 21, Issue 9, R294-R297, 10 May 2011
doi:10.1016/j.cub.2011.04.033
summary and restricted access to pdf file

Always happy to send pdf "reprints" if anybody wants to read it and can't get access.

vernier's chemistry

2011-05-09T04:38:00.000-07:00

The only German piece out this month is a news story on Harry Anderson's "Vernier chemistry" using the mathematical principle of the Vernier scale (a device consisting of two scales with different numbers of divisions lacking a common denominator, e.g. 9 and 10, invented 380 years ago) for the construction of well-defined molecular rings.

Schieblehre inspiriert Aufbau von Nanoringen, Spektrum der Wissenschaft Nr 5, S. 21

The beginning of the text and a link to the PDF (restricted access) is here.

As you can tell from the number of reader's responses, I got the explanation of the Vernier scale the wrong way round. In fact, the additional, slightly different scale is squashed (typically by 10:9), while I wrote that it was stretched. I think I had this wrong version in my head since the age of five or so, so it didn't occur to me to get the caliper out and check.

how sickle cell trait protects from malaria

2011-05-04T01:50:00.000-07:00

New insights into the mechanisms by which the sickle cell trait protects carriers from malaria point to an enzyme that produces carbon monoxide. So will we use this toxic gas as a malaria drug in the future? Read my news story in Chemistry World:

New hope for malaria drugs as sickle cell protection unravelled

european women in chemistry

2011-04-29T03:16:00.000-07:00

I wrote a "long essay review" on the book European women in chemistry, which, by definition, is more of an essay than a review. I've conjured up a book review variant of the time traveller's paradox (the one about going back in time and killing one's grandmother): If my grandmother had pursued a career in chemistry after her degree, she might have ended up in this book, but I wouldn't be here to review it ... You can find my essay review in Chemistry & Industry issue 8, p26 or online here (restricted access).

Some critical remarks about the book itself:

I love the idea of compiling these biographies in a volume celebrating the year of chemistry and centuries of women’s contribution to chemistry, but I think the editors could have done more to provide some added value, seeing that the bare-bones info is easy to find on the web these days.

For instance, a simple thing that someone could have done during proof-reading would be to cross-reference the names of women who have a chapter of their own, but are also mentioned in other chapters, such that readers have the option of navigating the network of the female chemists. Then, somebody should have checked the references. Those at the end of Marie Curie’s chapter include German translations of biographies published in English and French. Where a full-length biography exists, it should definitely be mentioned, but I noticed that Brenda Maddox’s tome on Rosalind Franklin has been omitted. I suspect there must be a dedicated biography of Irene Joliot-Curie as well, which we aren’t told about.

The uninspiring prose doesn’t really invite the reader to read the book from cover to cover, which is a shame. However, what I hope the chapters will achieve is to tickle people’s curiosity sufficiently to ensure that they go and find out more about those of the chemists they find interesting.

third generation genome sequencers

2011-04-27T12:56:00.000-07:00

I have covered the upcoming revolution in genome sequencing, i.e. the development of "third generation" sequencers that can read single molecules and/or use electronic instead of optical base detection a few times now (e.g. this feature in Education in Chemistry and this essay review in C&I), so I'm really excited that we now reach another milestone in this development.

Today, Pacific Biosciences announces the full-scale commercial release of its single molecule sequencer, the PacBio RS.

Without any attempts at false modesty, the company PR declares: "The PacBio RS is a revolutionary DNA sequencing system that incorporates novel, single molecule sequencing techniques and advanced analytics to reveal biology in real time. The system delivers unprecedented sequence readlengths - over a thousand DNA bases on average. And unlike ‘second generation’ systems on the market today that typically take over one week to deliver results, the PacBio RS allows customers to obtain results in less than a day."

Details of how the PacBio machine works are included in my EiC feature, which is openly accessible here.

