Monday, December 31, 2007

back from my time travel

... having spent some time in the 17th century and beyond, I'll now return to the present and future ...

Have discovered lots of exciting things in the murky old swamps of history, for details click here. In particular, I was surprised how mobile people were in that time (mostly against their wishes, I suspect!) A year ago I thought that all my ancestors were German, and now I have a dozen people from Italy, Switzerland, and France on my records. A nice 1595 picture of two suspected swiss relatives is here. Unfortunately, these two haven't let me enter their website yet, am awaiting response to find out if and how they are related ...



Anyways, I've updated the website, hoping it will work for me while I'm busy with science writing and all that.

happy new year to all !

Sunday, December 30, 2007

playing dumb

There is an interesting comment on women playing dumb when trying to snare a man:

Men want us lobotomised
In speed dating I did a lot better as a simpering, giggly florist than as a dazzlingly literate lawyer
Tanya Gold
Saturday December 29, 2007

As you can see from the 321 responses, it must have hit a sensitive spot. (many are from offended blokes!)

I largely agree with the sentiment expressed in the piece, and have observed this kind of dumbing down myself on occasions.

The fundamental flaw in this "investigation" is, however, that sensible men who appreciate women in the bright-to-brilliant range of the spectrum will most definitely never ever attend a speed dating session. Or any other kind of meat market. So if the author really wants a man to discuss Heidegger with (which I somehow doubt) she should drop by the nearest university's philosophy department rather than any seedy bars.

Saturday, December 29, 2007

earthwatch expeditions

It's the best time to plan adventures for the new year ... The Earthwatch Expedition Guide 2008 has just appeared, and as always there are lots (around 120) fascinating research projects that you can support by taking part as a fee-paying volunteer (or with luck, on a bursary).

The projects, some of which I have covered in my articles, range from archaeology to biology and conservation. They are based on 6 continents and offer all kinds of excitement from scuba-diving through to mountain hiking. There are 10 new projects, including one studying biodiversity in the vineyards of the Bordeaux region. I'm sure participants will get to study the products of those vineyards as well.

You can order a copy of the guide from the Earthwatch office closest to you (UK, US, Australia or Japan) which you can find via the central Earthwatch website.

Friday, December 28, 2007

bacterial hair styles

... well, ok, let's return to some science for a change.

Many pathogenic bacteria, e.g. those that cause infections of the urinary tract, have very thin "hairs" allowing them to stick to cells of their host. Thanks to these hairs, bacteria can invade the urinary tract and avoid being flushed out with the urine. These are known as pili, and their protein subunits are stuck together like lego bricks, i.e. one end has a binding pocket, and the other has a spare bit of protein chain that fits in there, and contributes one strand to the beta-sheet fold.

Before they get assembled into this pile of lego bricks, the subunits are bound to molecular chaperones in the periplasm, which use the same binding mechanism. So how does the subunit get handed over from the chaperone to the neighbouring chaperone? Emanuele Paci and co-workers at Leeds and Gabriel Waksman's group at Birkbeck college London have now presented molecular dynamics simulation that support the so called zip-in zip-out mechanism, which involves one beta sheet opening up like a zip, and the other starting to zip up in a coordinated fashion. Which is just beautiful molecular ballet.

But it is also useful, as potential drugs that can stop pili from growing may soon become an attractive alternative to antibiotics. As they disarm bacteria rather than killing them, the hope is that they will not favour the evolution of resistant strains quite as much as antibiotics do, plus they give the immune system a better chance to train its forces against the bacteria.

The paper comes out in Journal of Molecular Biology, and with luck you may be able to read it via
Science Direct.

I've also written a full-length feature on this topic in German, which is due to appear in February.

Thursday, December 27, 2007

I try to be like Grace Kelly ...

I try to be like Grace Kelly
But all her looks were too sad ...

... well not really.

But if you want to check whether you're related to Grace Kelly, you can do it here.

I am, as I just found out. Our common ancestor is her no. 1822., Leonhard Treusch. Wonder what he looked like :)

Wednesday, December 26, 2007

spending xmas with the family

I've spent xmas with my whole family, all 420 of them. And by the end of the day there were 20 more. Magic.

