Thursday, 31 January 2013

A bonding experience

There's a fun article* in Angewandte Chemie Int. Ed. 's 'early view' this week:

One Molecule, Two Atoms, Three Views, Four Bonds?
Sason Shaik, Henry S. Rzepa, and Roald Hoffmann

This paper is a bit of an oddity. While Angewandte does occasionally publish articles about the history of chemistry and so on, which adds a bit of colour relative to most journals, this is really quite unusual.

It discusses the background to a paper recently published in Nature Chemistry (h/t @stuartcantrill). The work is about the electronic structure of diatomic carbon, C2. Sounds dry, right?** It's the kind of thing every first-year chemistry undergrad studies at length, and I'm not sure I could read a paper about this without my eyes glazing over.

What makes it unusual is that it's written as a conversation between the three authors. I really enjoyed this for a number of reasons.

It's always interesting to see the people behind the science, and the personalities of the authors really shine through this article. They bicker with each other, they quote scripture, they ponder how blogs fit into the peer review process. You also start to get a sense of community as they discuss which papers to cite in their bibliography, agonising over dropping a reference to a friend's work.

You also start to see how science is actually done. The authors derive ideas from students and blogs; collaborations arise from unexpected places; and seemingly well-established textbook facts are revised. The discussion of how ideas about this subject have developed from the early 20th century conveys the place of this work in the grand scheme of things much better than your typical research article. As the authors put it, it's "a reflection that our science is alive".

Probably the best thing about it is that it really conveys why this is an interesting subject. As I said, bonding in homonuclear diatoms is not very close to my heart. This article really allows the authors to convey their fascination with the subject, and it's infectious.

This is something I'd like to see more of: 'outreach' within the scientific community. Not scientists communicating to the public, but specialists communicating across disciplines. Whether a somewhat contrived "trialogue" is the best way to do this or not, I don't know. But I'd definitely like to see more chemists telling us about their niche in creative and accessible ways***.

*unfortunately, as with most chemical literature, it's not open access.
**with apologies to the spectroscopy community.
***blogs are, of course, great for this - In the Pipeline is a prime example from medicinal chemistry.

Tuesday, 15 January 2013

Actually, the secret of life will be cooked up in a chemistry lab

In the Guardian this week, the physicist Paul Davies wrote an article entitled "The secret of life won't be cooked up in a chemistry lab". It's a thoughtful piece and worth reading; the key point is summed up in the final line:'s origin can ultimately be explained by importing the language and concepts of biology into physics and chemistry, rather than the other way round
I absolutely agree! Work by biologists and theorists such as Davies is absolutely essential, to guide research, identify flaws and incoherence in hypotheses, and unify disparate data. Chemists can develop all kinds of ideas, but if they're physically or biologically irrelevant or implausible, what's the point? That said, allow me to mark some turf for the chemists working in this field.

As Davies notes, much of the work in this field has been carried out by chemists. Implicit in his article is the suggestion that these workers have had their ears closed to the rest of the world - that ideas from philosophers, biologists, and information theorists have not reached the chemical literature. This is simply not true.

Take, for example, the work of M. Reza Ghadiri and co-workers on self-replicating peptides. To distill a decade of research down to a tweet, Ghadiri looked at whether peptides can copy themselves, and what kinds of behaviour might emerge when many peptides interact. Much of this work was informed by the theoretical biologist Eörs Szathmáry. One of the most complicated systems published by Ghadiri (available here, open access) took a group of self-replicating peptides and analysed their interactions to build a large network. A small section of this network was then recreated experimentally, to confirm its behaviour. The point is: here is a chemist, guided by theoretical biology, speaking the language of network architecture. We're not as deaf as Davies implies.

Further, this is not an exception, an isolated example of a chemist looking beyond the fume hood. Pier Luigi Luisi's work on self-reproducing micelles and vesicles was prompted directly by the idea of autopoiesis, as proposed by Maturana and Varela - both of whom are biologists and philosophers. Autopoiesis is very much about the structure and flow of information through a system.

Of course, the ideas upon which Ghadiri, Luisi, and other chemists draw might turn out to be incorrect. Regardless, ideas from beyond the chemistry lab are at the heart of chemical research into the origins of life.

Both of these examples illustrate a second, more important point. It is necessary, but not sufficient, for theorists such as Davies to elucidate the form of living systems. These ideas must be made flesh, so to speak. This is certainly the work of chemists. By applying these ideas to physical substrates, their validity and generality can be tested.

Ghadiri's work is again illustrative. Both Ghadiri and other researchers, notably Jean Chmielewski, have reported extensive efforts to increase the efficiency of self-replicating peptides. According to Szathmáry, an exponentially-replicating species is required before Darwinian selection can occur. Reaching exponential replication turns out to be incredibly difficult. This is not unique to peptides; research on self-replicating nucleotides and small molecules by von Kiedrowski and Rebek has run into the same problem. I am not in a position to comment on the biological or theoretical merit of Szathmáry's work, but two decades of research suggest that it is unlikely to be relevant in real chemical systems. At the very least, it seems that it can only be achieved under demanding, prebiotically implausible conditions.

Any theory, however elegant or plausible, must be tested experimentally. We must see if it is a valid idea, and if so, how readily it is achieved. So, while I agree with Davies that chemists cannot work alone, it will ultimately be chemists who 'cook up' life.