Evolving by direct action

. . .I saw by the Inspector's face that his attention had been keenly aroused.

'You consider that to be important?' he asked.

'Exceedingly so.'

'Is there any point to which you would wish to draw my attention?'

'To the curious incident of the dog in the night-time.'

'The dog did nothing in the night-time.'

'That was the curious incident', remarked Sherlock Holmes.

It was once thought that organisms quite often arose directly, through transformations of matter that did not require the reproduction of previously existing organisms. Such spontaneous generation was thought to be commonplace: for example frogs were thought to arise de novo from mud, and maggots from decaying meat.

I now wish to draw your attention to the curious incidence of spontaneous generation as we now see it. There does not seem to be any.

Is that not rather odd? Once upon a time an evolutionary process started up, but there are seemingly no brand new beginnings any more. The tree of life flourishes: but apparently there is only one tree with no sign, even, of any recent saplings on the same ground. Why are there no signs of present or recent spontaneous generation?

The first answer that may come to mind is that organisms are just much too complicated. One can easily see the absurdity of spontaneous frogs or maggots, now that the 'high-tech' nature of such forms of life has become so apparent. Similarly for bacteria - E. coli is not really a simple thing either. And since bacteria are nevertheless among the simplest free-living organisms that we know of, why then, any spontaneous generation may now seem absurd.

But wait a minute: that line of thought by-passes the argument. The point is that we might have expected, on the assumptions that we have been making, that there should be some really simple kinds of organisms around us. After all we have been assuming (chapter 1) that the first organisms really did appear spontaneously on the Earth (with no miracles, freak events, frame-ups or alien infections). In that case there should at least have been organisms of a kind that could generate spontaneously. Remembering the limitations of pure chance as an engineer (chapter 6) such organisms would have been, chemically, child's play. Presumably the laws of Nature were not any different 4 billion years ago. So why are there not still such organisms to be found - self-starters, what I will call primary organisms? Why do we not know all about them?

Is it because the general conditions on the Earth have changed? Is it that the conditions for making and sustaining the first sparks of life are no longer suitable? This is a standard answer. But we have seen how insufficient this kind of answer is. Just having general conditions right would not have been nearly enough. Even with the most favourable general conditions imaginable, key molecules of even quite modest complexity - nucleotides, for example - could not have been made with anything like the necessary competence. To make molecules of that sort requires an intricate interference, an elaborate manufacturing procedure that only the prolonged operation of natural selection (or an experienced research chemist) could reasonably be expected to generate.

Anyway we should be able to do much better than just create suitable general conditions. We can set up manufacturing procedures and automatic machinery to carry them through. We can load the dice - we can contrive situations and devices that could by no stretch of the imagination have arisen de novo by chance. So if Old Fumble Fingers, pure chance, did indeed put together the first evolvers under the rules of chemistry and physics, why, for goodness sake, can't we?

If, as it would seem, the difficulty is not technical, it must be a difficulty of knowing which area of possibilities to explore, of seeing the appropriate design approach. Perhaps, in line with the whole drift of this book, research has been concentrated on the wrong materials and on the wrong natural phenomena? (Are new sparks too gentle to be easily seen, now, against the more general blaze?)

But if, as I have been saying, the key materials for primary organisms are inorganic crystals (so that the topic of the origin of life on the Earth is a branch of mineralogy) then the opening question of this chapter becomes rather sharp - all the more so now that the pre-vital Earth is being seen as having been more 'normal' than was thought previously (p. 6).

Nor is there a let-out in the explanation (given on p. 42) for why the single common ancestor for all life on the Earth should have been so highly evolved. That kind of explanation pre-supposes the absence of recent spontaneous generation. It says that if there was only one tree then almost any arbitrary combination of branchings and prunings would have led to a late last common ancestor. But with spontaneous generation we should expect there to have been not one tree but quite a little forest of trees of different ages, and in that case no single common ancestor.

