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

Free access to

HTML text

PDF

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:

As of 2021, the Flash view of the score disappeared, but this link is working.

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:

oxidation and procrastination

Ooops, now it's March and I haven't done the roundup of the German pieces published in February yet. Time, you're moving too fast.

So in Feb, we had quantum procrastination, reduction and oxidation at the sea floor, and cycloaddition with triple bonds:

Organische Synthese: Drei mal drei
Chemie in unserer Zeit 47, 6
FREE ACCESS (PDF file)

Neuartige Redox-Biochemie im Meeresboden
Nachrichten aus der Chemie 61, 134-135

Proquastination
Nachrichten aus der Chemie 61, 111

And talking of which, a late arrival: a short piece on addiction biochemistry that is nominally in the issue for the 4th quarter of 2012 of the magazine:

Trillium Report 10, 200-201
Die Biochemie der Sucht

hearts and minds

My latest feature in Current Biology juxtaposes a highly acclaimed project to simulate the function of the heart and a somewhat controversial, but well-funded one to do the same for the brain.

Simulating hearts and minds

Current Biology, Volume 23, Issue 5, R177-R180, 4 March 2013

doi:10.1016/j.cub.2013.02.032

Free access to the full text in HTML and in PDF format.

Here is a video about the Alya Red project featured in my article:

Alya Red: A Computational heart

This video recently won Science magazine's prize for science communication.

go further for fairtrade

This year's Fairtrade Fortnight in the UK starts today, details here. In previous years I rounded up all the faitrade products I could find in the household for a group portrait, but that might become difficult as the number keeps growing. Instead, here is a selection of fairtrade chocolates which a family member bought for a science project:

marine litter

Surely, palaeontologists of the distant future will label our slice of geological time the plastocene, as a layer of plastic waste will be our signature remnant. Plastic pollution already affects the oceans to an extent that scientists aren't sure what if anything can be done about it, and whether or not particles of crumbling plastic are entering the food chain and may end up on our dinner plates.

I summed up the sorry state of this situation in a feature which is out in today's issue of Current Biology.

It is freely accessible in

HTML and

PDF format

(at least for now, while the issue is current).

Photo by Bo Eide, via Flickr

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PS Bo Eide was also involved in making this lovely video on the problem of marine litter.

DNA nanotechnology gets real

DNA nanotech is a field I've followed from its very beginnings, i. e. Nadrian Seeman's DNA cube in the early 90s. Back then, it was playful "misuse" of the tools developed for molecular biology, but increasingly, the methodology has become more versatile and sophisticated, leading us to a point now, where people can design complex and useful things, like nanopores, self-assemble them rapidly and efficiently, and rely on getting the structure they designed. There aren't many molecules you can do that with on a scale of tens of nanometres. So, while it remains an oddity that people misuse an information molecule to build machines, DNA nanotech has grown up into a technology to be taken very seriously.

My latest feature on this field is out in Current Biology today:

DNA nanotechnology gets real

Current Biology, Volume 23, Issue 3, R95-R98, 4 February 2013

doi:10.1016/j.cub.2013.01.049

Free access to

HTML text

PDF file

(Image: with permission from Langecker et al., Science (2012) 338, 932.)

PS: I've also covered the same work in an article in German, published in May 2013:

Spektrum der Wissenschaft 5/2013, S. 16

Materialwissenschaft: DNA-Nanotechnologie vor dem großen Sprung

First para and limited access to PDF

Bach for cello and flute

Looking through the flute tag on tumblr earlier this week I came across an ancient video of Jethro Tull performing "Bouree" (not sure what happened to the second "r" but that's what they call the piece), based on Bach's Bourree from BWV996, which I played on the guitar many years ago.

As Jethro Tull play the Bach bit with flute and electric bass, I thought that should work for flute and cello as well, so I found a guitar version on noteflight and converted it to cello and flute, with both instruments taking turns in the repeats.

Sounds ok when noteflight plays it (though it doesn't do the pizz I wanted). Will try out with real instruments soon.

now and later

Written and directed by French director Philippe Diaz but filmed in Los Angeles and in English, this film juxtaposes a hippie-style, free love and social justice world view to the view of the financial/political/military power. It could have been called “Make love not war”, although the actual title is really quite lovely and clever as you will realise after about 30 minutes.

In principle, we have a chamber piece setting these two world views up against each other. In one corner we have Bill, a disgraced banker, representing the people who think that their money and/or power will let them get away with anything - but, having been ejected from the system he supported, he is now ready to change his views and indeed his life philosophy.

In the other corner, Angela (Shari Solanis), the illegal immigrant offering him shelter for a few days in her gorgeously hippie-styled penthouse flat on top of a derelict hotel, where both the toilet and the shower are completely open-plan and in plain view of everything else, and where part of the neon sign of the hotel serves as lighting for the single room. That room alone is reason enough to watch the movie.

Angela embarks on the re-education of banker Bill, trying to reconvert him into a useful member of society – although it will have to be the society of a different country, as the US authorities want him locked up. With her priorities firmly on her sensual desires, she goes in for the sex first, fitting in the political education later.

To me, as someone who has essentially grown up with the Nicaragua solidarity movement, her political lecturing was a tad over-familiar, although I appreciate that the vast majority of the US audience will not know (or in fact believe, if told) that the CIA sold arms to Iran to finance the removal of a democratically elected government in Nicaragua (it’s called the Iran-Contra affair, look it up). This scandal, which was exposed in November 1986, is kind of hard to reconcile with the prevailing US ideology that “we’re the good guys”, but I can confirm that it is true, I was alive (and young and angry) when it happened. Bill’s response “you read too many novels” was hilarious to me, but probably representative of what a vast number of people would say if confronted with these historical events.

People who don’t like the gospel she preaches may resent the dialogue, but, as washed-up banker Bill proves, Angela’s charm is irresistible, whether or not you share her political opinion. And her roof-top paradise from where she looks down on the social divisions on LA with eagle eyes, is equally seductive.

I’m not exactly sure that the film will convert many Bills to Angela’s views, not least because it is effectively being boycotted and hasn’t been released in the UK at all, neither in cinemas nor on DVD. In the US, it remained unrated and got a review in the New York Times in 2011, when a Manhattan cinema showed it as part of a series of unrated films. Still it remains important to uphold the opposition to the sexual, military and financial oppression of our age, and linking these three may help to broaden the horizons of people who were only aware of one or two.

amazon.com

After the explanations above, it is almost needless to say that the film did not get a release in the UK (and thus joins my fast-growing list of films not shown here). However, it is available on DVD in the US and also in Germany. I’m showing the US edition here, as the German one shows a photo at the top of the cover that isn’t from the film, and I have a nagging suspicion that somebody may have had racist reasons to put Bill’s ex-wife there in her bra (who only appears for 2 minutes in the film, sitting in a café, fully dressed) rather than Angela.

Update October 2024: rewatched the film 11 years later and still love it. A bit worried re what happened to Shari Solanis, she hasn't been in any movies since.