Friday, July 31, 2009

plastic electrodes plugged into brain

Among this week's Advanced Materials Early View there is a paper on using polymer electrodes to establish permanent electronic contact with living brain cells. The authors claim the quality of neuronal recording with their device is better than with conventional metal electrodes. This sounds very promising to me, both in terms of restoring function to people with nerve damage, and also with regard to sci-fi style brain-machine interfaces. As I've said before, the boundaries between electronic and biological systems are disappearing.


Interfacing Conducting Polymer Nanotubes with the Central Nervous System: Chronic Neural Recording using Poly(3,4-ethylenedioxythiophene) Nanotubes
Mohammad Reza Abidian, Kip A. Ludwig, Timothy C. Marzullo, David C. Martin, Daryl R. Kipke
Published Online: Jul 29 2009 9:30AM
DOI: 10.1002/adma.200900887

Thursday, July 30, 2009

ocean mixing by jellyfish

I love the ocean-mixing paper in today's issue of Nature (and on the cover). Essentially, researchers believe that turbulence created by fish swimming around doesn't do much for ocean mixing (as it's limited to small scale and gets lost in friction), but the authors find evidence for surprisingly large mixing effects simply from the layers of water that a swimming organism drags along (details depending on its shape, and the viscosity of the water).

This mechanism was first considered in 1953 by the grandson of Charles Darwin, who is confusingly also called Charles Darwin (the authors of the Nature paper never bother to tell us that it is not the Darwin they are talking about!).

Understanding ocean mixing is especially important today in the context of climate change, as the oceans have a much higher heat capacity than the atmosphere. They also store more carbon, and are instrumental in natural processes of carbon sequestration (e.g. calcite sediments).

Im just a bit worried what creationists will make of this story. Soon they will be telling us that the big bearded guy put jellyfish in the oceans to ensure proper mixing ...


Kakani Katija & John O. Dabiri
A viscosity-enhanced mechanism for biogenic ocean mixing
Nature 460, 624-626 (30 July 2009) | doi:10.1038/nature08207

News & Views by William Dewar on page 581

Wednesday, July 29, 2009

aptamers guide chemotherapy

Aptamers are single-stranded DNA (or RNA) molecules selected from millions of possible sequences for their aptitude to bind a specific target. Developed originally as an alternative to antibodies for biotech applications, they have recently found application in sensors and in the treatment of age-related macular degeneration.

Researchers have now very cleverly combined liposome packaging and aptamer targeting to direct chemotherapy (e.g. cisplatin) to tumour cells (e.g. breast cancer). All the known advantages of DNA aptamers apply (non immunogenic, easier to produce and handle than antibodies), and on top of that one gets the chance to call back the attack if it goes wrong, by injecting antisense DNA.

Read my story in Chemistry World (free access to all).

Earlier pieces about aptamers include Chemical Origami (Chem. World 2006, restricted), as well as a chapter in The birds, the bees and the platypuses. I've also reviewed a book about aptamers, review should appear soon.

Tuesday, July 28, 2009

climate change special

Today's issue of Current Biology is a special issue on "Biology and Climate Change", and very exceptionally I have two pieces back to back in the magazine section at the front.

First there is a news feature on climate change policies and debates in the US, UK, China, and Germany ahead of the climate change summit in Copenhagen:

Climate crunch year
As countries around the world prepare for the crucial climate change conference in December, China tries to boost its green investment, Germany debates the pros and cons of carbon sequestration, the US debate a groundbreaking energy bill, and the UK counts the cost of mitigating climate change in the developing world.
Current Biology, Volume 19, Issue 14, R537-R539, 28 July 2009
PDF file (restricted access)

The second is about an Earthwatch industry partnership to investigate how mangroves in Kenya can help mitigate the effects of climate change:

At the frontline
Mangroves are at the frontline in the fight against the consequences of climate change.
Current Biology, Volume 19, Issue 14, R539-R540, 28 July 2009
PDF file (restricted access)

Monday, July 27, 2009

early music and art

I managed to miss the story of the world's oldest flute when I was travelling in June, but found it in the August issue of Spektrum der Wissenschaft. I'm intrigued to learn that the earliest instrument was found just a few feet away from the world's oldest sculpture, in the Hohle Fels cave in south west Germany. Both date from around 35,000 years ago, i.e. around the time when Neanderthals disappeared from Europe.

