Thursday, January 31, 2008

stop heating the garden

Patio heaters have spread epidemically around here over the last few years, as a vivid demonstration that awareness of environmental issues is still negligibly small. As people won't listen to reason, it's welcome news that the EU is preparing a ban on these horrid things. Even though, of course, this risks helping the anti-EU camp in this country, which is almost as strong as the anti-environment camp. A voluntary government ban ahead of EU legislation would have been better.

Wednesday, January 30, 2008

graveyards for unread books

I learned from this commentary that pulped books are used for road building in the UK. As more roads tend to produce more traffic, I'd prefer any remainders of my books to end up in a more environmentally friendly graveyard. Maybe as home insulation material, or as railway seats ... Even though, in an ideal world, they would all get read so much and treasured that they never would have to be pulped at all!

Tuesday, January 29, 2008

threat or promise

The science of The Simpsons has been one of my favourite topics for a while, and as Paul Halpern has published a book about it last year, I jumped at the opportunity to review it. My review is now out in Chemistry and Industry, No.2, page 29-30. The title is "Threat or promise", and it comes with a nice picture of Frankenstein's monster ...

Monday, January 28, 2008

pumping out proteins

The synthesis of bacterial flagella (the "tails" they use to propel their swimming motion) served as the foundation of one of my most-cited papers:

Plaxco KW & Groß M (1997): Nature 386, 657-659 (17.4.1997)
Cell biology: The importance of being unfolded (News and Views)
PDF

where Kevin Plaxco and I proposed that the regulatory protein FlgM, which serves its function in an unfolded state, might just be one of many such "unfolded yet active" proteins. Which turned out to be quite true.

The group of Kelly Hughes, whose work our comment was based on, has now investigated the energy source of the process of building up bacterial flagella, which is quite intriguing as proteins are pumped out through the hollow interior of the growing structure. Surprisingly it's not driven by ATP, but only by a proton gradient.

It's in the current issue of Nature, page 489:

Energy source of flagellar type III secretion
Koushik Paul, Marc Erhardt, Takanori Hirano, David F. Blair & Kelly T. Hughes
doi:10.1038/nature06497

Saturday, January 26, 2008

hay amores

There is an official videoclip of one of the three songs that Shakira recorded for the soundtrack of the movie Love in the time of cholera:

Hay amores


(SonyBMG)

I love the song, but I'm not so sure about the lipstick ...

Haven't seen the movie yet, I understand the UK release date is March 21.



Oh, and talking of movies, if there is a "quantum of solace", as James Bond would have us believe, I wonder what physicists should call it, maybe a solacon?

Friday, January 25, 2008

snips to the people

Personal genome sequencing has arrived in Europe, as I learned from this Guardian report this week. The company 23andme offers analysis of SNPs (single nucleotide polymorphisms, i.e. the 1-letter differences in DNA that are a part of what makes each of us unique) for some medical information and the chance to compare DNA with other customers and possibly find out something about your genetic origins. Participation costs GBP 500, apparently, so I'm not very tempted to try it out. I would do it if there was a free trial for science writers ...

Thursday, January 24, 2008

methanol fuel

Methanol is known as the stuff that makes you blind when you drink it (instead of its next door neighbour ethanol, which is less toxic), but it is little known that it is quite useful as a fuel for cars. Some motor racing competitions, such as the Champ Car circuit in the US have used methanol for decades (mainly for safety reasons, as it doesn't produce black fumes when it burns in an accident, and doesn't explode quite as easily as petrol).

Industry makes methanol from CO and H2 on the tonnes scale, but it would be really useful if methane, which sometimes turns up as an unwanted byproduct (of oil production, landfill sites, cow's digestion!) that is just released or flared off, could be converted into methanol. So far, this reaction required a multi-step process with high temperatures and pressures, but researchers in Japan have now proposed a simpler way using fuel cells. Read my story here.

Oh, and way back in the 70s, my dad used to have a methanol-fuelled VW Golf as a company car -- his company used to make 800 tonnes of the stuff per day, he tells me.

Wednesday, January 23, 2008

a green solution

When I was asked to do this story about biofuels produced from algae, I thought there wasn't that much going on in this field. But I was wrong, there is a lot going on, and the algal approach, abandoned by the DoE a decade ago, is alive and kicking. The USP is that you can farm algae practically anywhere on the planet, including on desert land. And they grow fast.