The explanation is I spent a few hours googling some of my "orphaned" ancestors, i.e. those whose parents I don't know, I found some possible links, sent a grand total of 2 emails to check, and bingo, by the end of the day I had confirmation that I now have 20 people more ... plus a couple of new living (though rather distant) relatives.

One of them has a really nice website. Our most recent common ancestors are his no. 64 and 65. Hey, that's only 6 generations away.

Tuesday, December 25, 2007

white robe

For all who have heard "Do they know it's Xmas" a million times too often (it's on the radio right now!), here is a special present, a new video from t.A.T.u..

The title translates to white robe, but I'll need a dictionary and a lot of time to work out what the lyrics mean. The video is intriguing and stylish, as most of theirs are. They remind me of European cinema (Kieslowski etc.) more than of US/UK music videos. See, for instance: 30 minutes, all about us, not gonna get us -- all available on t.A.T.u.'s MySpace.

enjoy!


PS -- those were the days:

Monday, December 24, 2007

no trains at xmas

One of the questions that have also bugged me since comming to live in Britain has finally been answered: Why can't we have trains at Christmas?

Apparently, the last time a passenger train ran on Christmas day in this country was in 1964. Why? People seem to be forgetting that not all of us believe in Santa Claus. There are lots of muslims, jews, and atheists living in this country who might want to go somewhere on Tue Dec. 25th. If they started trains again, I'd use them just for the heck of it. (A few years ago I had to see a dentist on xmas day, and was really happy with the experience -- happy to see that at least one person was doing something useful, while the rest of the country was stuffing themselves.)

But as things are going rather the other way, we can look forward to a future where there are no trains on Sundays either.

Sunday, December 23, 2007

meet the family

This has been an amazing year for my little family: there are about 100 new direct ancestors on my records, which now go back to 1448 in one line, and to the early 17th century in many more. That's mostly due to the fact that my father is now retired, geographically close to the relevant places, and getting the hang of it. On top of that, my family history website has also helped to create new contacts with distant relatives who provided valuable information.

So over the holiday season I'll be busy updating the 120-pages tome that is our official family history, and the website which presents some extracts from that. To begin with, I have added some of the new family members to the list of last known ancestors. By and by, I will also edit / add to the other pages. Watch this space.

Saturday, December 22, 2007

matters of the heart

Peter Houghton, I learned from his obituary this week, lived 7 1/2 years with an artificial heart, and is thus the longest surviving patient with this device. Love the story of how a thief tried to steal his bag with the battery pack, but got scared off by the alarm (built in to avoid accidental unplugging, not theft!).

They don't mention what he died of, though. Nor which factors limit the survival times.

Friday, December 21, 2007

schengen land expands

"End of passport control as east meets west in EU without borders", according to today's Guardian.

The nine new members of the passport-less travel zone are: Poland, Czech Republic, Slovakia, Hungary, Latvia, Lithuania, Estonia and Slovenia, and Malta.

It's not quite the end of pass port control in Europe, though. We can travel from Talinn to Porto without a passport, but still not from Dover to Calais.

There is still no word on whether the UK will ever join the Schengen land, or indeed the Euro, or any other significant EU activity. I think British governments (and their puppet masters in the tabloid press) are content with their role of operating the brakes on anything European.

Thursday, December 20, 2007

trust me on the sunscreen

I'm a huge fan of the "Sunscreen" speech which secured a UK no.1 hit for film director Baz Luhrmann in 1999. If I'd been asked to write a speech addressed to high school or college graduates, it would have probably ended up very similar.

Favourite lines include:

Do one thing every day that scares you.
[although I only do that about once a year!]

Don't feel guilty if you don't know what you want to do with your life. The most interesting people I know didn't know at 22 what they wanted to do with their lives. Some of the most interesting 40-year-olds I know still don't.