So it all fits together, our ancestors had visual arts and music and all that, while Neanderthals got bored to death ...

PS original paper on the earliest flute is in Nature AOP

Friday, July 24, 2009

the platypus has landed

... at last a jpg file with the cover of the German edition of "The birds, the bees and the platypuses":

I much prefer this cover design to the one of the English ed., hope it will help the sales accordingly.

The book is available to pre-order at

the magic circle

Review of

The mercurial emperor – the magic circle of Rudolf II in renaissance Prague

by Peter Marshall

Pimlico Paperback 2007

Imagine the most powerful political leader in the world decides he’s not interested in politics and wars and all that and prefers to dedicate most of his time to collecting art and dabbling in science. Amazingly, it really happened: the leader in question was the Habsburg emperor Rudolf II, who presided over the Holy Roman Empire in the twilight years before central Europe drowned in the Thirty Years War.

In his very readable biography of the ruler who couldn’t be bothered to rule, Peter Marshall follows the interests of his subject by dedicating only a little bit of space to the politics, and focusing on the art and the science instead. To get the politics out of the way first, many have slated Rudolf as a hopeless leader, but Marshall tends to support the view that his inaction and openness for divergent opinions (especially on religion, where he refused to support hardline Catholicism) quite possibly delayed the inescapable disaster by several decades.

Rudolf’s credentials are much clearer in art and in science. His support for the most exciting astronomers of the day brought together the last and greatest naked-eye observer of the heavens, Tycho Brahe, and the best theoretician of the time, Johannes Kepler. Without Rudolf’s patronage, the movement of the planets (Kepler’s laws) might have remained unsolved for much longer.

Astronomers of the day still very much believed in astrology, or at least used it as a welcome source of income, so we’re looking at an important junction between the medieval world views we now call superstition and the emerging modern science. Thus there are also alchimists and magi like the Briton John Dee populating the pages of this book.

In art, Rudolf supported many great artists, including Arcimboldo, who famously portrayed the emperor as a jigsaw made of vegetables. Marshall says that Rudolf often left important political figures waiting for an appointment, as he preferred to spend his time in the workshops of his artists, discussing their current work.

Of equal importance, though, was his unprecedented activity as a collector. He sent expert buyers including Jacopo Strada and his son Octavio to Italy, to buy art of what we now call the late Renaissance and bring it to Prague, the city which owes the time of its greatest glory to him.

With chapters dedicated to subject areas (magic, art, old astronomy, new astronomy) and the key figures representing them, Marshall’s book is a very accessible read. Minor moans from my part include the fact that the Strada family have not been given a whole chapter as they would have deserved (I have a vested interest here, but I think it’s fair to say that they are at least as important for Rudolf’s circle as the visitor John Dee). I would have also wished the author to be more aware of points where the textbook history may be wrong: He uncritically refers to “Juana la loca” (Rudolf’s great grand-mother in two lineages) as having been mad, and to a strained bladder as the cause of Tycho’s death. In both cases, I would rather take side with the alternative views explained here and here, respectively.

