Friday, January 29, 2010

oxford night life

continuing my occasional "Oxford by Night" series, here's a view of Blackwell's bookshop, which is of course about a million times larger on the inside than it appears to be from the historic facade. Sign of the time, too, that the only writing one can read from the other side of the road says "buy one get one free".

Thursday, January 28, 2010

giant molecules

I have a long essay review out in the current issue of Chemistry & Industry, of the book:

Giant molecules: from nylon to nanotubes
Walter Gratzer
OUP 2009


Online access is for subscribers only I'm afraid, but here's a snippet:

"... the book gives an interesting account of the colourful history and present promise of polymers of all shapes and sizes. I believe there should be more books like this, giving the famous intelligent lay reader access to important concepts that have been neglected because they cut across the established structures of scientific disciplines."


You'll also find the full text in my review collection "The noughties brought to book" which is already available from Lulu.com:

Support independent publishing: Buy this book on Lulu.

even though I'll only start promoting it when I've received and checked my own copies.

Wednesday, January 27, 2010

anybody out there ?

I attended (most of) the Royal Society discussion meeting on

The detection of extra-terrestrial life and the consequences for science and society

on Monday and Tuesday. Here are some quick notes on what (I think) I've learned from the more scientific part of the meeting (there were also talks about impact of any ET discovery on society, religion etc. which are a bit less relevant to me but may find more coverage in the mainstream media):

Some notes from the RS astrobiology meeting 25./26.1.2010

Charles Cockell (Open University) about life in the lithosphere. He insists “there is no such thing as a biosphere,” as the living part of the spherical planet is so thin it should be called a biofilm covering the geosphere. (Not sure that helps, as biofilms are something else entirely.) Attempts to cultivate iron oxidizers from rocks not successful yet. Very difficult for microorganisms to make a living from lithosphere, which is thermodynamically tasty but kinetically inaccessible. Therefore, when looking for life, follow the kinetics. Example Chessapeeke impact crater. Lithospheric austerity can be overcome by tectonism, volcanism, impacts. Habitats in solar system: Europa would be promising, but we don’t know redox status of subsurface ocean.

Simon Conway Morris (Cambridge) talked about extremophiles and potential habitat, mentioned Venus clouds and high pressure biology. No good explanation why microbial life dominated for so long except if step up to complex life is unlikely. Convergent evolution on Earth, => ET life may have developed similar features to adapt to similar environments, e.g. will also have camera eyes and similar sensory systems as we have. Violent behaviour could also be convergent, => need to be very careful with any ETs we find.

Michel Mayor (Geneva) on hunt for exoplanets, how boundaries have shifted so that now we can detect Neptune sized planets and even super-Earths with 1-10 Earth masses. Surprising diversity of extrasolar planets. Importance of migration of planets to orbits far from where they must have originated, e.g. very hot Jupiters. Eccentricity of extrasolar planets: huge scatter in distribution of orbit parameters. Transit, Doppler, and microlensing studies cover different areas of the planet spectrum, thus complementary. In order to find Earth twin need to improve methods even further.

Malcolm Fridlund (ESA) on COROT mission and how to spot life on extrasolar planets. Take Earth as model, move it 10 Parsecs away, what would we see? Need 1-pixel observations of Earth from distant space probes, not published yet. ESA looking into possibilities since 1995. Challenge equivalent to studying a firefly next to a lighthouse from 10,000 km away. COROT looking at acoustic vibraitions in stars, operated more than 1000 days so far, studied over 20 exoplanets, mission extended for further 3 years. E.g. Corot7B: 1.58 Earth radii, 4.8 Earth masses, density 5.5g/cm3 similar to Earth, orbiting Sun-like star, but only 5 star radii away from star, so very hot. Competitors: Kepler (now running), Plato (due 2018).

Chris McKay (NASA Ames) on life in solar system. Why we want to find some: Two examples of life more powerful than one, and could do comparative biochemistry. Case for Mars: evidence of past water, atmosphere, dry climate means good preservation of traces. Downside: exchange of meteorites with Earth could confound case for separate origin, may just find distant relatives. Fossils not enough, need guts. Phoenix Lander at Mars North Pole. Found soil pH 8, carbonate buffered, with 1% perchlorate (totally unexpected). If perchlorates generally present in Martian soil, conventional methods of organics detection by combustion won’t work, as organics won’t make it to receptor. Sensitivity would be reduced from ppb to 0.1 %. Phoenix couldn’t adapt its protocol to presence of perchlorate, this speaks in favour of sample return mission. Phoenix also found segregated ice, indicative of past liquid water. Habitability of Phoenix landing site 5 Myears ago: only thing missing is nitrogen. Europa, Enceladus, Titan, better prospects for “second genesis” as much less likely to have shared bio history with Earth. On Enceladus all basic requirements for life are met: C, H, N, energy … If it’s like us, easy to spot, but not interesting. If alien, interesting, but hard to find.

