Tuesday, April 24, 2007

What is Chemistry? A Preface to an as-yet unwritten Book.

Chemistry is the science of things that we can see and that we can control.

When I was young, I never gave chemistry a second thought. I loved the grand sweep of biological evolution, with its single unifying idea and its endless ramifications, every twig on life’s branch subjected to a neat exegesis by my idol, Stephen Jay Gould. I loved the vastness of space, the unimaginably gigantic and inhuman universe subjected to the breathless exposition of Carl Sagan. I was brought up in an atmosphere suffused with geology, and I cannot remember ever not knowing that I lived on a thin chunk of crust moving inexorably towards Asia. These, the descriptive sciences, the historical sciences, were where I lived. I wanted to know where I was; I wanted to know where I was going.


It is not enough to know. If you actually want to do something, all of these sciences have serious flaws. You cannot crash galaxies together to see what will happen. You cannot evolve your own species of toothed whale. You cannot smear an archipelago onto the Pacific coast of North America. You can only watch, and collect data, and hope for a ‘natural laboratory’ which will test whatever hypothesis you have developed. The essential bits of the historical sciences, the most interesting bits, are inaccessible to our tinkering.

As I grew older, I grew to lust after the secret and paradoxical wisdom of the physicists, the world of Schrödinger’s cat and Lorenz’s butterfly and the modest goal of the Theory of Everything. Here again, I was driven by the desire to know what was going on. Once upon a time physics was a science where you could do things.

But now, alas, they have mostly been done. Now you need obscene amounts of money to do experiments and whatever result you get can be explained by the theoreticians. Is that falsifiability?

Actually, I must be honest. I cannot discount physics. I am a failed physicist. Somewhere among the ordinary differential equations I got lost, and fell off the mathematical billycart. When I say that the great achievements of what we call ‘Modern Physics’ ended in the 1930s, and that since then it is chemistry and its biological metastases that have transformed the world, you must discount it as sour grapes. Likewise, when I proclaim: ‘physics has given we chemists our tools, and now its job is done.’ Sour grapes.

Essentially, chemistry drew me in because it let me play with liquid nitrogen and fire.

If you actually want to do something, chemistry is the only science worth considering. With physics, we can control things, but we can rarely see them or even imagine them. We can see the subjects of the historical sciences everywhere, but cannot control them. Chemistry is the science of things we can both see and control.

Chemistry is called by some of its practitioners the ‘Central Science’, a term that I have always found naff. It is the ‘Human-Sized Science’.

A few more facts about chemistry:

Chemists are allowed to:

(a) Appropriate any part of physics they like and call it ‘physical chemistry’

(b) Invade and subvert any ‘softer’ science they like and turn it into chemistry.

It is no coincidence that so many Deans, Pro-Vice Chancellors, Vice Chancellors and Prime Ministers (e.g., Margaret Thatcher) have been chemists. Those whose job it is to manipulate matter naturally want to manipulate it wherever they find it.

Monday, April 16, 2007

An especially egregious example...

...of something that greatly irritates Marco is the language used in this popular science article.

The thing that greatly irritates Marco- and me too, for that matter- is the pervasive image of evolution as a 'ladder' leading step by step to 'more highly evolved' beings. Nothing can be 'more highly evolved' in general. A species can be 'better adapted' for circumstances X, Y, or Z; but circumstances are subject to review (by climate change, giant asteroids, motorways, etc.).

One thing that confuses me is the relationship between population size and genetic change mentioned in the extract below. It seems counterintuitive. Perhaps a real biologist could help? :)

Zhang's team found that 233 chimp genes, compared with only 154 human ones, have been changed by selection since chimps and humans split from their common ancestor about 6 million years ago.
The result makes sense, he says, because until relatively recently the human population has been smaller than that of chimps, leaving us more vulnerable to random fluctuations in gene frequencies. This prevents natural selection from having as strong an effect overall.

