Wednesday, June 30, 2010

science drives the plot

review of:

Experimental heart
By Jennifer L. Rohn
Cold Spring Harbor Laboratory Press 2009


Jennifer Rohn is famous for promoting the idea that we need more fiction with realistic scientists in leading roles, via her website lablit.com, and other outlets including Nature. In an effort to practice what she preaches, she has written a couple of “lablit” novels herself, of which Experimental heart is the debut effort.

As the “lablit” label suggests, the lab, located in an academic research centre in London, and the science conducted there (and in a small biotech company next door) play very important parts in the novel. It’s not just that the ambitions of a slightly mad scientist drive the plot, the scientific agenda also shapes the encounters of the characters, and science metaphors colour their speech and indeed the voice of the narrator.

I was wondering in the beginning why the author has chosen to slip into the skin of a male narrator, post-doc Andy O’Hara, but it soon becomes clear that he is the central atom entirely surrounded by a coordination sphere of intriguing females, including five scientists and his mother. I’m beginning to suspect that the name of the local pub where some of the events unfold, King Henry VIII., may have something to do with this bouquet of six women.

Not surprisingly, hard-working Andy is quite confused by the various attractive forces acting in this coordination sphere and it takes him 360 pages to figure it out and get all the bond lengths and angles right. In comparison, the thriller sub-plot with the mad scientist comes relatively easy to him, as he can use scientific methods and straightforward experiments to work out what is going on there.

To me, as someone who has grown up, lived, and worked in the science culture that this story is set in, the whole thing feels completely like home – sometimes even too close for comfort. The lab part aside, the lit part is also very nicely done, written fluently and convincingly, though not letting the style get in the way of the science.

Whether it works equally well for people who have never heard of Taq polymerase or transcription factors is another matter, and I wouldn’t be able to tell. I would imagine that avid readers of crime novels, who like to exercise their grey matter while reading, may be up to the task of following the science plot, while others may find it too much work. My guess would be that most of the readers who enjoy and finish the novel will be scientists (which is also the case for my books, so no criticism), but hey, if it gives us the feeling that we could be the heroes of fictional (but realistic) adventures, that’s a good thing, too.

I am certainly looking forward to the second novel, due out this autumn.



PS,the single lit window, as shown on the cover, is a recurring motif ...

Tuesday, June 29, 2010

a house and a family

The trend this summer seems to be to publish a book about the house you live in. Bill Bryson tried it, but I’ve read mostly bad reviews about his attempt to make the history of the world revolve around his Norfolk rectory.

Now Charlotte Moore, known to people in the UK interested in autism as the author of the Guardian column “Mind the gap” and the book George and Sam about her two eponymous sons with autism (she also has a son without), has a new book coming out on Thursday (1.7.):



Hancox: A house and a family. (Viking / Penguin 2010)

Judging by the snippet that appeared in the Guardian this weekend (All under one roof), I find it a lot more promising than the Bryson book. Her house has been in the family since 1888, and its inhabitants seem to have the genetic disposition to keep things, especially everything that has any kind of writing on it. (At that point I was beginning to wonder whether that phenotype is actually linked to the autism genes, or whether the author is a long-lost relative of ours.)

So using the documents and other memorabilia that her relatives have stashed away in the house for 120+ years, she traced the history of both house and family. I’m really looking forward to reading it. Maybe I can get a review copy ?

PS just discovered, there's also an appreciation of the place by her brother in the Observer: Hancox: so much more than just my home and a photo gallery.

Monday, June 28, 2010

shakira at glastonbury

... haven't found any good video, but here's a nice photo from ShakiraMedia.com:



With her playing in broad daylight and the rather undefined setting, where you can never tell which people are actually listening and which ones are just standing around in a field, I thought it looked more like a dress rehearsal for the upcoming tour.

Thursday, June 24, 2010

neanderthal debate

Also in this week's issue of Current Biology (apart from those 3 pieces by me) is an interesting dispatch on the Neanderthal genome, raising the issue that our insufficient understanding of genetic diversity within sub-Saharan Africa may mean there are other explanations for the genome results than those favoured by Pääbo et al.

Essentially, if African diversity was already geographically segregated at the time the Neanderthals migrated towards Europe, their similarity could simply mean that they derived from the same sub-group of Africans as the later Homo sapiens migrants that settled the rest of the world. If I understand it correctly, this would mean however, that the genetic differences within Africa should be as large as those between modern humans and Neanderthals, which is not what has been observed.

