Wednesday, May 24, 2017

armchair and time travels

A few months ago, I found the booklet about Colombia in a charity shop - but they didn’t have any other countries I was interested in.

Colombia - a booklet from the “Around the World Program” from the American Geographical Society. Copyright 1959, 1964.

printed in greyscale with green as additional colour throughout. At least 29 colour photos are glued in manually (numbered but not in order, so I may have overlooked one).

I’m wondering if this was based on some kind of subscription / collection model.

Now, at a fleas market, I’ve found a few more to start a collection. At the moment, I’m not quite sure if I’m collecting countries I’ve visited (neither Paraguay nor Uruguay) or Latin American ones, in which case Algeria would be the odd one out. How about subtropical ones? that might vaguely fit.

I’ve actually read the Colombian one (a few more pics of it inside and out are here), very touching how the 1950s perspective is blissfully unaware of essentially all problems the country would face in the following decades. Will also read the other ones at some point.

Monday, May 22, 2017

recycling retroviruses

Last October I went to an epigenetics conference at the IMB Mainz, and one of the things I discovered there was the importance of KRAB zinc finger proteins. This sounds terribly technical and I probably ignored the relevant papers when I saw them in Nature or Science, but as two speakers explained at the conference, it offers a fascination way of understanding how evolution repurposes things. These proteins evolved as defence against retroviruses before our fish ancestors left the oceans, and over time they and the sequences descended from the former viruses became an integral part of our gene regulation.

Fascinating if slightly complex stuff, read all about it in my latest feature:

How our genome’s foes became its helpers

Current Biology Volume 27, Issue 10, 22 May 2017, Pages R365–R368

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 large family of KRAB zinc finger transcription factors goes back to a defence mechanism that originated in a common ancestor of humans and coelacanth (Latimeria chalumnae). (Photo: Mordecai 1998, CC BY-SA 4.0.)

Thursday, May 18, 2017

musical connections

At first glance, my great-grandfather Heinrich Groß (1882-1958), who played oboe and tuba in the military until 1918 and then the cello in an amateur string quartet until the mid 1930s, looks like a one-off on that side of the family tree. His only child, my grandfather, didn’t play anything (although he left a modest record collection including several recordings of Dvorak’s cello concerto). My father only found out about his grandfather’s musical past when another cellist turned up at Heinrich’s funeral to play the Ave Maria.

But stepping sidewise and looking at the (half-) siblings of both the cellist and his wife as well as their offspring, we find an astonishing number of people who played or worked with music in some form or shape. The cellist himself had one sister, with three great-grandchildren (ie my generation but younger), one of whom studied singing and early music and now works as a soprano and music educator.

Heinrich also had a half-brother from his mother’s previous marriage. His niece (the half-brother’s only child, I think) married into a dance school, a tradition which is now running in the fourth generation.

The cellist’s wife, Maria Pfersching (1881-1961; see also this entry on the origins of her paternal ancestors), was also from a relatively small patchwork family, with three half-siblings from her father’s subsequent marriage after the early death (in 1886) of her mother. Her two half-brothers, Heinrich and Fritz Pfersching, were amateur musicians who used to play for local dance events, although we’re not sure what instruments they played.

Among the descendants of her half-sister, Anna Pfersching, we have three professional musicians, with instruments including viola da gamba, bass trombone and cello. I understand they credit their talents to the Pfersching lineage, as the family of Anna’s husband reportedly had no musical inclinations.

Although, considering how Heinrich wrapped up his cello and never played again nor mentioned it to his grandchildren, I would argue that you can never know if you had some cryptic musicians in your family tree. I find this more shocking the more I find out and think about it. Surely, with the number of musical people on both sides and some variety of serious music-making happening in all five branches of the extended family, it is fair to assume that some kind of musical interest must have played a role when Heinrich and Maria got together. (They had a double wedding together with Heinrich's sister, and there are plenty of songs in the "wedding journal" of which I have a copy.) A musical family just falling into silence is a scary thought.

All’s well that ends well, though: Heinrich’s cello (now also known by the name of Heinrich) has seen a lot of excitement since the young musician in my family grew into it in 2009, including everything from quartets to barn dances. I will write up its adventures some other time.

Heinrich's string quartet, photo by his son who was a keen photographer. We still don't know who the other members were.

Monday, May 15, 2017

merian memories

Open Archive Day

Maria Sibylla Merian died 300 years ago, in January 1717. Ahead of the anniversary, I wrote a feature on the role of illustration in the life sciences using her hugely influential work as a prime example.

This feature is now on open access:

Putting biology in the picture

Image source: Wikipedia

Saturday, May 13, 2017

old books

My tumblr blog has a focus on everything bookish, and in this spirit I have also photographed and shared some of the antiquarian books on my shelves. As these photos are diluted with lots of other bookish stuff on tumblr, I decided to share photos of my collection here as well, under the antiquarian tag.

It isn't a very systematic collection, but I inherited some antiquarian books from my great-aunt many years ago, rescued some from a skip, and bought a few at charity shops and fleas markets, so over time, they have accumulated. Moreover, as the years clock, up, some of the books that I once bought new are also beginning to look a bit antiquarian.

To start the new series, here is a lovely appreciation of Oxford by D. Erskine Muir with watercolours by Jack Merriott, which I recently discovered at the antiques fair on Gloucester Green. A bit of googling revealed that the D. in the author’s name stands for Dorothy, and the book appears to date from the 1950s. I actually read it in its entirety, it was hilarious in a “plus ça change” kind of way.