I have recently written two other features about third generation sequencers (one in English and one in German), which are now in press, so watch this space.

planet of the phages

2011-04-26T08:24:00.000-07:00

My feature about bacteriophages (viruses infecting bacteria), their chequered history and possible future as antibacterial therapeutics, is in today's issue of Current Biology:

Revived interest in bacteriophages
Current Biology, Volume 21, Issue 8, R267-R270, 26 April 2011

doi:10.1016/j.cub.2011.04.008

Summary and restricted access to pdf file

Among other things, I learned from the research for this story that there are a lot more phages on our planet than all other kinds of living things, so we cellular life forms really are a minority living on he planet of the phages ...

A horse chestnut tree in Headington Hill Park - these trees are infected by bacteria, which are in turn infected by phages ...

don't tell me that it's over

2011-04-22T09:31:00.000-07:00

I quite like Amy Macdonald's second album, A curious thing, not sure why it didn't get much attention around here ...

this appears to have been the lead single from this album, but I don't recall it getting any airplay.

solidarity poster

2011-04-20T03:19:00.001-07:00

love this solidarity poster I saw in Brussels this weekend, at the Centre International

It's from the Belgian Labour Party - more on their thoughts re Libya and the Arab revolutions here (in French).

cells, cells, cells

2011-04-18T06:41:00.000-07:00

There are now three competing approaches to regenerative medicine: embryonic stem cells, induced pluripotent cells, and transdifferentiated cells. In my latest feature article, out in last week's issue of Current Biology, I explored these three options and discussed the implications for medicine and society.

Since writing this piece, one notable side effect occurred to me that I hadn't thought of: the approach of "therapeutic cloning," much debated in around 2004-05, has completely disappeared from the agenda, now that there are options that are both easier and less problematic at the bioethics front.

Regenerative medicine spoilt for choice
Current Biology, Volume 21, Issue 7, R235-R237, 12 April 2011
doi:10.1016/j.cub.2011.03.062

Summary and restricted access to pdf file

"exceptional" fees

2011-04-08T02:38:00.000-07:00

both Oxford University and the former polytechnic, Oxford Brookes University have now announced that they will charge tuition fees of £9000 per year, the value introduced by government as an "exceptional" option, while most universities were expected to charge "up to" £6000, i.e. £6000 exactly. Over 30 other universities have also announced the £9k charge (listed here). Even the lowest-ranked university of all has announced a fee of £8450, well clear of what was supposed to be the standard.

Now I do understand that the universities feel they can't carry on without the exceptional fees, seeing the government is pulling the funding rug out underneath their feet. But in my limitless naivete, I would have hoped that instead of rushing to milk the students, the universities might have united in protest and made it clear to the government that they can't do their job of offering education to the people if they aren't getting proper (state) funding for it. I have a dream ...

chemistry all around the world

2011-04-06T13:30:00.000-07:00

The round-up of German pieces published this month includes a clever application of llama antibodies, celebrations of the International Year of Chemistry circling the globe, and debates over the circling of the square story from last autumn.

Streit um die Quadratur des Kohlenstoffs
Chemie in unserer Zeit 45, 82

In 80 Feiern um die Welt
Nachrichten aus der Chemie 59, 403

Mini-Antikörper für Maxi-Effekt
Nachrichten aus der Chemie 59, 435-6

I see a rainbow rising

2011-04-05T01:09:00.000-07:00

The unforgiving

Within Temptation

I’ve followed WT since The heart of everything, and love the Black Symphony recording to bits. But what might they do after something as dazzling as BS? The new album left me confused at first. I loved the sound from the beginning, but just couldn’t place it. Plus, I didn’t quite know what to make of the expanded videoclips (which they somewhat grandiosely call “movies”), where a figure called Mother Maiden brings people back from the dead to “put wrongs right”. I wasn’t sure I actually needed that. While I like the dark moods underlying much of their work, I don’t have to have it spelt out who killed whom and why. There’s enough darkness to go round for all, anyway.

Then, suddenly, it all fell into place. Listening to the track no. 6, Iron, for something like the 27th time, I realised that Mother Maiden had accidentally resurrected Ronnie James Dio, and the band now aimed at reviving the elegiac anthem sound produced by Rainbow when Dio was their singer (I actually saw them live, back in the last century!) . And guess what, it works amazingly well. Other tracks with Rainbowesque qualities include Iron, Where is the edge, and A demon’s fate – well I guess if I were to analyse it in detail, it would be most of the album.

