Monday, June 27, 2011

astrobiology - second edition

Back in 2006, Johns Hopkins University Press published Astrobiology: a brief introduction, which I had co-authored with Kevin Plaxco. Since then, the field has become quite popular. (I would love to take credit for it, but maybe it’s just dumb luck.) The quest for life or at least habitable planets in the rest of the Universe is now a universally supported endeavour to the extent that NASA now justifies much of its research and exploration work with that goal.

The discovery of extremophiles in the most unlikely locations here on Earth has played a large part in propping up our hopes that life may also exist elsewhere. Add to that the discovery of more than 500 extrasolar planets in just 16 years since the first one was reported, and you get a proper scientific gold rush.

Thus, our 2006 book was beginning to look out of date and there was a strong case for a new, revised and expanded edition, which we prepared over the last year or so. We have revised the entire text, added a glossary and lots of new illustrations. New discoveries are included up to and including last December’s arsenic eating bacteria. With all this, the book will be around 90 pages thicker than the first edition, but hopefully just as readable.

The cover design, which we all love, has been kept. Only the colour of the title will now be green instead of orange, so you can easily tell the second from the first edition. The new version should be available by September in the US, maybe a few weeks later in the rest of the world.




In preparation for the release, I’m also updating the astrobiology web pages, but that’s work in progress still. (At the moment the ISBN numbers and the cover are there, but the exact page number and amazon links are still missing.)

Saturday, June 25, 2011

hidden treasures

After the most-viewed flickr pix, here now a selection of the least-viewed and underappreciated. There are quite a few flowers, such as this tulip with dew drops:

tulip1102

water fountains, like this one at Barcelona:

Plaça de Catalunya by night

pedestrian bridges, like this one in Amiens:

passerelle02

and our local bumblebees, such as this one:

bee10

Some of the other bumblebee pictures are in double figure views only because I posted specific links on twitter - this adds 10-15 views in a minute.

But maybe I just haven't found the right flickr groups yet to promote these types of photos ? Some of the highly specific groups I'm in, specialising on windows, pedestrian bridges, fountains, etc. seem to have little effect.


Anyhow, a set of my hidden treasures is here.

Friday, June 24, 2011

suerte

Spanish/English mixed version of Jason Mraz' song Lucky, featuring the Mexican singer/songwriter Ximena Sariñana:




As luck would have it, I just found out that Ximena has an English album in the pipeline, due to be released in August. There is already a video for the first single, Different, and I love both the song and the video (and the cuddly yellow monster, too), so even though I only meant to post the Suerte video, here comes another one ,enjoy:



so, mucha suerte to Ximena, at least in the UK she will need it.

Wednesday, June 22, 2011

flickr winner

So, after one year on flickr, I'll now reveal what is by far and away the most-viewed of my pictures. Strangely, it's not one of my wonderful bumblebees, even though they are nice and fluffy, very colourful, and have six legs. Instead, it turns out to be a Homo sapiens female with only two legs and very short shorts. Who would have thunk.

browsing

I do like the picture, of course, partially because of the composition with the female figure cutting across the white table cloth, also because I have managed to disguise the face quite cleverly. But I wouldn't have picked it for the top spot. Oh well. Some of the underappreciated gems from my photostream to follow soon.

For the complete chart countdown, click the "flickr" tag below. Alternatively, visit my flickr set more than 100 views.

Tuesday, June 21, 2011

neuroscience in China

In a rare departure from my comfort zone, I wrote a big feature article about neuroscience in China, which (like much of Chinese science) has seen a massive boost in the last 12 years, to the extent that new institutes can now attract both Chinese researchers returning from the US and international experts willing to try a new experience.

From the epic list of addresses at the top of my thank-you email I gather that it took at least 12 kind and helpful people to help me find my way in this big topic, and during the four weeks when I kicked this around, I certainly learned a lot.

So, the result of all this is out today:

Boom time for neuroscience in China
Current Biology, Volume 21, Issue 12, R441-R444, 21 June 2011
doi:10.1016/j.cub.2011.06.001

and as it is part of some bigger event across the Cell Press journals, it is on open access here:

summary page / PDF file.

It is accompanied by a Q&A piece featuring Fang Fang (not mine, this interview was set up by the editors separately), which is also on open access.

Monday, June 20, 2011

I'm blue

The silver medal in my flickr countdown goes to an abstract architecture photo. This is a bit odd, as these pix, much as I love them myself, normally don't get more than the median number of views. My guess is that the group "Photography is not a crime" is mainly responsible for this. I mentioned in the caption that I got told off by a security guard, and people responded to that, so I guess some people will have clicked on the photo to read the story, rather than to appreciate the photo. But it's all good, they get a nice photo as a bonus:

blue01

This is in London, between Paddington station and Little Venice.