Saturday, April 14, 2007

Thursday, April 12, 2007

The Electrochromic Effect

We are very coy and subtle folks, sometimes, we scientists. The other day I was skimming through 'Molecules and Radiation' by Jeffrey Steinfeld while preparing some lectures and came across this sentence:

"The Hamiltonian for the interaction of an atom with a static electric field [called the Stark effect after its discoverer, Johannes Stark (1874-1957); also called the electrochromic effect by other spectroscopists who did not like Stark] is just the electric-dipole interaction:"

Other spectroscopists who did not like Stark?

Why should other spectroscopists not like Stark?

My curiosity was piqued, and it did not take long for me to discover why.

The electrochromic effect it is!

Friday, April 6, 2007

Twitch, twitch, twitch, twitch...

When will the world listen to reason?
I get the feeling it'll be a long time.
When will the truth come into season?
I get the feeling it'll be a long time.

- The Offspring

I can't take much more of this kind of thing, I really can't. I will burst a blood vessel somewhere. This unwarranted hyperbole about climate change is going to harm the reputation of science for generations. I used to think that the collective insanity of the early 20th century was caused by mass heavy metal poisoning of urban populations and we would see saner arguments and saner policies as we moved into the 21st century. But it appears I was sadly mistaken.

If we are worried about people in the poorest regions of the Earth suffering 'malnutrition, disease, and increased untimely death rates because of heat waves, floods, storms, fires and droughts', then the logical thing to do is to bring them to a standard of living so that they will suffer as little as we in the developed world do from heat waves, floods, storms, etc.

If we are worried about the alkalinisation of the oceans, we should take a deep breath and acquaint ourselves with how flimsy the evidence for this particular doomsday scenario is.

If we are worried about coastlines disappearing, we should get rid of those dams upstream and regenerate those coastal swamps we have cleared. And we should move people away from that dangerous big blue thing which is always going to twitch and kill people, no matter what the climate does.

If parts of the planet become too hot or too cold for traditional crops, then we should switch to different crops, shouldn't we? We do this kind of thing all the time.

I can't imagine any possible scenario where Bangladesh would run out of drinking water. Very dry poor countries with high population densities survive by economising on all the other things we do with water besides drink it. Very dry rich countries don't care, because if they want more water, they just build more desalination plants.

If we are worried about extinctions, we should address the primary cause of biodiversity loss- the dangerous fragmentation of habitats. We can move people out of marginal regions to amalgamate little reserves into big reserves. The little reserve is always vulnerable. If global climate change means your preferred habitat shifts a hundred metres uphill, in a large enough reserve you move a hundred metres uphill. Conversely, if a minor local event means your preferred habitat shifts a hundred metres uphill, in a reserve that is too small you're not going to be able to move.

Coincidentally, I just came back from holidaying on the seaside at a house with very little in the way of reading matter. There were three copies of the Readers' Digest there, the oldest from August 1974. This magazine had an article about the alarming drop in global temperatures of 0.5 C since 1940 and forecasts of the dire effects to come...

Thursday, April 5, 2007

In the beginning was the Metabolism

Being some comments on ‘The Origins of Order: Self-Organization and Selection in Evolution’, by Stuart A. Kauffman.

If I was arguing with one of the people Marco sometimes has to contend with- those who find the transition monkey --> man as implausible as the transition unlife --> life- then an exposition of how a ‘primordial protoplasmic globule’ (PPG) might have unfolded into the bewildering variety of life we know on Earth today might be of value. In the 19th century, or in the darker corners of the 21st century, a layman might suppose a PPG simple enough to have arisen spontaneously. For such a layman, an exposition of the pageant of evolution might seem to be a complete materialist description of the history of life, and might well shake their worldview to its foundations.

To the biologist, this pageant is far from a complete description. The biologist knows the complexity of the prokaryote, the PPG, and finds the unfolding of its descendants almost trivial. The PPG is not the simple explanation: it is the complicated thing that needs to be explained.