I’m firmly expecting a holographic rainbow rising above the stage on their next tour. But it’s all good, I still love the album, even though the Rainbow memories now make me chuckle at times.

amazon.co.uk

PS: the short video of the first single, "Faster" is here - this one also comes with a Rainbowesque chorus.

Temple Grandin

2011-04-04T02:21:00.000-07:00

trailer of the Temple Grandin biopic, which was shown on UK satellite TV yesterday (and I missed it):

Grandin is a household name for everyone involved with autism, following her memoir Emergence: Labeled Autistic, published in the 90s, but I guess it is a good thing to bring this remarkable life story to a wider audience, which will help raise awareness of autism as well.

There was a feature about Claire Danes, who plays Grandin in the film, in last Saturday's Guardian, which also contained some info about the film and Grandin's story.

chemistry landmark

2011-04-03T13:37:00.000-07:00

I just spotted this weekend that the Inorganic Chemistry Laboratory in South Parks Road has acquired a second plaque. The first one honoured the work of crystallographer Dorothy Hodgkin, and the new one some discovery that led to today's lithium batteries:

The date on the plaque is when it was handed over to the department (see a short news release here, but I'm quite sure it hasn't been mounted on that wall for longer than two weeks when I spotted it this weekend. I love the hexagonal design of the new plaques. Places that get several of these will be able to create interesting polycyclic compounds from them ...

Now if somebody could find out why the lithium battery in my camera, only two years old, only lasts one day (80 photos), that would be very helpful.

dot the i

2011-04-02T13:14:00.000-07:00

In my rapidly growing collection of films that did not get a cinema release in the UK although they are perfectly nice, this is one of the more puzzling examples. It was made in the UK, with support from the British Film Council (now being axed), and with dialogues completely in English. All nipples are duly covered up, as Carmen’s bra stays on even during passionate encounters. And apparently the film made a favourable impression at festivals including Sundance. The case against a release, I presume, was that the two lead actors, Gael Garcia Bernal and Natalia Verbeke, are relatively unknown here, and/or the fact that someone gets away with a serious crime. Take your pick.

What UK cinema goers missed out on is not so much a thriller (I never really feared for the well-being of the protagonist), but a nice little film about the disappearance of privacy in a world were cameras are cheap and plentiful, and where electronically enhanced voyeurism has become normal. Trust nobody, the take home message seems to be.

I’m wondering what the version shown in cinemas in Spain was like, seeing that Mexican Garcia Bernal has to pretend being Brazilian in order to justify that he isn’t speaking Spanish with the Madrid girl played by Verbeke. (Which still doesn’t justify the present of a Garcia Marquez novel in English translation! Aaaarrrrgggghhhh!) I wonder how the Spaniards got out of this language dilemma, and whether they got the actors to do their own dubbing.

I think it might actually be worth getting a DVD from the continent, as this UK edition has no bonus features whatsoever, just the inescapable anti-piracy ad and a couple of trailers.

amazon.co.uk

oddbins run dry

2011-04-01T08:35:00.000-07:00

the Guardian reports it's the end of the road for mildly eccentric wine merchants chain OddBins, which happens to be my age. I loved their crazy catalogue graphics and used to buy my Havana Club (Cuban rum) from there, but I have to say that at least in the last three years, when I did some exploratory wine shopping, they never had any Cotes du Rhone bottles that might have tempted me. I mostly ended up importing them from the continent or buying them at M&S.

Just recently, I picked up brochure called "Oddyssey" from one of the branches (we have three within easy cycling distance), which relates the intriguing history of the chain, now looking certain to be coming to an end.

Here is a photo of the branch on Oxford's High Street,taken just a few days ago:

PS Possibly one of the last bottles they sold before going into administration arrived at my house just yesterday, it was the prize for spotting the odd book title that won the Diagram Prize.