The authors also offer a more complicated model, involving human emigration from Africa, mixing with Neanderthals, return to Africa, and then emigrating again, which in my eyes falls victim to Ockham's razor, as it is needlessly complicated.

But anyhow, I agree that one should sequence a lot more African genomes, seeing that most of human diversity is between Africans, not between the groups wrongly labelled as "races".


Reference:

Neandertal Genome: The Ins and Outs of African Genetic Diversity
Jason A. Hodgson, Christina M. Bergey and Todd R. Disotell

Current Biology, Volume 20, Issue 12, R517-R519, 22 June 2010

summary and link to pdf file

Wednesday, June 23, 2010

first cannabis prescription drug hits the market

I'm very pleased to hear that the cannabis based pharmaceutical Sativex is being launched on the UK market now, after 11 years in the pipeline. I covered its early promise in this Current Biology piece in 2001, but haven't followed its progress in recent years.

Sativex® (as in C. sativa, and not Savitex, as the Guardian called it) is an oromucosal spray for the treatment of spasticity in patients with multiple sclerosis. Sativex contains two cannabinoids as active ingredients - THC (delta-9-tetrahydrocannabinol) and CBD (cannabidiol). It is the first cannabinoid medicine derived from whole plant extracts from the Cannabis sativa plant. The company expects Sativex to be approved in Spain shortly. Further submissions will be made in additional European countries during the second half of 2010 under the mutual recognition procedure.

At a price tag of 11 pounds per day, one does have to wonder, though, if allowing patients to grow their own might have been a more affordable solution ...



(photo: GW Pharmaceuticals)

Tuesday, June 22, 2010

biodiversity in focus

Today's issue of Current Biology has a special news focus on biodiversity, which includes an exceptional three contributions from me:

Tiger in the bank R495
Michael Gross
(re. the debate whether tiger conservation efforts are failing)
summary and restricted access to pdf file

Missed targets R496
Michael Gross, Nigel Williams
(re. the UN's recent biodiversity report)
summary and restricted access to pdf file

Forest alliance R497
Michael Gross
(re. rainforest research and conservation in Borneo)
summary and restricted access to pdf file



Borneo - photo by Jen Alger

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Monday, June 21, 2010

insect-plant interactions

I'm studying insect-plant interactions, or stalking bumblebees, and gradually getting better at photographing them. Found out that there is no need to climb into trees, as there is plenty of bumblebee-friendly stuff in the front gardens up and down the road. Which also made me realise that having an area with lots of very small gardens is good for biodiversity, as everybody has different preferences in what they plant (or allows to grow) in their garden.






(as always, click the images to see the large version - and a lot more detail on the bumblebees)

Also acquired an identification guide which is very handy, it's the
Field Guide to the Bumblebees of Great Britain and Ireland
by Mike Edwards and Martin Jenner
(Paperback - Sep 2009)
so I'm learning to read those colourful bar codes, although I understand that in some cases there are several possibilities. (These ambiguous cases, the authors assure me, can easily be distinguished by a closer look at the genitalia. But maybe I'll just live with the uncertainty!)

PS These and a few more of my recent photos can now also be found on flickr.

PPS A full-page article on bee research has appeared in the Guardian:
Bee decline could be down to chemical cocktail interfering with brains

Sunday, June 20, 2010

sale el sol

Update 3.9.2010 The album "Sale el sol" is now due to be released in October, here's the announcement from the official blog:


We're very pleased to report that Shakira will release her brand new album, Sale el Sol/The Sun Comes Out, on October 19th.
The album will feature Shakira's record-breaking global hit "Waka Waka (This Time For Africa)", as well as a new single "Loca". Recorded in the Dominican Republic, “Loca” is Shakira’s interpretation of Dominican artist El Cata’s song “Loca Con Su Tiguere". You can hear the Spanish version of the track, above. There will also be an English version, featuring a guest appearance from Dizzee Rascal, the UK's number one rapper.
Read more: http://blogs.myspace.com/index.cfm?fuseaction=blog.view&friendId=7490990&blogId=538767380#ixzz0yTKKLqVz


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

A weekend video to match both the weather and the fact that Shakira is due to play Glastonbury next weekend (Pyramid stage Sat. 18:45, but I don't have a ticket, will have to make do with TV/online). This one is from the recent "Rock in Rio" festival confusingly held in Madrid:



Thanks to Yami for the hint.