I didn't know anything about the history of this recording though. Only this week I found out that the thing has its own Wikipedia entry where the whole back story is explained. Fascinating stuff. I'll put that on my "I wish I'd written list", right next to Cien an~os de soledad and 99 Luftballons :)

Wednesday, December 19, 2007

counting citations

Once a year, typically around this time, I visit the science citation index to check up on my old research papers. So here is my updated list of citations. I have to say I'm really chuffed to see that people still cite nearly half of the papers, even though I haven't been involved with any of this stuff for almost 8 years. So I'm not travelling around the conferences to blow my own trumpet and all that. Considering they are out there on their own, the papers are managing quite well, I think.

PS I don't include the books in the stats, but they too get cited every once in a while.

Tuesday, December 18, 2007

king and queen

I've added the track "King and Queen" (Wyclef Jean feat. Shakira) to my MySpace profile. I didn't expect much from it (as Wyclef rather ruined the finale of the OF DVD), but found to my surprise that I quite like it.

capturing carbon

I've written a news feature on carbon capture and storage (CCS) technology, which is out today in Current Biology.

Initially, I really liked the idea of running the CO2 in closed cycles, and I was also impressed by the work the Norwegian gas companies do to minimise the CO2 released from their gas production. But the rest of the field left me rather disillusioned, as it turned out to be championed by all those dinosaurs who would like to carry on burning fossil fuels regardless. I mean, anything that the OPEC and the US government agree on can't be right, can it?

Sunday, December 16, 2007

sliding shakira

As I've been posting lots of text and very few images recently, here's something to compensate (borrowed, again, from Adri's wonderful slide page):

Saturday, December 15, 2007

two headlines

... that made me laugh. The first is from Nature:

1) Fetal load and the evolution of lumbar lordosis in bipedal hominins

clear as mud ? If you haven't figured out what it means, try the Guardian's version:

2) How women keep upright while pregnant

Friday, December 14, 2007

books for kids

If you're still wondering what present to buy for the bright young things in your life, Nature magazine has very helpfully reviewed stacks of children's books in yesterday's issue:

overview by Harriet Coles

101 ways to save the Earth -- and other books reviewed by Tom Standage and Ella (7 1/2)

Hawking for kids

... well, there's lots more, see for yourself. The web pages carry a label saying that you'd have to pay for full text access, but as far as I can see, the pages linked to above do give the full text for free.

Thursday, December 13, 2007

modelling the immune system

I heard an interesting seminar this week, on the efforts to better understand our immune system by modelling its function with computer programs. There is an EU-sponsored project underway, called Immunogrid (because it uses computer grids to model the immune system).

The web portal also provides access to educational resources where you (teachers, students, pupils, anybody, really) can have a play with the computer programs.

Wednesday, December 12, 2007

2007 reviewed

This time last year I did a review of research news of 2006, and as that turned out to be great fun, I did it again this year.

On page 26 of the current issue of Chemistry + Industry, you'll find my take on:

* genomes ranging from those of Watson and Venter through to the grapevine;

* chemistry in outer space;

* nanofluids;

* winding back the development clock;

* ... and immortality, of course.

Also, in the same issue, a book review of the tome: Nanoscopic Materials -- size-dependent phenomena. Enjoy!

Tuesday, December 11, 2007

Methane eaters from the gates of hell

Cows produce lots of methane, but our planet itself exhales large amounts of the greenhouse gas, too. Certain bacteria can use the geologically produced methane as a fuel and turn much of it into biomass – a very laudable contribution to our current concern of minimising greenhouse gas emissions. Soils in volcanic areas are often hot and acidic, so any bacteria gobbling up methane in those areas would have to be adapted to these extremes. Decades of research have failed to identify any species that can thrive on methane under such conditions, but now two independent research groups have simultaneously found two of them, and hints that there may be many more.

Researchers from Nijmegen in the Netherlands and Naples, found Acidomethylosilex fumarolicum in hot, acidic volcano mudpots in Italy. This bacterium can thrive in extremely acidic conditions, down to pH 0.8, and its preferred temperature is around 55 deg. C. Surprisingly, it is unrelated to any of the known methanotrophic bacteria, which are all found in one of two large phylogenetics groups, the alpha and the gamma proteobacteria. A. fumarolicum appears to belong to the phylum verrucomicrobia, only very distantly related to proteobacteria. The microbe hunters tracked it down by looking for a key enzyme of methane metabolism, methane mono-oxygenase. Eventually they found three copies of the corresponding gene in A. fumarolicum, but they were quite different from the ones in known methane eaters, explaining why the extreme bug hasn’t been found before.