Of course a random-branching-and-pruning picture of the growth of evolutionary trees is too simple. There would have been other factors at work. One of these was pointed out by Darwin: organisms no longer originate de novo because any brand new forms of life would be promptly eaten by evolved forms. No doubt this is so. But how promptly? If the very first forms had been inorganic crystal genes, they would have been unappetising to any organisms of the modern type. Darwin's point explains, perhaps, why there are no obvious well-developed saplings around the tree of life. But on the crystal gene idea should there not be myriads of very small saplings, near-starter organisms that have not got far enough to interact with modern organisms because not yet sufficiently like them?

And of course that could be a reason why primary organisms have not yet been recognised: because they are made of the 'wrong' materials, and because their appearance is not 'life-like'. I think it is quite possible that primary organisms are indeed all around us.

By chapter 9 we had arrived at the idea that the first organisms would most probably have been made from substantially different materials from today's biochemical materials, and we touched on the notion that these organisms might have been 'naked genes'. Crystals then seemed to be the best bet for such genes.

But would not the term organism be altogether too pretentious for, well, just a mass of tiny crystals? One might be inclined to insist on something more interesting before using the word organism to describe it.

That would be sheer prejudice. We are never going to find (or make) primary organisms if we have too high-flown ideas about what they should be like. They will be all potential with little or no achievement. Of course they are going to be rather boring, poor things. If our ultimate ancestor was indeed a product of the Earth then similar things that we might find now should be similarly mineral first and foremost.

For example, clay crystals growing in the pores within a piece of sandstone might very well turn out to be primary organisms. Clay crystals growing under such conditions have, often, distinctive and elaborate forms - such as the grooved kaolinite vermiforms that were described in the last chapter - and it is not too difficult to imagine circumstances in which simply the shapes and sizes of crystals could have a bearing on their ability to grow quickly, or break up in the right way, or stay in the right place, or survive difficult conditions - or otherwise be a success. Provided some aspect of the shape and size (e.g. a cross-section) is replicable, with occasional errors in the replication, then that aspect will be subject to natural selection: it will tend to become optimised in a way that is formally just the same as the way in which the parts of plants and animals become optimised through natural selection. The practical difference here between crystal genes and, say, trees or giraffes would be that for crystal genes shapes and sizes are so much more directly specified by the genetic information. Indeed for real beginners the messages in crystal genes may simply be aspects of shape and size. Naked genes are direct-acting genes and enormously simpler participants in evolution as a result (pp.66-7).

The shapes and sizes of clay crystals can greatly affect the porosity of a sandstone that contains them. This allows one to imagine a process of natural selection operating at a very simple level. Imagine a piece of sandstone that has initially two different crystal genes in it. Each of these soon makes a little zone containing thousands of tiny crystals, all the crystals in one zone having similar features of shape and size and hence giving a characteristic porosity to that zone. The crystals in one of these zones are so shaped that they clog the pores completely. The flow of nutrient (supersaturated) solutions stops in that zone, the flow now being channelled elsewhere. These crystals stop growing. The crystals in the other zone have a different characteristic shape which is being replicated - a rather spindly shape, perhaps, that allows the crystals to grow without completely filling the space in which they are growing, so that solutions can still flow through to continue the supply of nutrients. It is this second form which thus tends to spread to fill the sandstone with its characteristic mass of loosely woven crystals. Bits of this fabric break off, perhaps, to carry the secret of how to grow effectively to other pieces of sandstone, which then become infected. Inevitable mistakes in the replication processes would ensure that there was always some spread of types. I dare say the detailed shapes would not have much effect on performance: but real doggers would always drop out of the race, as would, for example, crystals that were too small and hence too easily washed out of the growth region altogether. . . In the end you would expect, not always one exact shape within the sandstones of a given region, but a general style or perhaps a few styles if there was a spread of types of sandstone, or a spread of flow rates, or more generally a spread of niches calling for somewhat different optimal shape characteristics.

Now imagine a slightly more complicated situation. Let us suppose that sometimes the flow of solutions through the sandstone becomes rather fast and that under these circumstances the waters are generally undersaturated having not had enough time to dissolve the hard rocks through which they had been flowing before reaching the sandstone. Now there is a new problem for the clay crystals: to avoid being re-dissolved when this happens. One idea would be to become impervious under these circumstances. It sounds like a tricky combination of properties, but when the flow becomes too fast and turbulent the laths fluff up into a tangle that cuts down the local flow rate.

This is but another plausible (I hope) story, strictly for illustration: to show how easy it is to imagine particular circumstances that could provide selection pressures in favour of crystals with some fairly simple characteristics of the sort that might be replicable. But I must confess to having had illite in mind for that last bit. These clays grow in vast amounts in marine sandstones as thin, flexible, seaweed-like structures having odd effects on the porosities of the sandstones that contain them. (And a great nuisance they are too for under-sea oil recovery. They tend to clog up oil-bearing sandstones.)

These illites, if they can be described as organisms at all, would certainly have to be put low on the evolutionary scale: as crystal genes with one-dimensional information their information capacity would be very limited since they only have a few - often only three or four - layers in them. (If you remember, in crystal genes of this sort the information would be held as a sequence of layers.) But that some putative naked-crystal-gene could hold only very little information would be less important than that this information was (1) replicable, (2) adaptive (that is to say affected the chances of success of the gene material holding it), and (3) could be further elaborated in the future.

Well, (1) and (2) are a good bit more than conceivable, as I have been trying to indicate in this chapter and the last; and (3) presents no problem in principle, even for humble illites. A hundred layers instead of four would provide a very substantial information capacity, far beyond the reasonable expectations of dice-throwers. So, partly, it would be a question of whether in some circumstances thicker crystals might be better than very thin ones: and then it would be a question of whether particular features of the stacking of layers made any difference to their properties - properties such as flexibility, modes of break-up, or rates of sideways growth. Again this would be more than conceivable. . .

We are already well beyond the stage of even trying to work out what must have happened. What does happen in evolution depends so much on particular circumstances that the course of evolution over the long term is about as predictable as the meandering form of a river or the exact shapes of tomorrow's clouds: one can only illustrate possibilities and indicate general expectations. Of course we cannot know which particular circumstances really mattered for the very beginnings of evolution. But we do know that the real world is full of particulars - structures, events, situations - and that such can be of critical importance in determining the course of evolution. Organisms do not just evolve, they are driven to it by their surroundings, by all sorts of detailed threats and opportunities.

Here is an example of the sort of thing I mean. At some stage in the evolution of plants the woody stem was discovered. This was tied in with the discovery of a strengthening material called lignin - quite a complex substance that can be manufactured in a few steps from one of the protein amino acids. Plants that could make lignin could grow tall and steal the sunlight from others. The characteristic shape and size of a tree, with its tall, rather open branching structure, no doubt depended on the discovery of a suitable strengthening material. But the tree was to create new threats and opportunities for other organisms. Take a walk in the woods and see. Or think about our ape-like ancestors. It is not so much that they chose to live in the trees, rather they were driven into existence by, among other things, the existence of trees: that sort of animal was partly caused by trees. So, then, were we. It is at least plausible that our eyes point forwards mainly because our acrobatic ancestors needed to be good at judging short-range distances; that our excellent hands were designed mainly to grip branches thick enough to support body weight; that our good sense of balance that allows us to learn and enjoy such extraordinary feats as skiing or cycling also harks back to a more necessarily acrobatic way of life. (Who would have thought that lignin had anything to do with cycling? Yet I think it is true to say that if lignin had not been invented then man, that package of curious abilities, would not exist.)

Such are the unforeseeable consequences of evolution - even of those parts of the process that are comparatively near to us. How can we say anything about the very earliest stages? We certainly cannot say exactly what happened, because all sorts of details of circumstance are lost. But principles are understandable: we should be able to understand the kinds of situation that would encourage evolution, and the kinds of direction that evolution might be expected to take.

In the search, here and now, for primary organisms, it is particularly important to think about the kinds of situation that would actively encourage evolution - just because primary organisms, unlike other kinds, can exist in unevolved states which may be difficult to recognise. If primary organisms are to reveal themselves, they should be exposed to threats and opportunities. We might look for evolved primary organisms in places that are adjacent to places in which clays can grow easily: where only clays with rather special properties will be able to survive. One can imagine primary organisms starting (all the time and all over the place) in easy regions and then (sometimes) evolving into more difficult regions.

