Wednesday, April 19, 2017

crispr sensing

The revolutionary gene-editing technique known as Crispr-Cas has been embroiled in a patent dispute between two leading US research institutions. In one corner, the University of California at Berkeley, where Jennifer Doudna discovered it in collaboration with Emanuelle Charpentier, and in the other, MIT’s Broad Institute, where Feng Zhang’s group first demonstrated its use in living cells.

Now the two institutions are competing against each other again, as both recently demonstrated the usefulness of a different Crispr system for the detection of pathogens. Doudna’s and Zhang’s groups had shown in 2016 that a Crispr-type enzyme called C2c2, now renamed Cas13, targets single stranded RNA, unlike the ones used in gene editing, such as Cas9, which edit double-stranded DNA. Moreover, it doesn’t stop cutting once it has destroyed its target. It goes on to cleave thousands of other RNA molecules that happen to be nearby. This collateral damage provides a useful amplification step enabling the sensitive detection of the original target RNA, whose recognition can be programmed just as in the gene-editing method.

Aiming to turn this into a clinically usable sensor, Zhang teamed up with Jim Collins, also at MIT, who was involved in the race to develop practical methods for rapid detection of the Zika virus.

Read all about it in my latest news story in Chemistry World which is out now (free access if you haven't read any other CW stories this week, they have a free quota):

Crispr enables rapid disease detection




Monday, April 17, 2017

disorder turns 20

Open archives


Today I’ll exceptionally present a feature from the archives that was published in Chemistry World, not in Current Biology.

The occasion is that today is the 20th anniversary of one of my favourite and most impactful papers from my research career, even though it did not result from actual research I did.

What happened back in 1997 was that my friend and colleague Kevin Plaxco happened to know about a paper from molecular biologists coming out on a weird mechanism controlling the growth of the tail (flagella) that certain bacteria use to swim. The tail is a hollow tube, and while it is being built, a certain signalling protein escapes through the tunnel and is lost to the cell. When the tube is finished and closed, the protein accumulates in the cell and thereby signals that no more bricks are needed to extend the tunnel.

What Kevin noticed was an aspect that left the molecular biologist authors of the original paper gloriously uninterested – namely the fact that to carry out its biological signalling function this protein needed to be an unfolded, 1D thread, as opposed to a complex 3D structure as all functioning proteins were supposed to be according to the prevailing dogma that sequence determines structure determines function.

So Kevin told me about this and suggested to write a News & Views piece for Nature, which we did, and which came out 20 years ago today. At the time there were only two or three other examples of “intrinsically disordered” proteins that are functional while unstructured. Mostly the evidence relied on NMR spectroscopy, which invites the objection that maybe the researchers didn’t get the conditions quite right and maybe the protein would be more orderly if they did x instead of y.

The beauty of the system we discussed was that the biological function of the protein made it absolutely necessary to unfold, as it wouldn’t fit through the tube in its folded state.

Anyhow, this turned out to be the beginning of a whole new research field which grew quite impressively over the next years, so in 2010 I had the pleasure of attending a research conference at Barcelona that was all about intrinsically disordered proteins.

And summarising what I learned at this conference, I wrote a feature about the topic which appeared in 2011, and which is freely accessible:

Anarchy in the proteome
Chemistry World, August 2011, pp 42-45
FREE access to PDF file




screenshot of our 1997 News & Views (PDF - if you hit the paywall, try this)

Friday, April 14, 2017

dulci tunes

our home-built hammered dulcimer is a year old now, and while I'm still struggling with the hand alternations, the young musician has performed some lovely music on it, so here are a couple of videos to prove it:

Blossom by Bob Pasquarello & New Year's Waltz by John Dipper

Duo: The sliding dulcimer (by Ed Pritchard, who also plays the other dulcimer and recorded the video)

... and a photo of dulci in action at the French session, James Street Tavern:

Wednesday, April 12, 2017

smelly socks

here comes the round-up of German pieces published in March and April, including serious science on zinc fingers and f group chemistry, and slightly less serious stuff on champagne and smelly socks.


f-Gruppen-Chemie: Opposition erwünscht
Chemie in unserer Zeit 51, 138-139
restricted access

Netzwerk Leben: Zinkfinger gegen Fremd-DNA
Chemie in unserer Zeit 51, 82
restricted access


Ausgeforscht: Große Blasen, kleine Blasen

Nachrichten aus der Chemie vol 65, p411
restricted access

Ausgeforscht: Socken mit Katalysator
Nachrichten aus der Chemie vol 65, 511
restricted access

Monday, April 10, 2017

secret life of trees

Open Archive Day

A year ago, I wrote a feature on communication and (almost) cognitive abilities of plants, citing the extremely successful popular science book by German forest ranger Peter Wohlleben Das geheime Leben der Bäume (The Secret Life of Trees) as evidence for the observation that this topic appears to resonate with the zeitgeist.

