my inner fish

I somehow managed to miss Neil Shubin's excellent book "Your inner fish" when it came out a few years ago. Now, however, I had the chance to read it and catch up with my inner fish on the occasion of the publication of the coelacanth genome.

Shubin's discovery of an intermediate fossil, Tiktaalik, and the genomic comparisons of coelacanth with other vertebrates tell us some amazing things on the transition from fish to land-living animals. What I find most mind-boggling, however, is this: If you look at the tree of life from the perspective of the coelacanth, you'll find that mice, chickens and humans are closer relatives than herring or zebrafish, or anything that lives in an aquarium, and never mind sharks and rays. Try to get that into your brain if you're just a fish.

By coincidence, the reference genome of the zebra fish was published almost at the same time, so I could combine one fish that tells us about our evolution with another that tells us about our development, into a feature that is now out in Current Biology;

What fish genomes can tell us about life on land

Current Biology, Volume 23, Issue 10, R419-R421, 20 May 2013

doi:10.1016/j.cub.2013.04.068

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Source (via H2origins)

cognitive enhancers

Not that I've felt the need for brain doping (beyond caffeine) so far, but I've been following the field of cognitive enhancers from a safe distance for a while now and have summed up the current state of affairs in a feature for Chemistry & Industry, which is out in the May issue:

Smart New World

Chemistry & Industry No. 5, pp32-35

Full text

In the same issue, I have a review of the book:

Gold nanoparticles for physics, chemistry and biology

on page 47.

Full text

Maybe the smart pills could magically convert me into this guy:

gut feelings

This week's issue of Current Biology has a special section of food and biology. My contribution is a feature on the gut microbiome and what it can tell us about widespread problems like obesity, diabetes and heart disease.

Does the gut microbiome hold clues to obesity and diabetes? Current Biology, Volume 23, Issue 9, R359-R362, 6 May 2013 doi:10.1016/j.cub.2013.04.047

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The issue looks like this:

censorship in the UK

The UK's Advertising Standards Authority has banned this ad:

according to this report in the Guardian, and I'm having a huge problem with this decision. The posters don't show anything at all apart from the drink, just words, and (as the ad slogan itself suggests) any associations are purely in the mind of the beholder.

If we've reached the point of not being allowed to use words that have several meanings because some readers may associate them with a meaning that they themselves will then find offensive, I think we've arrived in a kafkaesque nightmare of censorship. If people are offended by their own thoughts, it should be their own problem, right?

To use a visual analogy, if looking at a lighthouse makes you think of male genitalia, that doesn't give you the right to ask for images of lighthouses to be banned. The association is exclusively your own problem.

And that's essentially the point that the ad itself tried to make in a playful way. Clearly some people at the organisation in charge of such things were unable to grasp this subtle philosophical point.

imaginary maladies

During the preparations for the latest edition of the Diagnostic and Statistical Manual of Mental Disorders of the American Psychiatric Association, DSM-5, controversies have raged over the broadening of diagnostic definitions. Critics have argued that the new manual, due to be published in May, will turn more people than ever into psychiatric patients.

So I wheeled out Moliere's imaginary invalid and investigated whether the shrinks are letting normality shrink away into oblivion. The resulting feature has now come out in Current Biology:

Has the manual gone mental?

Current Biology, Volume 23, Issue 8, R295-R298, 22 April 2013 doi:10.1016/j.cub.2013.04.009

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A stage production of Moliere's Le malade imaginaire in Argentina, via Flickr.

online culture

Why is tumblr like ancient Egypt? How do you recognise if a twitter user is part of a specific tribe? Will edit wars on Wikipedia end in peace deals or carry on forever? And why have some social networks turned into ghost towns?

All these questions and more are addressed in my feature on the cultural evolution of online social networks, which is out now in Current Biology:

What makes people click?

Current Biology, Volume 23, Issue 7, R255-R258, 8 April 2013
doi:10.1016/j.cub.2013.03.047

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Twitter users grouped into tribes, annotated with words typically used by each group. Graphic: John Bryden, Sebastian Funk and Vincent Jansen

beer and spinach

In the round-up of German pieces published in April we have serious reports on teeth and on artificial enzymes, and not so serious ones on beer and spinach. The latter made the cover of Nachrichten:

Chemie in unserer Zeit 47, p 74
Neuartige Enzyme

Nachrichten aus der Chemie 61, p 407
Chiralität und Reinheit des Bieres

Nachrichten aus der Chemie 61, pp432-433
Spinat macht Skeptiker stark

Nachrichten aus der Chemie 61, pp440-442
Wie das Krokodil zu Zähnen kam

All on restricted access I'm afraid, but I'll be happy to send pdf reprints.

apps with inverted helices

After my recent blog post on DNA double helices that twist the wrong way (inverted helices), a reader (who prefers to remain anonymous) submitted a few examples of apps featuring such mirror-world DNA. Following the example set in that previous post, I'm showing the corrected versions here:

I'm sure you can still read the text to work out who the culprits were ...

digging deep

The Deep Carbon Observatory is an international interdisciplinary project studying the hidden carbon fluxes deep within the earth, along with implications for life in the subsurface and on planet formation and development.

I've written a feature about this work which is out in Chemistry & Industry:

Carbon deep

Chemistry & Industry March 2013, pp 32-35

The full text is freely accessible here.

The article is also featured on the cover of the issue:

In the same issue, I also have a review of the book "Synthetic biology: a primer", which appears on page 50.

how to design new enzymes

Scientists are now able to design new enzymes to catalyse reactions for which a natural enzyme doesn't exist. I've rounded up some of the first success stories in enzyme design for my latest feature which is out now:

Evolving new types of enzymes

Current Biology, Volume 23, Issue 6, R214-R217, 18 March 2013

doi:10.1016/j.cub.2013.02.054

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Beethoven rondo

Moving on from first movement of the Beethoven Duo no. 1, we're now trying to play the third movement of the same piece, which is actually a little bit easier.

Here's the score:

This is mainly adapted from the Kalmus edition for violin and viola. A slightly different version is included in the duets for violin and cello from Editio Musica Budapest.

PS: Note that I added the first bar just to count me in and allow me time to get my hand back to the flute after pressing start.

the curse of the inverted helix

I've now figured out what to do with DNA double helices of the wrong chirality, which I frequently see in print and online. Earlier I started compiling a hall of shame, but that might reinforce the wrong image (eg by adding to the already considerable proportion of wrong helices that show up in google searches for double helix).

Instead, I'm now going to flip the images that also contain text, such that the DNA will be the right way round and the text will be mirrored. This way, I can signal-boost the correct structure while also exposing the error.

So, for example, a poster I received yesterday now looks like this:

much better, huh?

The same treatment for the historic blunders of Nature and Science yields: