Sunday, April 27, 2008

Show me the metabolism! Part Three.

Kauffman 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.

Kauffman’s network and Eigen's hypercycles are susceptible to the well-known ‘747 Argument’ of Fred Hoyle et al. and can only plausibly have arisen in two ways:

(1) Through a long and complicated process of prebiotic development containing all the most interesting parts of the story of the origin of life.

(2) As a system created by someone or something.

I don’t intend this as an argument in favour of intelligent design [see definition 1], still less of Intelligent Design [see definition 2]. Ockham’s razor suggests we should stick with explanation (1) unless we should find some very compelling evidence for (2). At any rate, the essential requirements of the pre-biotic processes leading to life based on the chemistry we know are going to be the same as the requirements of pre-biotic processes leading to life based on different chemistry.

What I am arguing is 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. There is no reason to expect that living systems today preserve the same chemistry of the first living systems. It makes much more sense that we have pulled ourselves up by our own bootstraps, as one phase of pre-biotic evolution succeeded another, perhaps as one phase of pre-DNA-life succeeded another. At each stage, we have doubtless destroyed our history more effectively than any Red Guards- for all less successful implementations of life qualify as food. Looking at RNA and Protein is the equivalent of looking under the streetlight for the keys we dropped out in the darkness.

It is as though we are trying to reconstruct the invention of the telegraph, knowing only the mobile phone. Arguing about whether RNA or Protein came first is something like arguing: Which came first, the handset, or the system of towers dotting the landscape?

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. If we want to understand where chemicals came from, chemistry is useless to us. We need to use physics. If we are researching the origins of culture, anthropology itself is little help. We need to use evolutionary biology. If we are researching the origins of life, then biochemistry- with its specific, fragile, optimised reactions, the product of ever-so-many years of pre-biotic and biotic evolution- is not the place to start. We need to plant ourselves on a solid base of physical chemistry, stop worrying about designing elaborate systems for allowing pre-biotic reproduction, and concentrate on nutting out a possible proto-proto-metabolism simple enough to arise spontaneously.

Definition 1: ‘intelligent design’ = ‘life as we know it was created by entities based on some different sort of chemistry’

Definition 2: ‘Intelligent Design’ = ‘life as we know it was created by God in some ‘supernatural’ fashion’

Show me the metabolism! Part Two.

What are the requirements a catalytic system of complex polymers (CSCP) must have in order to be relevant to the origin of life?

The CSCP must be secured from the overwhelming tendency of matter and energy to become more randomly distributed in the universe.

Condition 1: An Edge.

The easy part of securing the CSCP from the tendency of matter and energy to become more randomly distributed 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. It is not very hard to think of a plausible container that could possibly arise to keep polymers in.

Condition 2: A Proto-metabolism.

The hard part is allowing the CSCP to increase the disorder of its surroundings in order to persist in time. The energy to maintain the CSCP must be coming from somewhere. The CSCP must be part of an overall system of spontaneous reactions that is converting a relatively unstable chemical reactant (or reactants) into a relatively stable chemical product (or products). The CSCP polymers must be intermediates in this net of spontaneous chemical reactions, somewhere on the path between energy-rich ‘food’ and energy-poor ‘waste’.

Condition 3: A Selectively Permeable Edge.

The energetic requirements of this net of reactions also make the easy part- the physical barrier around the CSCP- 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. Biological membranes have evolved extraordinarily complex ways of getting the right things in and keeping the wrong things out. I am having a devil of a time trying to make a non-biological membrane to do just one thing: let ethanol through more readily than water. The tendency of matter and energy to become more randomly distributed makes generation of selective membranes a tricky business.

Condition 4: A Complexifiable Proto-Metabolism.

Not just any thermodynamically favourable driving reaction will do. This central driving reaction must proceed relatively slowly, so there are plenty of intermediate molecules around. This reaction must also have many steps, with many intermediates capable of being transformed in various ways. 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 this net of thermodynamically favourable reactions. I have only shown a few intermediates in the picture, but very many are required...and the relative sizes of the energy barriers and depths of the energy wells must be such that reasonable quantities of all the substrates present for making catalytic polymers are present.

I believe these 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 instances:

(1) Living systems

(2) Systems we have designed ourselves with a great deal of effort.

The question of how systems meeting these requirements can spontaneously arise is the key question for the origin of life.