The failure to acknowledge the possibility of Tycho’s murder is especially unfortunate as Marshall reveals further links between Tycho and Shakespeare’s Hamlet: The astronomer, whose research centre at Uraniborg was within eyesight of Hamlet’s Elsinore, had cousins named Rosenkrantz and Guildenstierne. Which rather fits in nicely with the murder case that Peter Andersen makes and that Shakespeare may have known about. As the bard said, there are more things in heaven and on earth …

Thursday, July 23, 2009

platypuses reviewed

There is a new review (in German) of my book The birds, the bees, and the platypuses, in Treffpunkt Buch Plus, a shared review supplement that appears with the entire family of "in unserer Zeit" magazine, i.e. Chemie in unserer Zeit, Biologie iuZ, Physik iuZ, etc. While each of the magazines has a very modest print run, I reckon the sum total should be quite reasonable, somewhere between Spektrum der Wissenschaft and New Scientist. The review appers on page IV.

Talking about platypuses, the German version of the book, Der Kuss des Schnabeltiers, is on track for publication in September. We have a lovely cover design which I'll put online as soon as I get a jpg file.

Wednesday, July 22, 2009

guardian technology & the dead tail of blogging

Recently, I've been looking through a pile of Guardian technology sections which I had piled up for a rainy day, and found a comment by technology editor Charles Arthur (Blogging's long tail is dying), where he explains how he tracks blog entries that comment on content of his technology section. So I reckon he must find this -- hi Charles, *wave*.

Anyhow, to Charles's point about blogging, his conclusion is based on two observations: 1) the reported finding that 95 % of blogs out there haven't been updated for 120 days, so are presumed dead. I don't find that terribly surprising, as there are lots of people who try opening a blog, post two entries with their favourite song lyrics, and find it's not for them, leaving the ruin standing for eternity. In MySpace alone one finds thousands of ghost blogs like this.

Observation no. 2) is that the comment tracking device that Charles set up is giving fewer hits than it used to (and being the editor of the section, he hopes it hasn't become less inspiring over the years). So I'll make a point of regularly commenting on the section to buck this trend :)

At least where I'm standing, which is probably somewhere in the middle of the long tail of blogging, I still feel that blogging is alive.

PS: I forgot to mention that I'm now on twitter:

Tuesday, July 21, 2009

Copenhagen conference reframed

As I mentioned earlier, I learned lots of interesting things at the Copenhagen conference on Framing Research.

Some of it I reframed as a news feature for Current Biology, which appeared last Tuesday and is available here (restricted access, but email me if you want a copy).

Another item published while I was away is my review of:

A short guide to the human genome,
by Stewart Scherer

This is in Chemistry & Industry, issue 13, 13.7.2009, page 30


In his “short guide”, Stuart Scherer has addressed around 80 such questions, using the available database tools and the published literature to give today’s best estimates, pinning the genome and its proteins down as precisely as possible. Regarding the number of genes in our genome, his answers range from 18,357 to 25,685. Each of these “genome FAQs” is addressed in a very short chapter of just one to four pages, often presenting the answer in the form of a table or graph, together with an explanation of how the results were obtained and what factors still limit their precision.

Monday, July 20, 2009

in praise of TGVs

It really only struck me when I was back in Oxford, Friday afternoon, and realised I had been in Avignon, Provence, the very same morning. Without using a plane. It struck me that these days the TGV (Train Grande Vitesse, or High Speed Train) only takes 4 hours and a bit from the top to the toe of France, i.e. from Lille to Avignon. On the way down it took us 4 hours and 13 minutes. And you never even notice you're moving very fast. And the train arrived precisely on time.

A quick comparison with the UK: the distance corresponds to that from Brighton (on the south coast) to Inverness (on the shores of Loch Ness), and the quickest train connection I can find right now takes 9 hours 49 minutes. which means that most people would take the plane to go up to scotland.

Plus, the new generation TGV trains, some of them double deckers, offer you an amount of space that you would only get in first class carriages in the UK. At one of the stations I spotted a magazine for (UK) railway enthusiasts with the cover page reading: "High speed trains: what we can learn from Europe". Well, ahem, short answer: everything.

The UK has only one high speed line, that is the bit that connects London St. Pancras to the Euro Tunnel, which opened a couple of years ago (before that, the fast Eurostar trains crept very slowly into Waterloo station). Seeing that the Paris to Lyon TGV line opened in 1981, we're about a quarter of a century behind.