Nicole's second debut

2011-03-24T04:55:00.000-07:00

Killer love - Nicole Scherzinger

I loved the video releases Heartbeat and Don’t hold your breath (not to mention the first PCD album and all 7 videos from it), so I came to this album with high expectations. It didn’t quite live up to my hopes, but it’s been growing on me after repeated listening. Like the title track and the other single, Poison, both co-written by Nicole, as is Everybody.

The big revelation of the album is the final track, AmenJena, which she co-wrote with Trina Harmon, who is referenced in the acknowledgements as “my teacher and friend.” She recorded this with Harmon playing the piano as the only accompaniment. Finally we get to appreciate Nicole’s voice … Now I have an idea: could the two of them get together and record an unplugged album with the best of PCD and from this album? That could be truly spectacular.

amazon.co.uk

PS: What really annoyed me is the sticky label on the box, saying “Debut solo album from …” Some of us remember that there was a debut solo album called “Her name is Nicole,” which got delayed several times and then disappeared from the radar. I wish record companies were honest about this kind of thing.

It's my turn to speak

2011-03-23T08:06:00.000-07:00

review of

Swallow
by Sefi Atta
Interlink books 2010

The book opens with a dialogue between two friends on the bus, on their way to work, after narrowly escaping a possible accident. Rose talks a lot, and preferably about what her friend Tolani should do with her life and her boyfriend, while Tolani herself only gives laconic replies. Both face an uphill struggle trying to survive in the chaotic metropolis of Lagos, Nigeria, in a society dominated by men who tend to be unreliable, molesting, or even criminal.

Tolani doesn’t appear to be very good at getting her way through dialogue, even though there is a lot of it going on. Somehow, it never goes her way, and she always ends up swallowing her pride. Her employers kick her around, her useless boyfriend squanders her savings, her mother tells her everything except what she needs to know, and her friend Rose signs the pair of them up for a trip as drug mules, which, again, requires Tolani to swallow her pride, not to mention a condom filled with cocaine.

With its colourful representation of everyday life in Nigeria, this short novel (like Atta’s debut, Everything good will come) is very engaging - at least in the short term, for 10 or 20 pages. I especially enjoyed the swipes at us western people (“oyinbo” seems to be the Yoruba equivalent to “gringo”), such as: “… oyinbos write theories about things they can’t understand, and by the time they finish, you can’t understand either, even if they’re writing about you.” (p. 167) However, given the very slow pace of the progress our heroine makes, the reading experience is also a little bit frustrating in the longer term. This may very well be intentional, reflecting the frustration that this woman suffers every day. (Atta's debut novel was a coming of age story, so there naturally was a bit more of direction to it.) Only in the very last paragraph she seems to have picked herself up. “It’s my turn to speak,” she says. About time, too.

amazon.co.uk

data deluge

2011-03-22T02:52:00.000-07:00

As I may have mentioned before, advances in genome sequencing are moving faster than those in computing (still following Moore's law, i.e. doubling capacity every 18 months or so). In the long term, of course, this means that scientists are going to produce more data than they can store or handle. Similar problems also arise in other fields e.g. neuroscience.

I've written a feature on the data deluge and how biologists are hoping to cope with it for Current Biology, which is out today:

Riding the wave of biological data
Current Biology, Volume 21, Issue 6, R204-R206, 22 March 2011
doi:10.1016/j.cub.2011.03.009

summary and restricted access to PDF file

One of the sources of the data flood: second generation genome sequencing machines at the Wellcome Trust Centre for Human Genetics, Oxford.

origin of life revisited

2011-03-21T13:19:00.000-07:00

Origin of life researcher Jeffrey Bada and his team have analysed a set of old samples inherited from Stanley Miller. It was the first simulation of origin of life conditions to include sulphur, yet Miller never reported results. With modern methods, Bada's group show he missed out on something interesting.

Read my news story in Chemistry World (open access).

faster

2011-03-18T10:07:00.000-07:00

Friday Video:

Within Temptation's new release Faster, from the album "The Unforgiving", out in Germany next Friday, 25.3.