Colin Pillinger (Open University) on chemical methods to find life. Involved in Apollo 11 sample analysis, made proposal for Viking analysis but wasn’t selected. Favours C isotope analysis, as (terrestrial) life has preference for 12C over 13C. analysis of Martian meteorite EETA79001, with carbonate inclusions (light) and organics (heavy). Step combustion can find every C atom in every form. Organics from ALH84001 very enriched in 12C, would fit methanotrophic organisms. Analysis of Nakhla meteorite (fell 1911) – 80% of organic matter contains no 14C. Beagle2, or how to shrink 1t of equipment to 5.5 kg. Would have detected C isotopes by 2 independent methods.

Paul Davies (Arizona State Univ) Shadow biosphere on Earth as test of cosmic imperative. Chance or law, or where on the spectrum in between ? There may be 1020 Earth like planets, but odds against could easily exceed that number. Looking for “second genesis” on Earth. As 99.9 % of microbial species remain uncharacteriseed, there may be extant or extinct second type of life, which could be ecologically separate or integrated with the kind we know. Places to look: extreme conditions, high atmosphere. Tested for “mirror life” looking for organisms that can digest mirror nutrients, found Anaerovirgula multivirulans which is normal but can live on mirror nutrients, not sure yet how it metabolises the sugars. Looking for “arsenic” life with As instead of P in arsenic-rich environments, results expected soon.

Frank Drake (SETI institute) on 50 years of SETI. 50 years ago, only considered sun-like stars, but now know that M stars also have planets, and multiple stars may have planetary system as well, so range of targets has expanded. How to look – radio signal still most promising, and today 14 OM more powerful than 1960. also consider picking up laser pulses from civilisations that actively try to communicate. Problem: progress in our communications technology means Earth radio has become much fainter than it was in 1960. Search parameters still based on old technology. Advanced civilisations may emit much less radio waves than thought.

PS my tweets from the meeting are tagged #outthere

PPS Oops, I just noticed I already used the title for a blog entry in September, will try to remember not to use it for a third time ...

students go mild

There have been simmering student protests across Germany since last June or so, but they were rather mild compared to the historic events of 1968. Mainly ignited by the measures surrounding the Bologna process and the introduction of new, more streamlined degree courses, the protests cover a range of other criticisms of the education system, such that even the politicians of the ruling parties can find something to express sympathy with (while blaming the other parties).

I've tried to make some sense of events in a news feature out this week in Current Biology:

Bologna resistance
Current Biology, Volume 20, Issue 2, R39-R40, 26 January 2010
doi:10.1016/j.cub.2010.01.004

summary and restricted access to PDF file

Saturday, January 23, 2010

going deep

Today marks the 50th anniversary of an exploration that is probably equivalent in scope to the first moon landing but has received much less attention.

On Jan 23, 1960, Jacques Piccard (son of Auguste Piccard who was the real life inspiration for Tintin's Professor Calculus / Tournesol) and US Navy Lieutenant Don Walsh reached the bottom of the Challenger Deep in the Mariana Trench, some 10.9 km below sea level with the Bathyscaphe Trieste designed by Auguste Piccard.

Down there, the hydrostatic pressure is roughly 1100 bar, and as somebody who has used this kind of pressure in the laboratory, I can state very firmly that I wouldn't want to be there, not for all the fame and glory in the world. It's bad enough keeping 1100 bars inside your equipment when you're on the outside, but the reverse situation doesn't bear thinking about.

Understandably, nobody has come forward to repeat and expand on this exploration, so the deep sea is still a territory about which we know next to nothing. We do know that there is life down there, but biological excursions with submarines such as Alvin have typically been limited to a range of around 4,000 metres.