Meanwhile, the UK government keeps subsidising the expansion of airports, undermining its own climate targets, as George Monbiot keeps reminding us.

PS couple of pix to throw in, this is the main hall of the TGV station at Avignon:

... and this is what the sunrise over Provence looks like when you move at more than 200 km/h:

PS I've now uploaded a few more photos to a dedicated MySpace album.

Saturday, July 18, 2009

olives and lemons

I'm back from a very quick TGV visit to my relatives in Provence, have uploaded a few pictures to my VIEW profile, mainly impressions from Avignon, where the festival was in full swing and theatre was spilling over into the streets to an extent that made it really difficult to work out where the theatrical ended and real life began. Now was that a real street sweeper with the rubbish trolley over there, or an actor wheeling a prop around?

olives at Nyons, not far from the world centre for olive cultivation.

Near the Pont du Gard, an olive tree which looks as if it might be nearly as old as the famous aquaeduct

More impressions to follow ...

Friday, July 10, 2009

women doing it for themselves

There was a huge fuss in the media this week about the first sperms to be made from human stem cells. It's not at all surprising that it can be done, of course. As pluripotent stem cells can be made to produce any kind of cells (with the right incentive), they can also produce eggs and sperms.

(added 30.7. -- I hear this paper has now been retracted over plagiarism allegations, according to science magazine )

But why would one want to make artificial sperm when the natural thing is the one resource we have in zillion-fold excess over demand? There is only one reasonable answer -- people behind this are working towards making men redundant. In the future, one could easily make sure that only girls are conceived, and in order to keep fertilisation going, one would need to make sperms from stem cells. Easy as that. You can imagine the consequences (mainly positive, I happen to think) for yourself, or read this.

In a world without men, women will of course have to provide their own stimulation, as it were, and this is what this commentary is about. One of the authors used to live in our neighbourhood for a while, and I actually like her books, so I am sorry to see the imprint close down. I think the publishers have failed to read their crystal ball correctly ...

Thursday, July 09, 2009

how to regenerate

Ever wondered how Dr Who regenerates ? Well, ok, I know they just hire a different actor. But if and when the Doctor happens to get an arm amputated during his regeneration phase, it grows back, allegedly. Which is exactly what happens with a range of different animals, including salamanders.

Surprisingly, research in last week's issue of Nature shows that the axolotl does not use pluripotent stem cells to regenerate amputated limbs. Fluorescent labelling and tracking of cell fate reveals that the secret is in a sophisticated system of getting the right kinds of cells to the right places, and not in making cell pluripotent again.

Probably a disappointment for stem cell people, but intriguing nonetheless.

The original paper is here:

Cells keep a memory of their tissue origin during axolotl limb regeneration p60

By using an integrated GFP transgene to track the major limb tissues during limb regeneration in the salamander Ambystoma mexicanum (the axolotl), it has been possible to demonstrate that each limb tissue produces a different set of progenitors with restricted potential. Thus, the blastema—the collection of cells that regenerates the diverse tissues of the limb—is composed of a heterogeneous collection of restricted progenitor cells instead of dedifferentiated pluripotent cells, as previously thought.

Martin Kragl, Dunja Knapp, Eugen Nacu, Shahryar Khattak, Malcolm Maden, Hans Henning Epperlein & Elly M. Tanaka


there is also an excellent News & Views piece about this research:

Developmental biology: A cellular view of regeneration p39
How the salamander regrows an entire limb after injury has flummoxed the wisest of scientists. A closer look at the cells involved in limb regeneration shows that remembering past origins may be crucial for this feat.

Alejandro Sánchez Alvarado


I'm surprised they didn't mention Dr Who, though.