Read my story in Current Biology.

Tuesday, January 22, 2008

music of the sephardim

I've just "discovered" (for myself) the singer Yasmin Levy, who specialises in reviving (and adding to) the music of the Sephardim, i.e. the Jews who lived in Spain before the "reyes catolicos" cleared the country of all non-catholics in 1492.

Although I'm neither Spanish nor Jewish, nor 550 years old, I just love this music. It also has had some influence on the origins of flamenco, which I like too.

Yasmin Levy has a MySpace page with a few of her tracks and a new album out with Harmonia Mundi, which I'll check out pronto.

There was also a piece in the Guardian about her. The Guardian made a big fuss about Ladino being a distinct language that hardly anybody speaks any more -- but to me it sounds just like spanish with a bit of a weird accent.

Monday, January 21, 2008

old school

This is the old "Lateinschule" (grammar school) at Trarbach, Mosel, Germany:




I've just found out that two of my ancestors were teachers there, namely Johann Jacob Ebner from 1686 till 1708, and his son Philip Nicolaus Ebner from 1708 to 1720. Both had the title "conrector", meaning they were qualified to teach the final year students, preparing them for university.

A short history of the school (in German) is here.

Saturday, January 19, 2008

special delivery

researchers in Japan have used the established electrospray (ES) process (from mass spectrometry) to deliver DNA into living cells.

It kind of makes sense, as mass spectrometrists have spent more than a decade turning ES into the gentlest method of transferring biomolecules from solution to the gas phase and firing them at a target, so nowadays they can do miracles with that method, spraying very sensitive assemblies and all kinds of things.

So using this for gene delivery as well looks like a very promising idea to me. And it will be important once gene therapy takes off.

Source: Angewandte Chemie online - DOI: 10.1002/anie.200704429

Friday, January 18, 2008

bare feet

As Shakira's birthday is coming up at the beginning of February, here's a reminder that her foundation, Pies Descalzos supports children in Colombia who would otherwise have no access to education.



People in the US (and Colombia) can donate directly through the website of the foundation, which has an English version and a US bank account.

In the rest of the world, it is easier to go via
conexion colombia which accepts credit cards over a secure server.


Thursday, January 17, 2008

trapping uranium

Researchers in Edinburgh have found an elegant way to catch the highly inert uranyl cation and make it react. Read my story here:

Chemists tame the uranyl ion

Wednesday, January 16, 2008

rock star

I don't normally post song lyrics on my blogs, but in protest against another outrageous instance of censorship by MTV, here's the full text of Nickelback's Rock Star, with the censored passages in bold:

I'm through with standing in line
to clubs we'll never get in
It's like the bottom of the ninth
and I'm never gonna win
This life hasn't turned out
quite the way I want it to be

(Tell me what you want)

I want a brand new house
on an episode of Cribs
And a bathroom I can play baseball in
And a king size tub big enough
for ten plus me

(Tell me what you need)

I'll need a credit card that's got no limit
And a big black jet with a bedroom in it
Gonna join the mile high club
At thirty-seven thousand feet

(Been there done that)

I want a new tour bus full of old guitars
My own star on Hollywood Boulevard
Somewhere between Cher and
James Dean is fine for me

(So how ya gonna do it?)

I'm gonna trade this life for fortune and fame
I'd even cut my hair and change my name

[CHORUS]
'Cause we all just wanna be big rockstars
And live in hilltop houses driving fifteen cars
The girls come easy and the drugs come cheap
We'll all stay skinny 'cause we just won't eat
And we'll hang out in the coolest bars
In the VIP with the movie stars
Every good gold digger's
Gonna wind up there
Every Playboy bunny
With her bleach blond hair

Hey hey I wanna be a rockstar
Hey hey I wanna be a rockstar

I wanna be great like Elvis without the tassels
Hire eight body guards that love to beat up assholes
Sign a couple autographs
So I can eat my meals for free

(I'll have a quesadilla on the house)

I'm gonna dress my ass
with the latest fashion
Get a front door key to the Playboy mansion
Gonna date a centerfold that loves to
blow my money for me

(So how ya gonna do it?)