Friday, January 22, 2010

language learning from bad to worse

There was an incredibly depressing round-up of the disaster zone that is language learning at UK state schools in the Guardian this week:
Languages are becoming 'twilight subjects' at state schools

Essentially, the government abandoned the obligatory foreign language from age 14 in 2004, with the promise that in exchange, earlier start would be introduced. However, the earlier start for 7- to 11-year-olds will only be introduced in 2011. Between those that turned 14 in 2004 and those who will be under 11 in 2011, there are at least ten year groups that may only get three years of foreign language education.

Considering that even at A level (year 13, after up to 7 years of language learning) the standards are appalling, and at GCSE (year 11) the kids are far from being able to speak the language they have allegedly learned for 5 years, 3 years is practically nothing (I have one child in the second year of learning French right now, and I know they learn nothing).

Reducing the minimal time from 5 years to 3 has turned a bad situation into a disaster zone. As the Guardian article points out, it also helps private schools, which are aiming at much better standards, apparently.

Of course it is right to start earlier, but what on earth were they thinking, moving the tail end first and the start date only seven years later?

The "New Labour" government started with the slogan "Education, education, education!"

Today it feels more like "Education, err ... education ? ... what education ???"


PS in a small accompanying piece, the Guardian credits Shakira with the increased popularity of Spanish (at the expense of German) in schools. I'd love to believe that, though it seems implausible, as her records aren't that successful around here (not a patch on what's going on in Germany), and anything she's recorded in Spanish doesn't even get to the shops. But ok, there probably are a few kids who have taken inspiration from her, good on them.

PPS I corrected the year of the change of policy, it was 2004, not 2000 as originally stated.

PPPS (8.10.2012) A visitor to this blog had posted a comment including a link to the site languagesoftware.net. I just received an incredibly rude email from the company requesting me to remove this link ...

"because your domain may fit within one or more of the following categories: infected with malware; low quality site; paid link provider; manipulative link activity; link exchange networks; or simply not a good fit for LanguageSoftware.net."

I have removed the comment, as it was anonymous and may very well have been a dodgy attempt to spread links to that website, but am wondering whether they actually have a right to stop me from linking to them. Any views? Of course I wouldn't link to their site now.

Thursday, January 21, 2010

book reviews collection

I've collected all my book reviews from the noughties into a book which is now available from Lulu.com:

Support independent publishing: Buy this book on Lulu.

Haven't even started to create a website for the new book yet, it all went so quickly. I'm also looking into the option of making it available at Amazon (may have to pay for that, and I get less money from each book, but for the buyer it has the advantage of free P&P). I think what I'll do is to wait for my own copies to arrive (takes two weeks or so), check whether they are ok, and then step up the marketing a little bit. Meanwhile here's the cover:



And yes, this picture is connected to the contents -- there is an essay review about blue skies research in there somewhere.

Wednesday, January 20, 2010

Y - the missing link

In my collection The Birds the bees and the platypuses, I have included articles about the chimp genome (as compared to our own, of course) and the confusing hall of mirrors that is the human Y chromosome. Now, released online in Nature last week, the missing link has also been brought to book: the Y chromosome of the common chimp.

Surprisingly (but then again, not that surprisingly), the chimp's Y chromosome is massively more different from ours than the rest of the genome. Rapid change in the Y chromosome is easily explained by the fact that -- unlike all other chromosomes -- it doesn't have a matching partner that can serve as a quality control and backup copy. While it has evolved its own internal control mechanisms, which are responsible for the large number of repeats and mirrored sequences seen in the Y, this still means that it is much more vulnerable to mutation.

The news item in the current print issue of Nature tries to put a positive spin on it, saying it evolves faster. Well, it certainly changes faster, but not always for the better. There is a school of thinking saying that it decays and is on the way out in the long term. Lucky that our species will self-destruct before that time anyway.

Reference:

Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content
Jennifer F. Hughes, Helen Skaletsky, Tatyana Pyntikova, Tina A. Graves, Saskia K. M. van Daalen, Patrick J. Minx, Robert S. Fulton, Sean D. McGrath, Devin P. Locke, Cynthia Friedman, Barbara J. Trask, Elaine R. Mardis, Wesley C. Warren, Sjoerd Repping, Steve Rozen, Richard K. Wilson & David C. Page

doi:10.1038/nature08700

Tuesday, January 19, 2010

pulling power

In Angewandte's online release last Thu there was a lovely paper about AFM studies of the enzyme titin kinase (TK), which is naturally activated by pulling force, a bit like a christmas cracker, but reversibly (that bit was known, but I wasn't aware of it before).