Why should they do that? Why should they not just stay in the easy regions? Why should they not just stay unevolved?

Most of them would, I dare say. The question is why some should take a more difficult path. Well, one might as well ask why some animals came out of the sea onto dry land (a far more difficult place to live): or why the ancestors of birds took to the air; why our own ancestors took to the trees; or why we will sooner or later colonise Mars. It is not for the sake of an easy life exactly, as a great deal of difficult technology has to be developed in each such case. But, given the technology, there are then new opportunities for the organisms that have it. It is clearly an important direction of evolution that organisms gradually come to occupy more and more difficult niches -that they aquire the means to survive where others cannot. This is not a question of innate ambition: it just happens as a consequence of natural selection operating in a complicated and heterogeneous world.

Another principle, and a trend that goes hand in hand with increasing control of the environment, is from more direct to less direct means of genetic action. In chapter 7 we considered how the consequences of this are built into the common control structure of all the organisms that we know about. Indirect action makes a lot of sense. By acting so indirectly - through RNA, proteins, cells, higher-order structures - those dry DNA messages develop rich and varied meanings: a dull-looking score is orchestrated and performed.

Now primary crystal genes evolved by direct action to begin with, but would they not too have moved towards a more indirect control? A genetic material has quite enough on its hands holding and accurately replicating its messages. It is unreasonable to expect it to be the last word as, say, a membrane material or a catalyst as well. To have one material, DNA, as the information replicating specialist, and a quite different material, protein, as the Jack of most other trades, is wholly comprehensible as an eventual outcome of evolution. Many, many more properties can be controlled by working indirectly like this. For evolving primary organisms the tactics could not have been through protein or anything like that. But surely the general strategy would have been similar, because the logic is similar for organisms at any stage of evolution. Indirect operation is always likely to provide a route to a greater variety of means of control, and in a complicated and heterogeneous world that means a greater variety of places to thrive in.

Trying hard to remember that the first organisms had no sight of the DNA-based machinery that lay in the distant future, we might now ask in what sorts of ways gene-1 might have extended its control. What sorts of separate phenotype structures could it most easily contrive, and for what purposes?

Different kinds of clay mineral crystals may grow in collaboration, one kind affecting the conditions for others. This may happen through new crystals forming on the surfaces of crystals that are already there - a kind of seeding. Or it may happen more indirectly through one clay altering general conditions, such as flow rate or local acidity, which then favours the formation of other clays that might not otherwise have formed. In so far as replicable features (e.g. shapes, sizes, surface patterns) of crystal gene clays could affect the formation of other non-gene clays, and in so far as the non-gene clays might be helpful to the gene clays, then the non-gene clays would be properly described as phenotypes of the gene-clays.

Picture these now somewhat evolved organisms as consisting of masses of crystal genes embedded in a watery matrix of other clay or clay-like material. It is not difficult to imagine uses for such a matrix material. It might provide mechanical protection against damage (growing crystal genes must break, if you remember, but only in the right way); or it might act as a glue, holding the genes in the right place. Or the matrix might provide protection against the effects of fluctuations in concentrations of nutrient solution: if the helper materials were to grow and dissolve more quickly than the gene

Seven clues to the origin of life materials, then the helper materials would have such a stabilising effect on the waters in their surroundings. Or again the matrix material might tend to hold on to metal ions that would interfere with the growth of the crystal genes. . .

It is almost too easy to imagine possible uses for phenotype structures - because the specification for an effective phenotype is so sloppy. A phenotype has to make life easier or less dangerous for the genes that (in part) brought it into existence. There are no rules laid down as to how this should be done.

We are now moving away from the relative security of unevolved primitive genes where possibilities are constrained by more or less well-known characteristics of materials - of crystals and molecules. We are moving away from direct-acting genes to a new playground, to convolutions of indirect genetic control that seem to be without limit.

'Ah! my dear Watson, there we come into those realms of conjecture, where the most logical mind may be at fault.'

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