Conversely, microbiologists from New Zealand, Hawaii, and China, using samples from a geothermal area known as Hell’s Gate in New Zealand, cultivated a microbial strain first, which they baptised Methylokorus infernorum, and which can metabolise methane at pH as low as 1.5. Being unable to identify the methane mono-oxygenase enzyme in this species, they went on to sequence its genome (as you do, these days) and found three copies, again. Like A. fumarolicum, this new methane eater is classified off the beaten track of methanotrophs, in the phylum of Verrucomicrobia.

Now that we know what acid-loving methane eaters look like (genetically speaking), there may be many more new species to follow. The Dutch group has already looked at unrelated samples from Yellowstone National Park (US) and found evidence that similar extremophiles live there, as well. Although they have failed to be discovered for decades, these bugs may in fact be widespread.

References:
A. Pol et al., Nature 2007, 450, 874.
P. F. Dunfield et al., Nature 2007, 450, 879.

Related books:
Life on the Edge: Amazing creatures thriving in extreme environments
Astrobiology: a brief introduction

NB: This story is a blog-exclusive one. From now on, I'll label such stories with the tag "sciencenews", while those published elsewhere have the tag "sciencejournalism".

Sunday, December 09, 2007

embedding slide shows

I don't know much about slide, but I'm wondering, if I embed this code I found in Adri's slide page into my blog, will I really get a copy of her slide show?

Let's try it out:




PS woo-hoo, it works ! now I'll see whether I can do that in myspace too :)

a US general in the family ?

Way back in the early 80s, when Ronald Reagan kindly offered to station lots of Pershing II missiles in Germany, and we were involved in the movement trying to stop that from happening, we used to joke that the general John Joseph Pershing after whom the missiles were named, might be a relative of mine, as my great-grandmother was born Pfersching.

Now I've had a closer look at this, and while I can't quite prove it, the possibility appears to be quite real. The general, like most of the thousands of Pershings in America, is a descendant of Frederick Pershing (1724-1794), born Friedrich Pfersching in Alsace, who sailed from Amsterdam to Pennsylvania on the ship "Jacob" in 1749. While there is lots of information on the lives of Frederick and his descendants, I have found nothing whatsoever on his ancestors. Except that family traditions say they were French Huguenots (as the name Pfershing is definitely German, this tradition may refer to maternal lines?!)

My eponymous ancestor in that generation is Johann Leonhard Pfersching, who married Margaretha NN in Flehingen, Baden (just across the Rhine from Alsace!) in 1759. His father Johannes Pfersching was a cartwright, but I have no further information about him.

So beyond the name and geographic proximity, evidence for any link remains to be found ...

Friday, December 07, 2007

is heme a hormone ?

Well, the short answer is: probably not.

But this is a long story, and an intriguing one (at least for people interested in protein biochemistry). I spent much of this week researching, writing, rewriting etc. the news item which is based on a paper in Nature Structural Biology, this press release, and communications with five different experts in the relevant fields. Essentially, the researchers found that heme (or haem), the cofactor in haemoglobin and other important proteins, binds to the receptors REV-ERBalpha and REV-ERBbeta, which were known to influence circadian rhythm, but were "orphan" receptors, meaning that nobody knows which hormone controls them.

In the paper, the researchers just report that heme binds the receptors, suggesting it may have a signalling role linking metabolism and the biological clock. No objections so far. In the significantly sexed-up press release, however, heme is referred to as a "hormone" and all kinds of wonderful medical applications are promised. The trouble is, hormones normally travel around and convey information from one cell type to another, and there is no evidence of heme doing that. This aspect is discussed in detail in my news piece.

After the piece was finished I hit on another fly in the ointment. I found out that there are two crystal structures of the REV-ERBbeta ligand binding domain in the Protein Data Bank, which the authors of the NSB paper hadn't mentioned to me. According to the crystallographers, these structures include the hormone binding site. Now the authors of the heme paper say that the crystal structures don't include the heme binding site which they confirmed by mutagenesis.

