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.

4 comments:

Anonymous said...

Chris, I must admit that I cannot contribute much. My chemistry and particularly this type of chemistry is rather outdated. What about the hypercycles of Manfred Eigen? How would they fit in?

Klaus (I have had problems with logging into your blog earlier, when I tried to comment on your post: homeopathy. I therefore remain anonymous)

Dr. Clam said...
This comment has been removed by a blog administrator.
HelmutSchiretz said...

Hi Chris - you might find this of interest ?

http://sandwalk.blogspot.com.au/2013/04/dna-nature-celebrates-ignorance.html

HelmutSchiretz said...

I guess the main point you make, with which I entirely concur, is in your statement:

"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."

As Dawson said himself he was avoiding the "what came first the chicken or the egg?" analogy ...

He steps right up the evolutionary ladder as close to the chicken as he can get to propose "sufficiently complex organic molecules" to get the ball rolling - conveniently ignoring enzymatic catalyst processes and naturally occurring biopolmers and their evolution towards the higher order building blocks of life as is generally understood in basic biochemistry ...

Shoot me down in flames if you like - it's a free world :-)