Thursday, May 11, 2017

galician magic

I have been playing Galician folk music for nearly two years now, and (as Pablo Casals famously said about his cello practice in his 90s) I'm beginning to notice some improvement. In the last few weeks I have been spoilt with opportunities to improve further. There was a Galician session at the Folk Weekend, then the the regular monthly one, and a week later, advertised only by word of mouth, a special one, with a special guest. Only two days before the event I found out that the special guest was the most special one you could imagine.

If you read up about Galician folk anywhere, eg in this recent feature in the Economist, the one musician whose name will definitely appear is Carlos Núñez. So, well, he was around visiting friends in the UK, and he came to our special session to listen to us playing and then to join in, playing his whistles (not the bagpipes he's famous for), dancing, chatting and generally being amazing. People in attendance were a mixture of the regulars from the established sessions in Oxford and Cardiff, as well as a delegation from the newly launched Galician session in London, which also set the event apart from our regular sessions.

So, I think everybody (including the paella cook and a stray Morris dancer) felt it was a magical night, and rather than raving on, I'll link to my videos here:

0) Pablo Gonzalez sings Camariñas (before Carlos got involved - any wrong notes on the flute are mine)

1) some dancing

2) A rianxeira

3) Mazurca dos Areeiras (David, who played the whistles at the far side of the room in this video, also recorded a clip of this in which I appear, see embedded video below)

4) an Argentinian chamame, I am told

(These videos are "unlisted" meaning they can only be accessed via these specific links and will not show up in searches.)

Carlos Núñez talking to our group of pandeireteiras (tambourine players). The guy in white at the back is a stray Morris dancer - his side had a dance-out just before our event and he stayed on, playing the spoons.

Mazurca dos Areeiras, the view from the other side of the room:

PS more magic to follow soon. O Arame, the second ever opera to be written and performed in the Galician language will be premiered in Oxford in June, conducted by Tamara Lorenzo Gabeiras. You can see her dancing in my video no. 1). I spent the entire session standing close to her without realising who she was, even though I had seen her in a recital a year before.

Monday, May 08, 2017

microfluidics for all

There's no feature from me in today's issue of Current Biology - slight hiccup but normal service resumes in two weeks time.

Instead, here is one in the latest issue of Chemistry & Industry, on some amazing things that are being done with microfluidics these days, from counting molecules to building soft robots:

Microfluidics for all

Chemistry & Industry 2017, vol 81, no 3, pp 22-25
SCI members and subscribers access via SCI
Wiley Online Library (paywalled)

(NB issue 3 is dated 18.4., as there are only 10 issues spread through the year)

sneak preview of the first page (from Wiley Online Library)

Thursday, May 04, 2017

59th Galician session

Over a year ago, I raved about Galician folk and created a new tag for it, but then I didn't do much with the tag. So here, at last, are some videos from the April session, which was the 59th - from which I conclude the sessions may have started in spring 2012, but I only discovered them in 2015.

A glimpse of Muiñeira dancing

Muiñeira de Chantada

Pingacho performed by the Oxford Pandeireteiras

(These videos are "unlisted" meaning they can only be accessed via these specific links and will not show up in searches.)

Monday, May 01, 2017

curb car culture

Open Archive Day

A year ago I published a feature on the trend towards a world with 2 billion motor vehicles, predicted to be reached by 2030 - doubling the number of 2010.

Since then, we have learned more about how much damage Diesel fumes do, and how car manufacturers cheat to get away with toxic emissions, never mind their share of climate change. So, sadly the topic is still very much on the agenda. As far as I can see, there are only two movements opposing the ongoing fossil fuel madness, namely the indigenous land right activists in the Americas who are fighting pipeline project, fracking, and similar. And the World Naked Bike Ride (which in addition to environmental issues around cars also highlights a body positivity message). Which is as good an excuse as any to advertise this year's WNBR dates below and include one of my photos from last year's ride at Bristol.

First though, freshly released from the paywall, here comes my feature:

A planet with two billion cars

WNBR 2017

As far as I know, 16 UK WNBR dates are now confirmed for this summer, in chronological order:

27.5. Canterbury (Sat)
2.6. Southampton (Fri 6pm)
4.6. Bristol (Sun)
9.6. Manchester (Fri 6pm)
10.6. London
11.6. Brighton
17.6. Cardiff
17.6. Cambridge
24.6. Exeter
24.6. Chelmsford (Essex)
25.6. York
1.7. Folkestone
1.7. Newcastle-Gateshead
2.7. Worthing (near Brighton)
8.7. Colchester (Essex)
9.7. Portsmouth
15.7. Clacton (Essex)

still to be confirmed:
Edinburgh, Hastings, Scarborough

(WNBR Wiki also including dates from other countries, but not always reliably up-to-date)

Monday, April 24, 2017

arthropods at work

Both insects and spiders tend to have a bad press, so I collected up some examples of how insects make positive contributions to our world, apart from the pollinators which I have covered on numerous othr occasions. And to round it up I've thrown in the recent study estimating how many insects end up being eaten by spiders. The feature is out today:

How insects shape our world

Current Biology Volume 27, Issue 8, pR283–R285, 24 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)

Fairy circles in Namibia have caused lively debates. Recent modelling suggests that both feedback regulation of plant growth and competition between insect states play a role in creating these patterns. I just love this photo from Jen Guyton, check her website for lots more amazing wildlife photography.

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)
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