What is Life?:How chemistry becomes biology (18 page)

As we have discussed in some detail in
chapter 5
, we are lacking any direct information regarding that early prebiotic period. However there
is
one thing we can state with high assurance regarding that early period. It is that the laws that govern chemical behaviour have not changed over the past several billion years, and that means that studying the right kind of chemistry today can inform us about what might have happened billions of years ago. And the right kind of chemistry is systems chemistry, the chemical reactions of replicating molecules and the networks they create.
^29
,
56
Such study may provide us with insight into the
kinds
of reactions that prebiotic replicators might have undertaken, amongst them that early process of complexification.

What have we then learnt regarding simple chemical replicators? First, getting single molecules to self-replicate is inherently difficult. In fact the difficulty in getting so-called replicating molecules to replicate when no biological materials are added to ‘help’ things move along, has been viewed as one of the stronger arguments against a replication-first scenario for the emergence of life. But let us return to some recent results from the Joyce lab as they are illuminating. Despite the difficulties inherent in getting single molecules to replicate, Gerald Joyce was able to come up with an RNA molecule that was able to make copies of itself without enzymatic assistance. In that particular reaction, a replicating RNA molecule, let’s call it T, itself composed of two RNA segments, A and B, underwent a replication reaction by the template mechanism (described in detail in
chapter 4
). The RNA molecule, T, acting as a template, induced fragment entities, A and B, which were floating about freely, to temporarily bind to itself and then link up, thereby creating a new molecule of T. The overall result, a single T molecule
was able to make copies of itself by inducing its two component parts A and B, freely available in the solution, to connect up.
⁵⁷

Even though that replication reaction was possible, it was frustratingly inefficient. First, it was slow—it required seventeen hours for an initial sample of RNA to double in quantity. But slowness wasn’t the only problem. After all what is seventeen hours when compared to a billion-year time frame? An additional problem was that the replication reaction only proceeded for two replication rounds before grinding to a halt (due to certain side reactions), so it was not possible to continue the reaction, even when feedstock for further replication reactions (i.e., more A and B) was provided. But now to the interesting finding. When Joyce switched from a single replicating RNA molecule to a two-molecule system composed of
two
discrete RNA molecules that had been obtained in a careful selection process, then replication proceeded rapidly—the initial sample doubled in quantity in just one hour—and replication could be sustained indefinitely, provided the building blocks were available. How come? Why the difference?

Let’s start by stating what wasn’t happening. In the two-molecule RNA system each molecule was
not
making copies of itself. Rather, one RNA molecule was inducing the formation of the other, while the other molecule was inducing the formation of the first. In chemistry we call that cross-catalysis—each RNA molecule was catalysing the formation of the other. So the more complex system
is
self-replicating, but in a more complex way—each component of the system isn’t replicating individually, but the system as a whole
is
self-replicating. That distinction is important because holistic replication is the norm in biology; that’s what cells do when they replicate—the system as a whole makes copies of itself, as opposed
to each individual component within the cell copying itself. So what is the significance of this result? Simply this: what one simple replicating entity could only do
inefficiently,
a more complex one was able to do
more efficiently.

This chemical equivalent of ‘I’ll scratch your back, if you’ll scratch mine’ goes beyond the tit-for-tat exchange of favours, which is useful in itself. The deeper meaning is that what I cannot do well on my own, I can do more effectively in a cooperative way. Cooperation is win-win. No wonder cooperation is endemic in the biological world—biologists call it symbiosis. You see it wherever you look. So what Gerald Joyce discovered in those two RNA molecules was profound. Yet another piece of evidence that demonstrates how chemistry and biology are intimately connected. A process of
molecular complexification
has led to an enhanced replicative capability.

Let us take another look at Fig. 6 because it now takes on a new significance. Our discussion above has indicated that complexification facilitates both the molecular replication phase
and
the biological replication phase. In fact, the entire process when viewed over an evolutionary time frame is seen to be one of complexification. The main difference between the two phases is that the first phase, the chemical phase, is the
low-complexity
phase, while the second phase, the so-called biological phase is the
high-complexity
phase, all taking place within the context of replicating entities. The conclusion seems clear: complexification, primarily through network establishment, appears to be the
mechanism
for the transformation of
simpler chemical
replicators into more
complex biological
ones. In fact the recognition that complexification is a key process in evolution leads us to a surprising conclusion, namely, that the
causal sequence that leads to evolution needs to be modified. Evolution in biology is normally associated with the causal sequence:
replication, mutation, selection, evolution.
But we now see that an important step in that sequence has been overlooked. The missing step is complexification. The sequence should read:
replication, mutation, complexification, selection, evolution
and this is true for both the chemical and biological phases.

Some words of clarification are now appropriate. The previous discussion might suggest that the evolutionary process is based solely on complexification and this is clearly not the case. It is well established that in particular instances evolution follows a process of
simplification.
Biology in particular is replete with such cases—for example, cave-dwelling animals such as crickets and cavefish that lose their eyesight as they adapt to life in the dark. But, remarkably, in chemical systems precisely the same phenomenon of simplification can also be observed. Recall Spiegelman’s experiments on molecular evolution in which replicating RNA chains shortened because the shorter chains replicated faster.
²⁷
That classic study provides a
chemical
example of simplification. Just as cavefish lose their ability to see in dark caves, RNA chains (extracted by Spiegelman from the Q
β
virus) discard those parts of the viral genome that prove redundant in the artificial resource-rich test-tube environment. The very existence of a process of simplification in both biological
and
chemical evolution serves to
further
strengthen the chemistry-biology connection and provides yet an added piece of evidence supporting the unity of the evolutionary process of Fig. 6. Returning however to the present theme, regardless of those well-documented instances of simplification, it is clear
that complexification is the
underlying
tendency in evolution, in both the chemical and biological worlds.

In the light of the above experiments and arguments, the reader has hopefully been convinced that the processes of abiogenesis and evolution are actually one single physicochemical process governed by one single mechanism, rather than two discrete processes governed by two different mechanisms. That insight will turn out to be of utmost value as it leads to a whole range of both chemical and biological insights. If our conclusion is correct it means we can apply
chemical
insights from the chemical phase to better understand the
biological
phase, and we can also apply
biological
insights derived from 150 years of studying Darwinian evolution to provide greater insights into the
chemical
phase. Win-win for sure! But beyond that, the unification tells us that chemistry and biology are one, that there is a
complexity continuum
that connects them, that biology is just an elaborate extension of replicative chemistry. Interestingly, as noted in the prologue, Darwin, in his genius, foresaw the existence of some underlying principle governing abiogenesis and biological evolution. However, thanks to the inspiring work of gifted systems chemists these past decades, we don’t have to speculate about the nature of a general life principle—the life principle can now be formulated based on hard facts.

So what new insights does this merging of chemistry and biology provide us with? Before answering this question and in order to fully benefit from this conceptual merging, we now need to rephrase Fig. 6. Traditionally one would describe the first phase, the chemical one, in chemical terms, and the second biological phase in biological terms—each process in its own language. But, as we all know from foreign travel, a dialogue in two languages,
when the two parties do not speak the other’s tongue, may be frustratingly less than useful. Misunderstandings galore can arise. In order to avail ourselves of the deeper insight of one continuous process, the two phases need to be described in one language. So which is it to be—the language of chemistry, or that of biology? The answer is clear-cut: the entire process—chemical and biological—needs to be described in chemical terms. Let me explain why.

In an earlier chapter (
chapter 3
), I described how understanding in science is achieved at different hierarchical levels. Phenomena at a higher hierarchical level of complexity are normally explained in terms of scientific principles associated with a lower hierarchical level. Thus we conventionally explain biological phenomena in chemical terms and chemical phenomena in physical terms, not the other way around. Recall, Steven Weinberg’s comment: ‘Explanatory arrows always point downward.’
²⁴
To bring this point home and to illustrate how fundamental this hierarchical aspect of explanation is, consider the two sciences, chemistry and psychology, and how they might interrelate. Let us say you find some psychological phenomenon of interest and you tried to explain it in molecular terms. Scientifically speaking that is quite acceptable. For example, if you came up with a molecular explanation for schizophrenia that would certainly be of interest—drug companies would likely be knocking on your door! However, if one went the other way and attempted to explain some
molecular
phenomenon in
psychological
terms, that would only attract derision! Schizophrenic molecules? Neurotic molecules? No way! The message is clear: the temptation to interpret phenomena that are inherently chemical in nature in biological terms—fitness, natural selection, adaptation, survival of the fittest, cooperation, information, etc., should be firmly resisted. Open any chemical
text that deals with chemical reactivity and those biological expressions will not be found there. Chemical phenomena are explained in chemical (and physical) terms, as chemistry is the more fundamental science. On this basis a reinterpretation of Fig. 6 in terms of just one scientific discipline makes clear that the discipline of choice must be the lower-level one, chemistry, not the higher-level one, biology. So let us proceed to do just that. Let us reinterpret the entire process of Fig. 6—part chemical, part biological—solely in chemical terms.

When several replicating molecules are mixed with their component molecular building blocks, as described in
chapter 4
, they compete with one another, in much the same way as biological entities compete for a limited supply of food. But as explained above we shouldn’t discuss that competitive process as
natural selection at the molecular level.
Such reactions are dealt with by a specific branch of chemistry that deals with the rates of chemical reactions called chemical kinetics. That sub-discipline of chemistry, going back some 100 years to the pioneering work of Alfred Lotka, has no difficulty in dealing with the situation in which two replicating molecules compete for the same building blocks. It comes up with a clear-cut prediction that is applicable in most cases—the faster replicating molecule will out-replicate the slower replicating molecule and drive it to extinction. That result comes out directly by solving the relevant rate equations. In other words when two replicating molecules compete for the same chemical building blocks, the outcome is readily explained by a process that chemists call
kinetic selection.
Kinetic selection in everyday language just means
‘the faster one wins’. Since the faster replicator is capable of assembling building blocks into new replicating molecules more effectively (for a variety of chemical reasons), the number of those faster replicators grows quickly while the number of slower replicators drops until those slower replicators disappear entirely.

But that strictly chemical result does ring a biological bell. It sounds very much like the way in which natural selection operates in biology. When two biological species compete for the same resource, the one that can utilize that resource more effectively drives the other to extinction. That result is the basis for the competitive exclusion principle that we discussed earlier. But then, natural selection and kinetic selection are really the same concept, so let us state that explicitly:

natural selection = kinetic selection

Biological natural selection merely emulates chemical kinetic selection. Natural selection is the biological term, kinetic selection is the chemical term.

At this point the reader may ask why the chemical description is to be preferred over the biological one. Despite the earlier comment that explanatory arrows always point downward, aren’t the chemical and biological explanations really saying the same thing, that faster, and therefore more effective replicators, whether chemical or biological, will out-replicate less effective ones? Not quite. The reason is that the chemical explanation is more fundamental and probes the issue of selection more deeply. The chemical term is more quantifiable than the biological one because chemical systems are inherently simpler. That greater simplicity allows us to further break down the composite chemical replication reaction into the
individual reaction steps that go to make it up. The chemical analysis can tell you how long it will take for one molecular replicator to out-replicate the other. It will even tell you under what circumstances the two replicators may coexist. Coexistence between competing molecular replicators can also be observed under appropriate circumstances.