I'm gonna trade this life
For fortune and fame
I'd even cut my hair
And change my name

'Cause we all just wanna be big rockstars
And live in hilltop houses driving fifteen cars
The girls come easy and the drugs come cheap
We'll all stay skinny 'cause we just won't eat
And we'll hang out in the coolest bars
In the VIP with the movie stars
Every good gold digger's
Gonna wind up there
Every Playboy bunny
With her bleach blond hair
And we'll hide out in the private rooms
With the latest dictionary and
today's who's who
They'll get you anything
with that evil smile
Everybody's got a
drug dealer on speed dial
Hey hey I wanna be a rockstar

I'm gonna sing those songs
that offend the censors
Gonna pop my pills
from a pez dispenser
Get washed-up singers writing all my songs
Lip sync em every night so I don't get 'em wrong

Well we all just wanna be big rockstars
And live in hilltop houses driving fifteen cars
The girls come easy and the drugs come cheap
We'll all stay skinny 'cause we just won't eat
And we'll hang out in the coolest bars
In the VIP with the movie stars
Every good gold digger's
Gonna wind up there
Every Playboy bunny
With her bleach blond hair
And we'll hide out in the private rooms
With the latest dictionary and
today's who's who
They'll get you anything
with that evil smile
Everybody's got a
drug dealer on speed dial
Hey hey I wanna be a rockstar
Hey hey I wanna be a rockstar

Note that they did _not_ censor the sex reference (mile high club) nor the thing about not eating to stay skinny, which is certainly more problematic than the word "drug".


Oh and when I'm not busy pulling my hair out over the censorship issues, I really enjoy watching the video and trying to guess who the people are -- there is a wild mix of famous and unknown people. I spotted Nelly Furtado, Gene Simmons (of Kiss), Kid Rock, and a couple more who I knew I knew but just couldn't remember their names. For an amazingly complete list by somebody who clearly had too much time, click here.

PS just noticed they censored "assholes" as well. Maybe they felt it didn't really rhyme with "tassles"

Tuesday, January 15, 2008

the birds and the bees

... and most importantly the platypuses!

I think I can now reveal the cover design as it's only a few months till publication date (May). So the book is going to look like this:





more details to follow soon -- web page for the book being built.

Monday, January 14, 2008

gelatine for creamier gelati

A food scientist has suggested that peptides derived from gelatine, a common food ingredient, could serve to make frozen food last longer and keep ice cream soft and creamy. Read my story: Ice-cream without the crunch.

I really do believe that this is a very promising approach, as gelatine is such a cheap and cheerful starting material. However, the nerdy nitpicker in me insists on mentioning that the author of the paper exposed his scientific illiteracy when he wrote in the discussion:
"We hypothesize that these three oxygen atoms, which lie on a
plane, constitute the ice binding face of these gelatin peptides."
... and then went on for 2 paragraphs discussing the importance of the three oxygen atoms on a plane.

He should have known of course, that any combination of 3 oxygen atoms in the universe, or any 3 points, for that matter, lie on a plane. Unless they lie on a straight line as well, they also _define_ a plane. That's the reason why three-legged structures like easels can't wobble. So this "observation" doesn't prove anything, except that somebody didn't pay attention in their maths lessons. I am amazed that this got through peer review and into a journal published by the American Chemical Society.

Sunday, January 13, 2008

science in fiction

in the current issue of Nature there is a review of three books representing the rather rare species of "science in fiction", written by Jennifer Rohn, the editor of the website www.lablit.com, who is trying to raise the profile of this genre. Just wait till I get round to writing novels -- of course they will have scientists as their protagonists ...

Saturday, January 12, 2008

greed is bad for your mental health

It's always been kind of obvious to me, but apparently not to Tony Blair -- that greed doesn't make people happy. Psychologist Oliver James has explained this in a little more detail in his book "Affluenza" which came out a bit over a year ago, and now in a companion volume, which is a bit more academic, and which is called "The selfish capitalist: the origins of affluenza." Basically, James says that countries with a more social-democratic model of capitalism, such as Germany, have half the rate of depression and similar mental illness as the US, UK, and those that follow the "greed is good" philosophy of Blatcherism, so he concludes that a culture based on excessive greed and inequality is bad for people's mental health.

Basically, you'll probably find all the arguments in the works of Erich Fromm from the 60s and 70s already (e.g. To have or to be?), but if you need them spelled out in the modern context, take a look at these:

Affluenza (paperback edition) reviewed by Nicholas Lezard
The selfish capitalist reviewed by Madeleine Bunting
Selfish capitalism is bad for our mental health (an essay by Oliver James)

Friday, January 11, 2008

our man in havana

The former CIA agent who revealed to the world exactly what the agency did to Latin America, Philip Agee, has died aged 72. In recent years he lived in Germany and Cuba and ran a travel agency specialising on travels to Cuba (obviously). Read his obituary here -- it's more interesting than most.