Puchner and Gaub at the LMU Munich have done a three-step experiment involving
1) pulling to activate
2) allowing time to bind substrate
3) further pulling to analyse

In analogy to spectroscopic methods that involve "pumping" by laser light and then probing by spectroscopic measurement, they call this a "pump and probe" force experiment.

Intriguingly, they can see in the force measurements whether or not the substrate (ATP) has bound during phase 2. Plus, they can exactly define which energy barriers the pulling has to overcome to open the path for the enzyme activity.

Reference:
Exploring the Conformation-Regulated Function of Titin Kinase by Mechanical Pump and Probe Experiments with Single Molecules
Elias M. Puchner, Hermann E. Gaub
Angew Chem Int Ed 2010
Published Online: Jan 13 2010 10:57AM
DOI: 10.1002/anie.200905956

Monday, January 18, 2010

is big google watching you ?

Last week's cover story of the German news magazine Der Spiegel was all about the masses of information that google collects on its users, and the potential threat in that should the company one day go over to the dark side. Some of that really did sound scary, especially the quote from a top executive who didn't seem to have an understanding of the concept of privacy at all.

Personally, I am not worried that much, as I like to believe that my preferences and habits are sufficiently eccentric to confuse all market researchers that care to look at them. Amazon.com has been trying to figure me out for ten years now and aren't any closer to understanding what I really like, or to knowing what I haven't bought yet. They don't even understand that the same person can act as a writer, bookseller, and reader, and that in four different amazon markets (US, UK, France, Germany). So I'm not worried that the google robots, just from managing my blog, will figure out what I'm thinking (*wave to the nice robot*).

But I think that everybody should make sure they think about what information to reveal to whom, and, crucially, not to reveal all to the same company. I.e. if a given company is already handling my email and blog, I wouldn't want them to run my mobile phone and my bank account as well. It's just elementary "don't put all your e-eggs in one e-basket" kind of thing, but I think it can prevent considerable damage should one of the baskets go awol one day. Oh, and for anybody worried about what their search habits may reveal, there is ixquick.com a meta search engine that doesn't record customer details.

And come to think of it, my shiny new phone (not from google) doesn't have an off switch, but it does of course have a microphone and a camera. After reading this article I began to wonder whether the phone was maybe spying on me. Now that would be a big brother type scheme extremely easy to implement. I think the next few years in communications are going to be interesting.

PS some of the Spiegel content is online in English translation, but I don't think this article is.

Friday, January 15, 2010

cognitive enhancers -- the next war on drugs?

No German publications out in January, but there's one left to report for December, which only got printed late in the month and thus arrived here in the new year.

Together with Claudia Borchard-Tuch, I wrote the title topic of the current issue of Trillium Report, dealing with cognitive enhancement (i.e. drugs that healthy people take to boost their mental performance). While she handled the medical side, I had a go at the political aspects, and the risk of new drugs being made available illegally and thus starting a new version of the failed "war on drugs". While I'm not wildly enthusiastic about cognitive enhancers, I think sensible legislation is needed to avoid a rerun of the drugs disaster.



Read my article here:
Trillium-Report 7, Nr 4, 164-5
Drogenkrieg 2.0: Vom Schlafmohn zum Leistungskampf

PDF download (intro and CBT's article only)

Thursday, January 14, 2010

the best things in life are free

I enjoyed Katharine Hibbert's recent piece in the Guardian on how she survived with (virtually) no money in London for a year, living in squats furnished from skips etc. Have to say I like to check skips as well, it's just the permanent moving around from one squatted house to the next, taking all one's possessions along, which would be a little bit tricky for me at this stage of my life.

That piece was extracted from a book which I understand is out today:

Free: Adventures on the Margins of a Wasteful Society by Katharine Hibbert, published by Ebury Press


but obviously, I'll wait and see whether I can get it for free ... Coming soon to a freecycle group near you.

Wednesday, January 13, 2010

skating on thin ice

just a few more winter pix while the fun lasts (day 8 of the first proper winter we had here since arrival in 1993).

here's the setting of our local ice rink, also known as the Large Human Collider, or LHC:



Here is phase 2 of the LHC, with two rings joined to a figure of 8. By now there are three rings, with the third joined to the distal ring, going out towards the right hand side:



and here's yours truly, skating on thin ice:




PS Health & Safety advice: this is on a flooded field, so there's no danger whatsoever. It strikes me that the official police advice "keep the children off the ice" is about as sensible as "just say no to drugs". Instead of teaching children what is safe and what isn't, they go for the "don't do anything that may be fun" line and set themselves up for failure.