Sunday, June 19, 2011

summer legs (No. 3)

No. 3 in my flickr charts is one of my lucky ones, and one of my very first candid shots. The stripes caught my attention and I just hit the button. Only when I got home and looked at it on the screen I noticed that the legs are looking nice too, especially the way they seem to be forming arrows pointing downwards:

summer legs

Saturday, June 18, 2011

jogger on the fast track

This candid snap of a jogger who just sped past me is no. 4 in my flickr charts, and still gaining views and faves, so may make it to a higher position. While I have no particular interest in athletics or in athlete's legs, I like the way the jogger's shadow is enclosed in the triangle between the legs and the ground.

sporty

(click photo to see larger versions in flickr / click the "flickr" tag below to find other photos in my countdown)

Friday, June 17, 2011

Lady Gaga and philosophy

To my utter shock and bewilderment, I have just found out that neither of the two publishers that run book series on popular culture and philosophy has yet published a book about Lady Gaga and philosophy. In fact, searching the exact phrase “Lady Gaga and philosophy” I got only two hits, one to the twitter profile of someone who lists her interests and ends the list with these two items (as you would), and the other to a philosophy blog which also notes the lamentable absence of this title.

So, while we are all waiting with baited breath to find out what the serial philosophers will have to offer once they have woken up to the semiotic treasure trove that is the work of Gaga, I’ll start compiling a few suggestions of topics they may want to consider:


Is it music? Why Mozart might have written “Bad Romance” if he were alive today (for more about this, see here)

Is it art? The school of gagaism and its position in the development of occidental art

Baby you were born this way: The quest for sexual identity in the 21st century.

I’m in love with Judas: Gaga vs. God

Scheiße Scheiße be mine: the language and languages of gagaism

P-p-p-pokerface: The semiotics of make-up and masks

I am my hair: Hair style as a cipher for personality in postmodern society

I’m on the edge of glory: Feeding the reward system in the age of individualism

Papa paparazzi: Iconography and perceptions of fame

Monster ball: Identification and motivation of fans and followers

Gossip girl: The education of a cultural icon


All suggestions for additional chapters, and indeed authors, welcome.

I notice that Open Court have among their forthcoming titles "Rolling Stones and philosophy" (due to join a male-only club of artists like Bruce Springsteen and U2), so they are clearly catching up and might get round to the Gaga title in a few decades. My favourite title on their list of 59 books is "Woody Allen and Philosophy: You Mean My Whole Fallacy is Wrong?" (2004). The competitors at Wiley-Blackwell have Metallica as their only musical entry. Gaga apart, I really do think one of them should have covered the philosophy of Alanis Morissette by now.

Update June 2012: Open Court now list "Lady Gaga and philosophy" among their future publications, but without a date, so I'm guessing it will be 2013 before it comes out.

Update April 2015: Open Court still has it under "Forthcoming Titles: 2015 and Beyond" at the bottom of the list, now with a release date of 2017. These guys should get their priorities in order. Still no news from Blackwells.





Oh, and as bonus material, here are my random thoughts on the new album, jotted down a bit hastily after the first two or three times playing it:

Would I still enjoy this album if it had arrived in a brown cardboard sleeve and I knew nothing about the artist?
Actually, I think I would. Not all tracks are great, but there is an interesting variety and I sense the genuine artist's urge to express herself in many details. I'm not wildly excited by the first three tracks including the title track, but love the middle section starting with Judas (which I read as an attempt to recapture the glory of Bad Romance).

As someone familiar with several European languages, I find Scheiße interestingly disturbing - it mangles fragments of half a dozen languages into a meaningless but attention-catching pidgin pudding. Gets me every time. My attention tends to wander off after Bloody Mary, and come back for You and I, strangely.

Surely it's not to everybody's taste and will irritate many, but that's what art is supposed to be like. So please ignore the hype and try it with an open mind.

Thursday, June 16, 2011

cyclist, abstracted

No. 5 in my flickr chart countdown is a cyclist. There's no shortage of these in Oxford, and I've snapped a few that were unfortunate enough to cycle past my camera, but most of these snaps are a bit boring. In fact this one is the only one I posted on flickr, and I love it because the backlight, the perspective, the stripes, and the crop all work together to make it a bit more abstract and artsy. It also helps that the face and legs are out of sight so viewers (and even men) can focus on the photographic qualities.

cyclist1103

Needless to say that none of the qualities described are down to my planning. This cyclist just brushed past me on the footpath and I instinctively pushed the button.

Wednesday, June 15, 2011

Greens on course for federal government

I've just realised, somewhat belatedly, that Germany's Greens have become the second strongest party in the wake of the Fukushima accident and have stayed in second place quite firmly since then.