Friday, June 18, 2010

new finds from Dyson Perrins Laboratory

Back in the days when I worked at the New Chemistry Laboratory here, the building next door was the Dyson Perrins Laboratory (or DP), which was the codename for organic chemistry. When a new research lab was completed across the road, the chemists moved out, and some other departments moved in, including the Research Laboratory for Archaeology and the History of Art, which I always find sounds very interesting when I walk past it.

Now these guys have a paper out in today's issue of Science re. the carbon-dating of plant materials associated with specific phases Egyptian history. Here's the advance PR from Science magazine:

Nailing Down Ancient Egypt's Chronology:
For several thousands of years, ancient Egypt dominated the Mediterranean world--and scholars have busied themselves documenting the reigns of the various rulers of the Old, Middle and New Kingdoms. However, although the resulting chronologies have been quite precise in a relative way, assigning absolute dates to specific events has been a contentious task. Now, a detailed radiocarbon analysis of short-lived plant remains from the region is providing scientists with a long and accurate chronology of ancient Egypt that agrees with most previous estimates but also imposes some historic revisions. Christopher Bronk Ramsey and a team of international researchers collected radiocarbon measurements from 211 various plants, obtained from museum collections in the form of seeds, baskets, textiles, plant stems, and fruits, that were directly associated with particular reigns of ancient Egyptian kings. The researchers then combined this radiocarbon data with historical information abou t the order and length of each king's reign to make a complete chronology of ancient Egyptian dynasties. Their new chronology indicates that some events occurred earlier than predicted. It suggests, for example, that the reign of Djoser in the Old Kingdom actually started between 2691 and 2625 B.C. and that the New Kingdom began between 1570 and 1544 B.C. Bronk Ramsey and his colleagues found some discrepancies in the radiocarbon levels of the Nile Valley but suggest that it is due to ancient Egypt's unusual growing season, which is concentrated in the winter months.

Reference
"Radiocarbon-Based Chronology for Dynastic Egypt,"
C. Bronk Ramsey et al., Science 2010, 328, 1554.

Here's the old DP reflected in the new chemistry research building:



and here's the plaque commemorating its history:

Thursday, June 17, 2010

book reviews collection at amazon

It's taken me a while to sort out the tedious bits (I had forgotten the copyright page and had to re-publish), but now my book reviews collection

The noughties brought to book

has arrived at Amazon.com, and can be ordered here. Update: As of 1.7.2010, it is now also available from amazon.co.uk and amazon.de.

One can also order it directly from Lulu.com, but that may end up being more expensive, as they don't normally do free shipping.

Support independent publishing: Buy this book on Lulu.


Wednesday, June 16, 2010

finding the sculpture inside the tree

Last week I had a very interesting chat with a local artist, Dominique Lussier, who showed me some of the sculptures he's produced from wood, which he gets locally from tree surgeons. So branches cut off from people's cherry trees might turn into something like this:



(untitled - photo courtesy of the artist)

He very much works with the natural grain and structures of the wood, which often results in a mixture of abstract and human or animal forms, or a combination of art and nature, so to speak.

I really like the work, and the way he interprets the natural fabric of the wood (or liberates the sculpture inside, as Michelangelo famously said), my only problem is I don't have space to put up a sculpture. Oxford Colleges have a bit more space, so you can admire some of his work at Keble (in the Sloane Robinson Building) and at Wolfson.

Tuesday, June 15, 2010

bumblebee biodiversity in the backyard

I've written quite a few pieces about colony losses in honey bees (Apis mellifera), but have to admit I didn't really know who's doing all the pollinating work in my own small garden. This weekend, after noticing one of the trees being visited by lots of insects, I took my camera and had a closer look. I think I have spotted four different species (not counting flies). All identifications below are tentative, so any helpful hints appreciated:


I think this could be a Bombus terrestris, or buff-tailed bumblebee ?


Love the orange neck-scarf on this one, think it might be Bombus hypnorum, which apparently only arrived in the UK in 2001 (according to Bumblebee Conservation Trust)?



Don't recall seeing its rear end, but if it's reddish, it might be a red-tailed bumblebee (Bombus lapidarius) ? I've definitely seen one of those elsewhere in Oxford.


I think this one is an ordinary European honey bee Apis mellifera - we may be in reach of the colony housed in the Oxford University Museum.

Monday, June 14, 2010

astrobiology news

Lots of news at the astrobiology front.