So if heme binds in a place that is distant from the hormone binding site, to me that says loud and clear that heme is not the hormone that regulates REV-ERBbeta. If anything, it is a co-regulator, and the receptors are still semi-orphaned.

Oh, and the claim for medical applications isn't much better. I wouldn't want to take a drug that competes for heme binding sites. I guess the take-home lesson is never to trust a press release ...


PS, the whole heme story reminded me of a classic Irving Geis illustration, where heme is shown as the light source illuminating the protein cytochrome c from within. The picture is shown here as Fig. 2.

found in translation

Not many books, it appears, get translated into Arabic, or out of Arabic, for that matter. Now, the Kalima project aims to get 100 books each year translated from Western languages into Arabic by providing grants to pay for translation work and rights. I think a quarter of those books will be about science, but I don't think they'll bother with mine. In the long term, the project will also improve the success of works written in Arabic by getting them translated to other world languages.

Thursday, December 06, 2007

local authors

Writers in Oxford, our local writers' club, has about 200 members I think. Until recently, there were three of us living in my street. Mary, who interviews authors for the local newspaper, Tilly who writes erotic fiction, and myself. Here is Mary interviewing Tilly in full swing.

The most prominent member of our club right now is Philip Pullman, of course. The new movie "The Golden Compass" is based on his book "Northern Lights", and interviews with him are currently practically everywhere.

Wednesday, December 05, 2007

all things german

here's the monthly roundup of publications in German. This time I made fun of the people inventing pointless new names for companies (they are practically asking for it!) and covered the Nobel prize for knockout mice:

Groß M:
Nachrichten aus der Chemie 55, Nr 12, 1185
Kreativität und Selbsterneuerung

Groß M:
Spektrum der Wissenschaft Nr 12, 20-22
K.o.-sieg für Mäuse und Menschen

Also, a reminder that my German blog on the WissensLogs site is here:

http://www.wissenslogs.de/wblogs/blog/gro-klein

Tuesday, December 04, 2007

flash memory stacked higher

To me, the introduction of the USB stick (flash drive) was the point where the boundaries between technology and magic started to blur. How on Earth do you squeeze a 2 Gbyte memory into that ?

Now, scientists in Korea have developed a way of multiplying the capacity of flash memory devices, using stacked layers of nanoparticles. Read my story

here.

The story also gave me a chance to catch up with the fast-moving technology/magic boundary and to understand (for a fleeting moment) what a flash memory is and how it works. Don't ask me now, though, the moment has passed and I have a new story to write up.

Monday, December 03, 2007

drugs and mental illness

deutsche Version



I can get quite furious about certain parts of the media that want us to believe that drugs (e.g. cannabis) cause mental illness (e.g.schizophrenia), when there is absolutely no evidence at all that the observed statistical link is causal in this direction. There are at least two other interpretations of the same data, namely

1) that an as yet undiagnosed, early stage mental illness makes people more likely to try and enjoy mind-altering drugs, and

2) that both the mental illness and the drug addiction are consequences of the same or similar neural disorders.

A paper in Behavioral Neuroscience, published by the American
Psychological Association (APA), now presents evidence that -- at least in rats -- damage to the amygdala has effects that support explanation no. 2.

Wouldn't it be nice if this could put an end to the headlines screaming that drug X "causes" mental disease Y ? Sadly, I guess that this will be largely ignored by the press. (I proposed a news item on this but was turned down!)

Saturday, December 01, 2007

earthwatch

One of the perks of living in Oxford is the fact that the headquarters of Earthwatch Europe are here. Over the last few years I did a few nice stories about Earthwatch in general and about specific research projects.

Yesterday I popped round to the office to talk to Mark Huxham about his mangrove studies in Kenya and in Sri Lanka. See whether I can get a story out of that, too.

PS I forgot to mention that mangroves are a nice example of life under extreme conditions (high salt concentrations in tidal swamps) that I was unaware of when I wrote Life on the Edge. One day I'll need to write a sequel to that, to incorporate all the things I've learned since it appeared. "Life on the Edge and Beyond" would be a catchy title for that ....
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