Since then, his book has been published in English (The Hidden Life of Trees: What They Feel, How They Communicate-Discoveries from a Secret World; Greystone Books,Canada; Sept. 2016) and French (La Vie secrète des arbres; Les Arènes; March 2017) translations, I've seen the main evening news on France 2 running a major report based on the book and conjuring up holographic trees in the studio, and the original is still in the bestsellers list in Germany, so I'm guessing it still resonates.

As the feature is now in the open archives, here's a chance to read it for free:

Could plants have cognitive abilities?




The French edition of Wohlleben's book, published March 2017.

Saturday, April 08, 2017

highly charged

I have half a cover story in the new issue of Chemistry & Industry - as the cover is about future means to power transport, including biofuel and batteries. My feature is the one about batteries:

Highly charged
Chemistry & Industry vol 81, issue 2, pp 22-25

Open access to full text (HTML) via SCI website

Restricted access to PDF files via Wiley Online Library



Chemistry & Industry issue 2 / 2017

Monday, April 03, 2017

eastern evolution

Homo sapiens came out of Africa and conquered the world, more or less in one sweep, or so we used to think. Exciting new finds from China, however, suggest that a significant movement to the East - convenient inasmuch as it allowed people to stay broadly in the same climate and vegetation zone - happened much earlier than previously thought, and much earlier than the expansion into Europe.

I've discussed the latest discoveries from China, also including two archaic human skulls that have been speculatively linked to the Denisovans so far only known by their DNA, in my feature which is out now:

A new continent for human evolution
Current Biology Volume 27, Issue 7, pR243–R245, 3 April 2017

Restricted access to full text and PDF download

(will become open access one year after publication)


Magic link for free access

(first seven weeks only)





The Xuchang 1 (A, superior view) and 2 (B, posterior view) crania discovered at the Lingjing site. (Photo: Xiu-jie Wu.)

Monday, March 27, 2017

coming out

Open Archive Day

my gender transitions feature from last year has come out of the paywalled closet and is now freely accessible to all people of all genders and orientations, enjoy:


Transitions to new concepts of gender





Orange is the new something or other - gender divisions at the Science Museum, London (own photo).

Monday, March 20, 2017

robot ecology

robots are beginning to take over our planet, so it's time to start worrying what they will do to the existing systems, from ecology to economy. Which was a sufficient excuse for me to write a third robot feature (previous attempts date from 2015 and 2013), which is out now:

How will robots integrate into our world?
Current Biology Volume 27, Issue 6, pR199–R201, 20 March 2017

Restricted access to full text and PDF download
(will become open access one year after publication)

Magic link for free access
(first seven weeks only)




The robot exhibition at the Science Museum, London (own photo). I'll also add some of my pics from that exhibition to my flickr photostream.

Wednesday, March 15, 2017

misa campesina

As part of Oxford twinning link with León, Nicaragua, it has become a tradition that the Misa Campesina Nicaragüense, a folk mass emphasising workers rights and their suffering under capitalism, is sung here once a year (although the most recent press report appears to be from 2011). To give an impression of the music, here's a 3-minute potpourri of the misa performed by Nicaraguan singer Katia Cardenal.

I managed to miss this in the last 22 instalments, but this year there was an official call for people to join the band and choir, which the young musician forwarded to me, so I got to play the lovely tunes on the flute, plus a few bars worth on the guitar.

There were a few people from Nicaragua in the audience, including a woman in the first row who watched us (the band) very closely. Before the last piece she got up to make a speech - turned out she is Guisell Morales, the Nicaraguan ambassador to the UK.



The choir warming up (own photo). The Nicaraguan embassy has shared some photos (of me even) on twitter.

Related to this, the Oxford Leon Link has an exhibition on the occasion of the 30th anniversary of the town partnership. This is at the South Oxford Community Centre in Lake Street, although I'm not sure about times and dates.

We also had a visit from a coffee farmer from Nicaragua who gave a talk during Fairtrade Fortnight.





Monday, March 13, 2017

dances with science

Open Archive Day

I hear Rambert (formerly Rambert Dance Company) are on tour and perform at the New Theatre Oxford this week (Wed-Fri), so it's a good excuse to dig up a feature I wrote in 2011 about their work with scientist in residence Nicola Clayton (whose research field is corvid intelligence, hence the title):

Dances with magpies



image source



Monday, March 06, 2017

losing ground

Even after the international year of soils (which was in 2015, in case you missed it), the world cares too little about the ground we stand on and which actually feeds us. On current trends, most fertile soils may disappear well within this century, and food security with them. It's a global problem that political leaders could fix with sensible regulations, if they weren't so busy deregulating everything.

My feature on the state of our soils is out now:

Losing the soils that feed us
Current Biology Volume 27, Issue 5, pR163–R166, 6 March 2017


Restricted access to full text and PDF download
(will become open access one year after publication)

Magic link for free access
(first seven weeks only)



We often dismiss soil as the dirt below our feet, yet it is a vital resource for food production as well as a highly complex and insufficiently understood ecosystem. The image shows farmers in Kyuso, Kenya terracing part of their land in order to minimise erosion losses. (Photo: ©FAO/Thomas Hug.)
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