In a similar way, to the chemist, the unfolding of Kauffman’s ‘complex system of catalytic polymers’ (CSCP) to give rise to something recognisable as life seems almost trivial. The CSCP is the complicated thing that needs to be explained. Kauffman’s statement: ‘the origin of life, rather than being vastly improbable, is instead an expected collective property of a complex system of catalytic polymers and the molecules on which they act’ should become: ‘the origin of life, rather than being vastly improbable, is instead an expected collective property of a vastly improbable complex system of catalytic polymers and the molecules on which they act’.

I will now try to justify this assertion by considering the requirements a CSCP needs to have in order to be relevant to the origin of life.

Firstly, the CSCP must be secured from the overwhelming tendency for matter and energy to become more randomly distributed in the universe. This has one easy part and one hard part.

The easy part is the barrier to separate the system from the surroundings: something to draw a surface around the CSCP and keep it together. Kauffman mentions vesicles and protein coacervates as possible CSCP microcontainers for the early terrestrial environment, and plenty of other possibilities have been canvassed.

The hard part is whatever reaction allows the CSCP to increase the disorder of its surroundings in order to persist in time. The molecules making up the CSCP cannot be just any old polymers we happen to be fond of. They must be- if the system is to persist in time- intermediates in a spontaneous chemical reaction. This is whatever reaction converts energy-rich ‘food’ into energy-poor ‘waste’. The requirements of this net of reactions also make the easy part less easy: the low molecular weight intermediates have to stay in, not just the polymers. The ‘food’ has to get in. The ‘waste’ has to get out. Some selectivity is therefore required in the barrier separating the system from the surroundings.

Secondly, not just any thermodynamically favourable driving reaction will do. It would be preferable for this central driving reaction to proceed relatively slowly, so there plenty of intermediate molecules around. This reaction must also have many steps, with many intermediates capable of being transformed in various ways- because a great deal of complexification of the net of reactions must take place before we arrive at a CSCP. Before a CSCP can form, all of its constituent parts must be present as intermediates in a net of thermodynamically favourable reactions.

I believe this set of requirements allowing a CSCP to persist in space and time are very difficult to meet. Nothing approaching them has ever been observed, except in two common instances: living systems, and systems we have designed. The question of how systems meeting these requirements can spontaneously arise is the key question for the origin of life.

Kauffman, understandably invigorated by the Central Dogma1 of molecular biology like so many in the last half century, is chiefly concerned with reproduction as the defining feature of life. He makes only a superficial discussion of metabolism that does not consider its central thermodynamic requirements. But ultimately, metabolism is what is most important. Without petrol, the most splendidly engineered automobile will just sit there. Without a plausible metabolism, the most elegant net of autocatalytic reactions is an empty exercise in symbol manipulation.

I don’t intend this as an argument in favour of intelligent design2, still less of Intelligent Design3. My main aim is to defend a strongly held view that both the ‘RNA world’ and the ‘Protein world’ are historically late phenomena, and that the critical events for the origin of life lie much deeper. We are trying to reconstruct the invention of the telegraph, knowing only the mobile phone: Which came first, we argue, the handset, or the system of towers dotting the landscape? It is an unquestion. We have pulled ourselves up by our own bootstraps, as one phase of pre-biotic evolution succeeded another, as one phase of pre-DNA-life succeeded another. At each stage, we have destroyed our history more effectively than any Red Guards, as we cannibalised previous stages for chemical substrates. Perhaps there have been shifts in pre-DNA evolution radical enough that unassimilated chemical traces of previous stages remain, somewhere. Perhaps we will be lucky, and find somewhere out there traces of pre-DNA intelligent designers. But as far as the ultimate origin of life is concerned, it is useless to try and work backwards. We need to work forwards, by considering the necessary requirements for a CSCP to arise and where and how such a system might realistically arise.

1: I hate this term, 'Central Dogma'. Similarly, when Kauffman describes his theory as 'heretical'. This quasi-religious language makes scientific discussions sound very silly to outsiders, I am sure.

2: Defined as manipulation by, for instance, Jumba Jootika, vide infra...

3: Defined as manipulation directly by God.