The CoRoT probe has reported half a dozen new planets (Oxford University press release). More on this later.

News from exoplanet Beta pictoris b (BBC news).

Martian ocean continues to make waves (although I'm not sure that 30 cubic miles justify the use of the word "ocean" - I think that's just over twice the size of Lake Constance, which has 55 cubic km). Anyhow - Guardian report

And there may be evidence for life on Titan!

Oh, and it is probably safe to reveal now that at some point next year there will be a second edition of "Astrobiology: a brief introduction" by Kevin Plaxco and myself. More details to follow in due course.

Saturday, June 12, 2010

live the dream

a special birthday post for a faithful reader and blogging friend:



have a good one and may your wildest dreams come true ...

PS: I was going to post the original video, but within the last 3 days they have blocked the embedding, but you can watch it here.

Friday, June 11, 2010

one goal

there will be absolutely no football coverage on this blog, but here is one goal I can relate to:



You can join 1goal here or follow their tweets.

PS - I pinched the photo from Wendy's blog.

PPS: While I'm at it, I'll also throw in a video of Shakira's appearance at the opening ceremony:

Thursday, June 10, 2010

copy number counts in autism

I recently wrote a news item for the Wellcome Trust Centre for Human Genetics, about the genetic work done on autism:

Autism genes: combinations and copy numbers

This work is mainly about finding out which genetic variants are truly linked to autism and which not. While many such associations have been reported, there is a great deal of uncertainty regarding which of these are really important for a significant number of cases.

What I also learned during my research for this piece is that copy number variations, e.g. gene duplications or deletion of duplicate copies, are now regarded as an important factor in autism genetics. As it happens, the WTCHG has another paper out in Nature online today dealing with the impact of CNVs in autism:

Functional impact of global rare copy number variation in autism spectrum disorders
D. Pinto et al., Nature (2010) doi:10.1038/nature09146 Published online 09 June 2010


For my previous pieces on autism research, click here.



photo: NHG

Wednesday, June 09, 2010

bhopal - the disaster continues

Following on from my earlier rant re. the 25th anniversary of the Bhopal disaster, there is further depressing news about this in yesterday's Guardian. A trial has come to an end but the disaster continues.

Seven convicted over 1984 Bhopal gas disaster (news report re. the outcome of the trial)

Editorial including an enlightening comparison with the current BP disaster.

Comment by Indra Sinh who says: "The people most responsible for the disaster in Bhopal were not in the courtroom today when the verdict against eight Indian employees of Union Carbide India Limited was announced."

Tuesday, June 08, 2010

drug delivery

My review of the textbook

The physicochemical basis of pharmaceuticals
Humphrey Moynihan, Abina Crean
Oxford University Press 2009

is out in this week's issue of Chemistry & Industry (should turn up here very soon). Found the book very readable and interesting, so the review is broadly a recommendation.

Here's a snippet:

The authors focus on the well-established drugs and delivery routes, so they are mainly concerned with organic molecules, using classical drugs like aspirin, paracetamol, and ibuprofen as examples, and creams, pills, injections, etc. as the standard delivery methods. [...] the book is very good at delivering exactly what it says on the cover, namely giving students a physicochemical basis for understanding the formulation of pharmaceuticals.

Monday, June 07, 2010

blue river

The river Cherwell as it appeared after a late shift at the library:

 





 



PS I uploaded a larger version of the photo to fotocommunity.

Saturday, June 05, 2010

german pieces in June

exoplanets, synthetic fuels, ESR spectroscopy, and the double life of Dicer, it's all in a month's output:

Astrochemie: Chemie ferner Planeten
Chemie in unserer Zeit vol 44, No. 3, p. 166-167

Biochemie: Häcksler bekommt Nebenjob
Chemie in unserer Zeit vol 44, No. 3, p. 171

Ausgeforscht Traumreisen in ferne Welten
Nachrichten aus der Chemie vol 58, No. 6, p.633

Kraftstoffe Fischer-Tropsch-Synthese: Wiederkehr im grünen Gewand
Nachrichten aus der Chemie vol 58, No. 6, p.653

Blickpunkt Biowissenschaften ESR-Spektroskopie: Was der Spin verrät
Nachrichten aus der Chemie vol 58, No. 6, p.659

Friday, June 04, 2010

lablit up and coming?

Jennifer Rohn writes in the current issue of Nature that lablit (i.e. realistic novels with scientists as central characters shown to engage in scientific research) appears to experience a boom, with an increasing number of lablit novels being published every year since around 1990.