Wednesday, April 23, 2008

Show me the metabolism! Part One.

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

I thought I would expand my central criticism of Kauffman’s model a bit in the hope of clarifying what I was saying and starting a fruitful discussion.

My thesis is that the network of catalytic polymers and substrates that Kauffman postulates as an initial self-organising complex system which can give rise to more lifelike systems is so inordinately complex and unlikely that it in no way addresses the crucial problem of the origin of life.

Specifically, what is first needed is not a mechanism for self-replication and complexification, but a plausible metabolism enabling some tiny corner of the universe to dump entropy outside itself and accumulate order within.

My initial statement of the thesis:

Marco sometimes has to contend with people who find the evolutionary transition monkey → man as implausible as the transition unlife → life. If I were arguing with one of those people, then a clear 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 from the PPG to the diverse biosphere we see around us might seem to be a complete materialist description of the history of life.

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 do not think I am alone here. I think if you were to show Kauffman’s system to any chemist anywhere in the world, there is a 99% probability they would find it unsatisfactory. Not because such a system could not exist, but because ‘it just happened’ is an entirely implausible explanation for its existence. Saying 'it just happened' is hardly more satisfactory than pointing at a functioning cell and saying 'it just happened'. (The remaining 1% would be those who have a quasi-religious faith in the self-organising properties of matter.)

Any chemist would ask: 'What is driving this cycle of reactions? Where is the energy coming from? What is preventing this system from dissipating?'

There is no such thing as 'Order for Free'. That is the Law. If you want order at point A, you need to dump your disorder at points not-A. Should anyone claim there is such a thing as 'Order for Free', let them be unto you even as the homeopaths and the creationists.

The Curious Incident of the Dog in the Night-Time

Some graduation ceremonies are very dull. Others are dead interesting, and provide enough material for numerous anecdotes. If you are Jenny, you already know two anecdotes about the graduation ceremony I went to a few weekends back. This is a third one.

The main speaker at the graduation was John Ellice-Flint, distinguished alumnus, ex-CEO of Santos, and 2020 summiteer. He talked about climate change. He did it ably enough that he never had me offside. I shall give a very rough paraphrase of his speech, as it is not the done thing to take notes, and my memory is not what it once was.

He didn’t waste any time emoting about environmental catastrophe, and stated at the outset that he was going to set to one side the whole debate about the nature and extent of global warming.

He pointed out that the large developing nations were not going to abandon fossil fuels, whatever we did: we would have to accept that fossil fuels were going to be a major part of the world energy mix for some time to come.

He gave an internet factoid about the number of wind turbines China would have to build every day in order to equal the number of coal-fired power plants it was building.

He said the only way we could hope to make an impact on carbon dioxide emissions in the short-term was to throw barrow-loads of money at scientists and engineers- the one outcome of Global Warming hysteria that I have always felt to be an unqualified good.

He said he felt confident that the new government would rise to the challenge of providing these barrow-loads of money, and that in achieving world-class expertise in these areas Australia would soon earn it back many times over.

He talked a bit more about renewables, and a bit more about carbon-capture. I forget exactly what he said. I was waiting for him to mention the ‘N’ word.

But he didn’t!

Not once.

The word ‘nuclear’ did not pass his lips.

He is obviously on top of the whole big picture of greenhouse-gas abatement. He is obviously a clever bloke. He is obviously well-connected.

And it is pretty obvious that the nuclear option is one that is going to be adopted by a lot of our neighbours in our Near North, whether or not an ice age starts tomorrow, because we are going to run out of coal eventually, no matter how clean it is. It seemed obvious to me that the arguments he made with respect to developing expertise in renewables and carbon-capture applied equally well to expertise in nuclear power. And it seems obvious to me that since we are already involved in the nuclear industry as a supplier of uranium, we have not only an economic opportunity but a moral duty to take responsibility for the whole fuel cycle: to provide processed fuel to our customers (to reduce proliferation concerns) and to take back their waste (because it was ours to begin with, because we have ideal political and geological conditions to store it, and again, to reduce proliferation concerns).

But Mr Ellice-Flint didn’t mention nuclear power at all.

I am sure it didn’t just slip his mind.

I am sure he had some perfectly good reasons not to mention it.

But unfortunately, by not mentioning it, he couldn’t help but come across as someone pushing a narrow carbon-capture agenda, rather than an honest broker surveying the challenges of our energy future.