Thursday, January 10, 2008

cent ans et un jour

how very rude of me to have missed the 100th birthday of Simone de Beauvoir yesterday. I believe I have read all her novels as a teenager, but I never got round to reading Le deuxieme sexe, which sits on my shelf waiting for me.

Wednesday, January 09, 2008

love is a battlefield

... and even chemical warfare seems to be quite common.

What I've learned from the current edition of Nature is that Drosophila males have a peptide in their semen, known as the sex peptide, which drastically changes the behaviour of copulated females, such that they reject any further offers they may receive.

Researchers have now found a receptor for this peptide, which is not only of interest for the fans of Dr Tatiana, but also in a more general sense as a model for a very clear connection between a chemical switch and a change of behaviour.

The sex peptide seems to be widespread among insects, so there is the chance that an artificial mimic could be used to control insect populations. Also, while it hasn't been identified in mammals yet, it is quite possible that similar mechanisms exist even in our own species and remain to be discovered.

PS: Evidence that flies and people aren't that different:
Drunken flies get hypersexual
Chronic boozing sends male flies chasing after any and every potential mate.

Tuesday, January 08, 2008

sesame street on the brain

Rule no. one of science: if you give boring names to the things that you discover, nobody will pay any attention. So researchers studying the development of the brain have named two key proteins ERNI and BERT (obviously, as Sesame Street was also supposed to serve the development of the brain, and as these proteins tend to fight each other), and bingo, they got my attention. I have to say in my defence, though, that it was a very slow news week for science last week, so there wasn't much else really.

Anyhow, here's their story:

BERT and ERNI proteins control brain development

Scientists at University College London have discovered how two proteins ¬called BERT and ERNI interact in embryos to control when different organ systems in the body start to form, deepening our understanding of the development of the brain and nervous system and expanding our knowledge of stem cell behavior.
The new research published this week in the open-access journal PLoS Biology solves the puzzle of how vertebrates prioritize the order in which they begin to develop different sets of structures. During development, only a few signals instruct cells to form thousands of cell types, so the timing of how cells interpret these signals is critical. An international research team led by Professor Claudio Stern of the UCL Department of Anatomy & Developmental Biology has shown that the first stage of development of the brain and nervous system is, paradoxically, a block on its progression.
The scientists describe a sequence of reactions that take place when vertebrate embryos are only a few hours old that together act as a timing mechanism, temporarily preventing the development of neural cells (cells that go on to form the brain and nervous system). This gives a head start to other cells in the embryo that will go on to create the body’s internal organs and skin, and prevents the nervous system from developing prematurely.
Dr. Costis Papanayotou of the Stern laboratory discovered a new protein, BERT, which then binds with the protein ERNI (also discovered by Professor Stern’s team) and other proteins to unblock a gene called Sox2, which gives the green light to cells to start forming the brain and nervous system.
Professor Stern said, “Scientists have been looking for a long time for the switches that determine when cells in the embryo take on specific roles. Our work shows that the proteins BERT and ERNI have an antagonistic relationship: BERT is stronger and overrides ERNI’s suppression of the Sox2 gene, which has a crucial function in setting up the nervous system. As the Sox2 gene is also needed for stem cells to retain their ability to take on a variety of roles in the body and to renew themselves, this research also advances our knowledge of stem cell behavior in adults, which could have implications for this growing area of medical research.”


Citation: Papanayotou C, Mey A, Birot AM, Saka Y, Boast S, et al. (2008) A mechanism regulating the onset of Sox2 expression in the embryonic neural plate. PLoS Biol 6(1): e2.doi:10.1371/journal.pbio.0060002

Monday, January 07, 2008

books for cuba

on my visits to Cuba I was impressed by the high level of scientific research conducted there in spite of extremely difficult conditions. The advanced biotechnology R&D in Cuba represents a real opportunity for the country to overcome isolation and poverty by exporting products that the majority of the world population desperately need but can’t afford to buy from the big pharma corporations (Current Biology vol. 14, no. 11, pp R401-R402, 2004). Surprisingly for me, the access to information (both electronic and printed) was at least as significant a problem for researchers in Cuba as the shortage of hard currency for the import of instruments.