Wednesday, July 08, 2009

chernobyl -- the next generation

I was amazed to learn from the Guardian last week that there are still children with radiation-related diseases in the Ukraine, a generation after the Chernobyl disaster. Something to consider before we solve our CO2 problems by switching everything to nuclear. Equally amazing the fact that they still get treated in Cuba, for free:

Revolutionary care: Castro's doctors give hope to the children of Chernobyl

Monday, July 06, 2009

round-up of German pieces

It's very rare that I get artwork from my own production published along with my text, so I'm thrilled to see that my recent feature on farm animal genomics is illustrated with the photo of our local horse population, snapped maybe 100 metres from my doorstep. Note that the origin of different colours in horses is part of the subject matter of the piece, and the horses belonging to the local riding school display a nice range of colours.

I'm also pleased to have acquired a new outlet for my writing in German, in the shape of the medical magazine Trillium Report. My contribution is an essay on the possibility of higher cognitive function emerging in computer networks.

So there are 3 pieces in German this month:

Tycho Brahes Elemente, Nachrichten aus der Chemie p. 741
more about this

Genomik auf dem Bauernhof, Nachrichten aus der Chemie p. 779

Der Geist des Netzwerks Trillium Report 7, Nr 2, 57

Friday, July 03, 2009

Jacko's Simpsons appearance

I've been wondering since I saw the episode with the "big white guy who thinks he's the small black guy" whether this was really Michael Jackson doing the voiceover. Am glad to hear that it really was him:

Jackson's Simpsons episode to re-air as tribute

after all, who better to parody MJ than the man himself ?

Thursday, July 02, 2009

cheerleader or watchdog?

Last week's cover of Nature confronts me with an uncomfortable choice: are science reporters cheerleaders or watchdogs? Well I don't like either of the metaphors, I would be more likely to describe my activity as that of building bridges, translating, communicating, interpreting ... Although there are occasions when I feel that certain parts of science are grotesquely underappreciated so I get out my pompoms and do a bit of cheerleading. More rarely, there are also occasions when I feel that scientists are going against the best interests of society, and I bare my teeth and let out some growling watchdog-like noises. But on the whole I am too busy building bridges across the Two-Cultures-Canyon to be bothered with either the cheering or the barking.

The reports and comments in Nature add to my increasing awareness -- which I talked about at the recent Copenhagen meeting and in my lectures in Germany -- that science reporting is changing quite drastically and rapidly, and we really need to think about how to ensure that the result we want to achieve, i.e. a reasonable level of public understanding of science, and public appreciation of the role science plays in our lives, doesn't fall overboard.

PS What I really don't understand is why the three cartoon characters on the cover had to be all male. Obviously they wanted to avoid the clichee of a female cheerleader, but a female watchdog would have looked really nice next to the male cheerleader ...

Wednesday, July 01, 2009

Schrödinger's Jacko

I had a very weird media experience on my way back from Germany. Having been cut off from electronic media since Thu afternoon, I arrived at Paris Fri morning and looked through the newspapers, both French and international ones. Only one of them (it may have been Le Figaro) had Michael Jackson's death on the front page.

I thought that was really weird -- surely, if he had died he would be on all the front pages, and it would be very difficult for one paper to get the story exclusively? Might they have been caught out by a hoax?

Unable to resolve this in situ, I took the Eurostar to London with a kind of Schrödinger's Jacko thought on my mind, wondering how he could be dead and alive at the same time. By the time I arrived at London, though, all the British papers whose early, Jacko-alive editions I had seen in Paris had changed their front pages, and he was all over the place. On the Guardian front page, poor old Farah Fawcett had to be dropped to make space for him.

So if future generations start asking where were you when you heard ... I'll have a more interesting story than on similar occasions (there are at least two catastrophic events which I heard about while sitting on the toilet, having walked past the radio and switched it on for the morning news!).

Anyhow. I can live with or without him and don't have strong feelings about his music one way or the other.

More importantly, I'm very excited that the first single from Shakira's new album is now online at her Myspace site. It's called "loba" (as in female wolf) and features her howling like a wolf :) Check it out.