Come to think of it, I haven't read all that many books that fit her definition. Off the cuff, I can remember:

Carl Djerassi: Cantor's Dilemma (which also got Rohn interested in this)
Carl Sagan: Contact
Daniel Kehlmann: Measuring the world


Missing from the LabLit list is German author Karl Aloys Schenzinger who is a pioneer of the genre:

Anilin. Roman eines Farbstoffes (1936)
Metall (1939)
Atom (1950)
Schnelldampfer (1951)
Bei I.G. Farben (1951)


but who is somewhat discredited by being also the author of Hitlerjunge Quex (1932), a novel glorifying the Nazi youth organisation.


An Austrian refugee working in Canada, Charles Wassermann (1924-78) novelised the discovery of insulin in the book:

Insulin (1966)


Also missing is Jules Verne. Looking up by topics, one can find loads of novels about scientists, eg about Kepler the German wikipedia entry lists:
Rosemarie Schuder: Der Sohn der Hexe – In der Mühle des Teufels. Berlin: Rütten & Loening 1968
Wilhelm und Helga Strube: Kepler und der General. Berlin: Neues Leben 1985
Johannes Tralow: Kepler und der Kaiser. Berlin: Verlag der Nation 1961



As for the reasons for the increase over the last 20 years, I reckon that Djerassi's success with Cantor's dilemma may have triggered something like a chain reaction.

On second thoughts, the graph shown in Nature would also be compatible with the interpretation that lablit novels decay with a half life of 10 years.

PS Many years ago I read a book that comprehensively analyses the image of scientists in literature - I vaguely remember I found it quite inspiring at the time (need to read it again at some point). That's "From Faust to Strangelove" by Roslynn Haynes, Johns Hopkins University Press 1994 (Paperback 1995)

Thursday, June 03, 2010

parisian memories part 1

a la recherche du temps perdu ... collecting up some memories of various cities I have visited more than once, starting off with

PARIS

1. Just walking through

During the first 20 years of my life, I spent probably more than 10% of my time in northern France, but never got to see much of Paris. By age 20, I had seen all the “big six” gothic cathedrals of the north, except Notre Dame de Paris. Lille, where my aunt used to live, was the biggest city we went to, and even there my parents managed to get lost every time.

I think I once went to Paris as a child accompanying my cousin who had some business to attend there, but can’t remember seeing any of the city’s attractions (my only memory is of a side road with a door where my cousin rang to deliver something, maybe there was a postal strike).

At 17 I went hitchhiking / camping with a gang of 7 along the Atlantic coast, from Saint-Jean-de-Monts (near Nantes) down to Soulac-sur-Mer (near Bordeaux). Love the Atlantic coast, it’s the only place in France where you get a proper ocean with proper waves, the southern part of the coast is a popular destination for surfers. I travelled back alone to stop by at my aunt’s place at Lille. I spent a day hitchhiking back up from Soulac to Nantes, then took the night train from Nantes to Paris (Montparnasse, I guess). With my trademark unwarranted optimism, I assumed I would be able to sleep on the train, but ended up having just enough space to crouch down outside the toilet door, so I arrived in Paris in less than perfect condition at some ridiculous time like 5 am. As I was travelling on an extremely small budget and there wasn’t any particular hurry, I decided to walk across Paris to the Gare du Nord to catch a train to Lille from there.

After all these years I still remember some glimpses I had while walking across the city with 18kg of luggage including a tent on my back (I know this number for certain because I weighed it when I arrived!). It was great fun watching the city wake up and rub the sleep from its collective eyes, market traders setting up their stalls, bin men doing their rounds very early such as not to hold up the traffic too much. So on that occasion I saw more of Paris than in my lifetime before and in quite a few years after, and I enjoyed it greatly. What I also remember of that trip is that on the train to Lille (that being before the times of TGV, it would have taken three hours or so) the conductor had to shake me to wake me up when he wanted to see my ticket. Oh, and just for the heck of it, I walked the 4 km from Lille station to my aunt’s place as well (and, unlike some people I know, I didn’t lose my way).

... a suivre ...

Wednesday, June 02, 2010

elephants in london

On a trip to London this week I found out that lots of elephants are out and about in the capital, advertising the charity Elephant Family. Apparently, there are 258 of them, all different designs. Here are a few of the dozen or so that we saw:









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