Today's Forsa poll indicates that in response to the "Sonntagsfrage" (what would you vote if federal elections were held next Sunday?), the votes were distributed as follows:

31% CDU/CSU (conservatives)
26% Green
23% SPD (labour)
9% Linke (left)
4% FDP (liberal)

source, and additional polls from previous weeks

This would give a putative green-red coalition a solid majority, as the FDP (currently Merkel's junior partner) would fail to get into parliament, staying below the 5% threshold.

For someone who first voted in 1983, these figures just look crazy. Having been a member of the Greens from the early 80s to 2001, I never thought I'd live to see this happen.

Mind you, it's only a partially due to voters becoming greener, and a large part due to the party becoming more mainstream and normal since the days that I witnessed.

Tuesday, June 14, 2011

candid portrait

No. 6 in my flickr charts is again untypical, as it is a candid portrait - this person stood right in front of my camera at a pedestrian crossing and I couldn't resist the early morning sun playing with her hair:

candid portrait

Most of my candid shots do not contain a recognisable face though - if only because we tend to have strong opinions on human faces and it is difficult to appreciate the qualities of a photo when we're busy responding to the face.

Although it has attracted more than 100 views, this photo hasn't done particularly well considering that it is in more than 25 groups, so there have been only 4 clicks per group. Anyhow, I do like it, still.

Monday, June 13, 2011

Medem medley

All seven of Julio Medem's feature films are mashed up in this six-minute clip, highlighting recurring themes. Must-see for all fans:

Saturday, June 11, 2011

flickr charts no.7

According to the stats I recorded in the first week of June (there has been a fast riser since then) No. 7 of my most-viewed photos is my Escheresque self-portrait. As will become clear in due course, this picture is rather untypical of the top 8, but still my self portraits have generally attracted more viewers than most of my pix.

with apologies to Escher

Click the image to see larger versions in flickr.

I'm counting down from 8 to 1 - use the "flickr" label below to find the other entries.

Friday, June 10, 2011

rabiosa

One wouldn't be able to tell from the UK media, but Shakira has a new video out from the Sale el Sol album, called Rabiosa. The Spanish version features El Cata, the English one PitBull. Here's the Spanish one:



Oh, and the Sale el Sol tour is still going strong too, sadly I can't attend at the moment ...

Thursday, June 09, 2011

top 8 flickr pix: No. 8

As I'm approaching the first anniversary of my flickr photostream, I'm going to post some of the best-clicking pictures here, and also some of my favourites that may not have been appreciated by that many flickr visitors so far.

Counting down the top 8 most-viewed pix, we start with No. 8, taken on a rainy evening at Lyon:

lyon21
(click image to see larger versions in flickr)

This has done reasonably well thanks to the award-driven group "Photography in the Rain".

Wednesday, June 08, 2011

sticky stuff

My long essay review of the monograph

Biological Adhesive Systems: From nature to technical applications
By Janek von Byern, Ingo Grunwald (eds.)


is in this week's issue of Chemistry & Industry (No. 11), page 27. It's premium content, I'm afraid, so only the lucky few with a subscription or institutional access can read it online here. For the rest of us, here's a snippet describing the most entertaining part of the book:

The prize for the most accessible chapter goes to the Australian frogs of the genus Notaden. Apparently these creatures are so well-rounded that they can’t cling on to each other with their short limbs during mating. Which is why they need glue, literally, in order to stick together while they are exchanging body liquids. The author tested the adhesive power of the frog secretions by sticking two full, cold and humid beer cans together, lengthwise in one experiment and bottom to top in another.


Tuesday, June 07, 2011

bees, ETs, ACGTs, and old samples

Among the German articles published in June we have bees, ETs, re-evaluation of Stanley Miller's samples, and third generation genome sequencing:


Rückkehr zum Ursprung des Lebens
Chemie in unserer Zeit Vol 45, No 3, page 158
Article first published online: 6 JUN 2011 | DOI: 10.1002/ciuz.201190041
limited access to PDF file

Genomsequenzierer. Die dritte Generation
Chemie in unserer Zeit Vol 45, No 3, pages 184–187
Article first published online: 6 JUN 2011 | DOI: 10.1002/ciuz.201100553
limited access to PDF file
most recent English article on this topic

Ausgeforscht: Und täglich grüßt E.T.
Nachrichten aus der Chemie Vol 59, No 6, page 605

Biowissenschaften: Keine Ernte ohne Bestäuber
Nachrichten aus der Chemie Vol 59, No 6, pages 629-631
most recent English article on this topic


Summary: Das Sterben ganzer Bienenvölker und der Artenschwund bei Hummeln bedrohen die Landwirtschaft in Europa und Nordamerika. Daran sind vermutlich mehrere Faktoren beteiligt, auch Pflanzenschutzmittel stehen unter Verdacht.