Tuesday, January 12, 2010

stem cell progress

Last year, scientists have made significant progress in making the production of induced pluripotent cells either safe or efficient. However, experts warn of fundamental problems with applying stem cell products to patients. Thus, the advent of replacement organs grown in the lab is still years away.

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

Stem cell moves
Current Biology, Volume 20, Issue 1, R3-R4, 12 January 2010
Progress with both embryonal and induced pluripotent stem cells is bringing clinical applications a step closer.


summary and limited access to pdf file

Monday, January 11, 2010

51 years of Asterix & Obelix

Brussels is not only the capital of the European Union, but also the capital of the European comic strip, as I found out last week when trying to find a book shop that also sells normal books without drawings. So I felt obliged to bring back a copy of the Asterix & Obelix "Livre d'or" (Golden Book) published on the occasion of their 50th anniversary last year (which I missed completely, living on an island that's very well insulated from European culture).

Although I started my writing career with a lengthy piece about Asterix volumes 1-24 in my school magazine 30 years ago, I'm not going to review this one in detail. It's great fun, but it also struck me that dear old Uderzo is about as subtle as Obelix (which, I believe, is not a coincidence). All the graphic jokes which might have served a deeper meaning if Goscinny were alive, are just thrown around for the heck of it. But what can we do. It's the best we can get without René so we might as well enjoy, as my 12-year-old clearly does.

Wednesday, January 06, 2010

snow pix

... quickly before the UK's Internet provision collapses under the weight of snow pictures that everybody uploads to facebook and emails to their local media outlets, here are some of my snaps from this morning. I measured 20 cm snow on the top of our dustbin (which of course wasn't collected today, like everything else was shut down as well).






PS This blog service is of course severely disrupted by the extreme weather conditions. Every morning I have to clear the snow off the ice so we can get some ice-skating done. Expecting to resume normal service next week.

Sunday, January 03, 2010

cancer genomes

I was really excited to see several papers on "cancer genomes" appearing just before christmas. There were two in Nature's advance online service mid-December, widely hyped in the press, and then another one in the print issue of 24.12.

However when I read the lung cancer paper I found it quite disappointing. As I understand it, the authors sequenced 25-year-old cell lines from a patient whose smoking history is unknown. While there is a 97 % probability that his cancer was caused by smoking, this also means that there is a 3% risk that the conclusions are just wrong and the mutations relate to a different cause. And for any specific mutation one might be interested in, one simply doesn't know whether it developed in the cancer or in the cell culture, and whether it's a "driver" mutation (i.e. promoting the cancer) or a "passenger" mutation that just hitched a ride. Also, the control sample will have developed somatic mutations as well, so one would have needed several controls to figure out what is a relevant mutation. The authors admit somewhere that the various rates of somatic mutations aren't very well understood yet.

As millions of smokers get lung cancer every year, I really don't understand why the researchers couldn't get a fresh sample linked to a well-documented case study. Insiders tell me that it's tricky to sort out the legal side of doing such studies on a real patient, but then again, that's what the whole thing is for, namely ultimately to be able to analyse a patient's cancer, to find out how it can be treated most efficiently. And if I went through all the trouble of sequencing two human genomes (cancer and control) several times over, I real would want to make sure that the information I get can be interpreted meaningfully.

The second online paper also used cell lines, this time from a melanoma (so at least there is no doubt that the patient has been exposed to sun light, though again, we probably don't know any further details).

The paper in the print edition of 24.12. (vol. 462, p.1005) doesn't look at complete genomes but samples rearrangements of genetic material. This time, at least, there are several "fresh" samples included among the 24 separate breast cancer cases studied. So it can be done, and I think this is the way forward. The other two papers only show that one can analyse the genomes of cell lines - which I think we all knew before. Now we need lots of genomes of lots of real tumours, with real case histories, and then we can start discussing what caused these cancers, and which are the "driver" mutations, and which the "passenger" mutations.

In the newspaper coverage I read, the two online papers based on cell lines were represented as if they were based on actual living patients, so this subtlety clearly got lost in translation.
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