It occurred to me that I have lots of scientific books that I don’t really need, e.g. books that I reviewed, or ones that I once needed for a long-forgotten research project. I have therefore taken up the monthly (or so) routine of sending one of these books to a friend in Cuba who has agreed to make sure that each book is made accessible and useful for as many researchers as possible. (It appears that the copies of my own books which I brought on my visit are now making a complete tour of the island!)

If you have any science books (in English) that you no longer need and that take away precious shelf space, I encourage you to do the same. A typical book (800g) will cost around GBP 3 to send (surface mail from the UK) and it will be immensely valuable and useful for scientists there. (The packaging comes free as I recycle cardboard boxes and jiffybags in which I have received books myself.) If you would like to send some books too, please contact me and I can provide suitable mailing addresses.

Sunday, January 06, 2008

magic and danger

The first two albums that Shakira recorded as a teenager, Magia and Peligro, are officially buried and will never be released again. Thus I was pleased to see that they are at least represented in MySpace:

Magia:


Peligro:


Each site has six tracks from the respective album. Which together would make a nice CD ...

Saturday, January 05, 2008

mathematics

... apart from being the year of the frog (as I mentioned earlier), 2008 continues the series of science years in Germany as the Mathematics Year. Events and PR fun will be spread throughout the year, presumably, following the recipe successfully applied to the recent years of physics (2005), humanities (2007), and chemistry (errr, I should remember that one, I think it was 03 or 04).


... and then there is an anniversary to celebrate ... I have no idea how I came to be included in this mailing list, but here is what I received:

January 5, 2008 marks the
60th anniversary of the publication of Sexual Behavior in the Human Male.

To learn more about this groundbreaking book, the history of Dr. Kinsey's work,
and the evolution of the Kinsey Institute,
visit our website at: http://www.kinseyinstitute.org/about/history.html

You can hear Dr. Kinsey's brief comments on his research through a video clip,
or read some of the selected findings from the first 'Kinsey Report.'


... well, it may have to do with my two-day stint as a sexpert, around valentine's day 2006 :) As Kinsey also used statistical methods, I guess that counts as mathematics too.

Friday, January 04, 2008

proteins linked to autism

There is a news story on Chemistry World (not mine) about the crystal structure of the complex formed by neuroligin with beta-neurexin. Apparently, mutations in these proteins have been linked to autism.

Obviously, the crystal structure is not going to provide any quick answers about the disorder, as there are at least a dozen genes contributing to the symptoms of autism, but it's good to see things are happening at the molecular scale, and one day we might even understand how it all fits together ...

Thursday, January 03, 2008

have heart, will travel

organ transplants are a rather messy feature of modern medicine -- the donor organs can only be stored very briefly on ice, and they may not reach the patients who need them on time or in a reasonable condition.

Researchers are now developing devices that keep donor organs alive in physiological conditions, so they can be kept for longer and can be tested for their functionality before being implanted. Devices for hearts and kidneys are already available, but the big challenge, and the area where such a device could save many lives, is the liver. I've written a feature article about this work which is in the January issue of Chemistry World:

Portable organs
A combination of medical research and engineering could bring an end to the era of putting precious human organs on ice to keep them alive for longer.
... but sadly with restricted access. Should work from university libraries, though.

Oxford research towards the "portable liver" is also discussed in my earlier feature for Oxford Today.

Wednesday, January 02, 2008

from bad to worse

way back in 1999 I applied for a few London-based jobs, thinking that I would be able to commute in, as the trains could only get better. Since then, they have become worse, and worse, and worse still. And they keep increasing the prices at 2-3 times inflation every year, just to add insult to injury. I believe that under Thatcher (when they were still state-owned, British Rail), there was an official policy of "pricing off demand", i.e. raising the prices to turn people away from the overcrowded trains. Now it seems to work very similarly, only that nobody admits it. Here's today's bad news, but I'm sure we'll hear tomorrow that more lines have to be closed because the wrong type of snow has fallen onto them.

On the plus side, am I glad I never got a job in London. It's already a challenge to go there once a month ...

Tuesday, January 01, 2008

year of the frog

According to a news report out in Nature, 2008 will be the year of the frog. Oh, and also of the potato, greek feta, sanitation, and 1/3 of the year of Planet Earth.

Very confusing all this, but have a good one anyway !
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