PS: The bees article also features my photo of a Bombus hypnorum (tree bumblebee):

bee 31

(click image to see larger version in flickr)

Wednesday, June 01, 2011

protein portal

Gabriel Waksman's group at the Institute for Structural and Molecular Biology (shared between Birkbeck College and University College London) has an exciting article out in tomorrow's issue of Nature, on the molecular machine which builds pili, i.e. the "hairs" that pathogenic bacteria use to attach themselves to their host. I wrote the following summary for the ISMB website:


The ability of bacteria to cause diseases in humans or animals depends, among other things, on their ability to stick to their host in order to be able to establish an infection. Many kinds of bacteria do this with the help of very thin protein hairs, known as pili. Like our hair, these pili grow from the root. With a detailed structural analysis of how this growth happens, ISMB researchers have now laid the foundations for medical applications.

E. coli strains causing urinary tract infections are one of many examples of bacteria depending on pili, as they would otherwise get washed away with the urine. The outermost end of their type I pili is a sticky protein that attaches itself to the surface of the urinary tract, using the host’s carbohydrate receptors.

Following the pilus from the tip inward, we first find two linker units FimG and FimF and then a large number of copies of the main hair builder, FimA, which is anchored in the outer membrane. In 1999 and 2002, the team of Gabriel Waksmann (then at Washington University Medical School in St Louis, USA and now at the ISMB) showed that these subunits fit together like pieces of a linear jigsaw puzzle. Each protein subunit has a well known structural pattern (the same that is also found in antibodies), but one bit of this structure is missing. The following subunit brings along the missing bit that latches into the hole and completes the structure.

This structural incompleteness of each single subunit means that each of them on its own is unstable in the periplasm, the space between the outer and the inner membrane of certain bacteria (only Gram-negative bacteria have this feature), where pili are manufactured. Therefore, they are being looked after by molecular chaperones, i.e. proteins that can protect these contact points from aggregation.

Now Waksman’s group has elucidated the detailed structure of a complex involving the outermost, “sticky” FimH subunit of an E. coli pilus, as it is being exported through the outer membrane by a specialised protein export machine (the FimD usher) and still being guarded by such a chaperone, FimC. The structure, which shows the pilus tip protein lined up inside a hollow cylindrical channel of the usher protein, is unique in that it is the first such structure of a complete protein export machine including the proper protein to be exported.

Previous biochemical studies had implicated the front end of the usher protein, the N-terminal domain, as a binding site for the pilus proteins to be exported. The new crystal structure, however, shows this site to be idle, while a second site, near the other end of the usher protein, the C terminus, binds the FimH-FimC complex. The authors conclude that the usher has two binding sites such that the growing pilus can remain anchored to one, while the next subunit to be added to it docks to the other.

The authors also conducted a crystallographic analysis of the empty FimD usher for comparison (although the structure of a similar, empty usher, PapC, had been solved before). They found that the binding of the substrate proteins induces a major structural rearrangement. The empty usher has an oval pore sealed by a specific part of the protein, the plug domain, while in the presence of FimH-FimC, the protein adopts a perfectly cylindrical shape, and the plug domain moves out of the way to open the channel for the substrate proteins.

Because this highly complex mechanism by which E.coli and similar bacteria assemble their pili has no equivalent in higher organisms, it appears to be a very promising drug target for new antibacterial therapies. Researchers hope that structural details of this mechanism, such as those revealed in this study, will help them find a way of stopping bacterial hair growth. This may offer a fundamentally new way out of the current crisis caused by drug resistant bacteria, which seem to be spreading ever faster.

The crucial difference is that drugs targeting a non-vital virulence factor such as the assembly of pili, will not kill the bacteria, which has two significant advantages. Firstly, there is less evolutionary pressure in favour of resistance genes, and the evolutionary pressure only applies in the location where the pili would normally anchor the bacteria, e.g. the urinary tract. For the survival of bacteria outside this location, the pili aren’t necessary, so any drugs leaked into the environment don’t breed resistance – in marked contrast to leaked antibiotics.

Secondly, the “disarmed” bacteria may remain present in the organism for long enough to allow our immune system to learn how to fight them most efficiently, such that they act as an immunization against the disease.

Some substances targeted at pilus formation are already under investigation as potential drugs, but the detailed molecular understanding of the process will certainly help to address this target more systematically.

Reference:

G. Phan et al, Nature 2011, 474, 49–53 doi:10.1038/nature10109


Background:

Gross M:
Education in Chemistry 2008, 45 No 4, 141-143
Better than antibiotics?

Groß M:
Nachrichten aus der Chemie 2008, 56, Nr 2, 148
Blickpunkt Biowissenschaften: Bakterien am Schopf gepackt
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