Here in the UK we have to wait till Monday ...

march for the alternative

2011-03-17T09:30:00.000-07:00

metropolitan police are expecting guests next week, I'm sure they are putting the kettle on ...

But seriously, it's important to keep the protests going, this government needs strong opposition, or else it will wreck the country in no time.

PS Speaking of which, welcome back to Science is Vital, the movement against research spending cuts.

how volunteers help science

2011-03-16T07:51:00.000-07:00

Tomorrow's Earthwatch lecture:

Many hands, new knowledge: The value of citizen science
Thursday 17 March, 7pm (doors 6pm, event end 8.30pm)
Royal Geographical Society, 1 Kensington Gore, London, SW7 2AR

focuses on the breadth of tasks that volunteers can perform to help field science.

Chris Newman from Oxford's WildCRU (wildlife conservation research unit) will talk about the volunteer experience on the mammalian ecology projects in Wytham Woods and in Nova Scotia. William Megill will explain the challenges of observing whales and sea turtles in the Pacific Ocean, where both robots and volunteers come in handy.

More details and free tickets here.

PS a related BBC news story is here

jewish prayer

2011-03-13T14:29:00.000-07:00

Cellist Sonia Wieder-Atherton performs her "Jewish prayers" at the Kings Place, London, next Thursday. Here's a taster:

She also appears, with different programmes, on Friday and Saturday, details are here.

Genghis Khan's winning ways

2011-03-10T01:18:00.001-08:00

I’m so excited – just found out I’m in the shortlist for a literary prize. Well, errr, a book title that I suggested for the Diagram Prize (oddest book title of the year) is on the shortlist: Managing a Dental Practice the Genghis Khan Way. And last time I checked the online votes, it was leading by a large margin. [Update 28.3.: turns out Genghis Khan and I actually won the award! Woo hooooo!]

Still haven’t checked with my dentist whether she’s following this approach. We should be told.

The six titles on the shortlist are:

8th International Friction Stir Welding Symposium Proceedings
Various authors (TWI)
The Generosity of the Dead
Graciela Nowenstein (Ashgate)
The Italian's One-night Love Child
Cathy Williams (Mills & Boon)
Managing a Dental Practice the Genghis Khan Way
Michael R Young (Radcliffe)
Myth of the Social Volcano
Martin King Whyte (Stanford University Press)
What Color Is Your Dog?
Joel Silverman (Kennel Club)

I love the last one, actually, as it shows how you can achieve absurdity with very simple means, without using a single unusual word.

A collection of 50 book covers from the shortlists of the first 30 years of the prize was published in 2008: How to Avoid Huge Ships: And Other Implausibly Titled Books. Sadly my personal favourite "Procrastination and task avoidance, a practical guide" (shortlisted some time in the late 90s) isn't included.

Recently, oddity lovers in Germany have also set up a prize: Kuriosester Buchtitel. With my most recent title “9 Millionen Fahrräder am Rande des Universums,” I might be at risk of getting nominated. Which would be ironic and nicely circular, as the original Diagram Prize is covered in one of the chapters, greek rural postmen and all.

PS I don't think I own a single book from the Diagram shortlists. Maybe I should get this one, it got glowing reviews at amazon:

amazon.co.uk

20 años de Ecos

2011-03-09T01:46:00.000-08:00

Ecos de España y Latinoamérica, the magazine for learning Spanish, is 20 years old this month (as is a member of my family). Funny that. I've already praised the magazine here, so I'll just add "many happy returns" to that. Our household does in fact have a subscription at the moment, so long may it prosper.

Ecos Online

PS in other Latinamerican news, biochemist Alberto Granado, Che Guevara's travelling companion of Motorcycle Diaries fame, has died aged 88. There is an interesting obituary in the Guardian

fairtrade fortnight

2011-03-07T01:47:00.001-08:00

In the UK, fairtrade organisations are celebrating fairtrade fortnight (28.2.-13.3.), so I rounded up some of the fairtrade products I use regularly - turned out to be all coffee, chocolate, tee. There weren't any fairtrade fruit around at the moment, and I forgot to include the orange juice (fruit passion):