What is Life?:How chemistry becomes biology

by Pross, Addy

  Life’s dynamic nature

  One of life’s striking characteristics is its dynamic nature. We commented earlier how within the space of some months you are no longer who you were. Materially you are now largely composed of new stuff—a new you! Your blood cells, billions of them, are replaced daily, your skin cells continually turn over, the protein molecules that do most of the work in getting on with life are all continually being degraded and regenerated in a never-ending dynamic process. But how can this ephemeral and dynamic nature of living systems be explained? In fact, this particular aspect of life is one of the easiest to understand. Recall our analogy of a replicating population and a water fountain. The fountain is stable (persistent) even though the water that makes up that fountain is turning over continuously. Different water, same fountain. For any replicating entity the same proposition holds. Because the replication reaction is unsustainable, regardless of what it is that is being replicated, a replicating system that achieves stability would be one in which the rate of replicator generation and decay would be in rough balance, one in which a steady state is established. This would be true of molecules, microbes, or monkeys, or any other replicating entity one would care to mention. In other words it is the population that is stable, with the individual entities that make up that population constantly turning over. And this continual turnover holds at all levels of complexity—molecules within cells are constantly turning over, cells within organisms are constantly turning over, and, of course, all organisms are constantly turning over. That simple fact clarifies the role that death plays in the life process. In a 2005 commencement speech to Stanford graduates, Steve Jobs, the hitech innovator said:

  No one wants to die. Even people who want to go to heaven don’t want to die to get there. And yet death is the destination we all share. No one has ever escaped it. And that is as it should be, because Death is very likely the single best invention of Life. It is Life’s change agent. It clears out the old to make way for the new. Right now the new is you, but someday not too long from now, you will gradually become the old and be cleared away. Sorry to be so dramatic, but it is quite true.

  Death then is not just something bad that happens to us living things. Death is part of the life strategy. Seeking eternal life? The term is an oxymoron. There can be no eternal life because the very basis of life is its transient and dynamic nature.

  Life’s diversity

  Though Darwinian theory was able to relate all living things to one another, the source of life’s spectacular diversity remains unresolved. As we discussed in chapter 1, Darwin himself remained uncertain on this key point. In his Origin of Species Darwin did propose a Principle of Divergence, but whether that principle was independent of his principle of natural selection, or derived from the principle, was left open and, interestingly, the issue continues to preoccupy modern biologists. However, the theory of life that we have described, based on the DKS concept, seems to offer some resolution of this issue. It turns out that the key to understanding life’s extraordinary diversity lies in the topologies of the two chemical worlds—the ‘regular’ and replicative worlds, and the difference between them. Let me explain.

  I have already explained that all chemical systems are directed toward their most stable form. That means that different chemical systems that are composed of the same elements will all want to end up at the same place, just like different balls rolling down a hilly terrain from different locations on that terrain will all want to end up in the same location—the lowest point in the valley below. If you take any mixture of hydrocarbons—that’s just a chain of carbon atoms joined to hydrogen atoms, such as we find in gasoline—and react that mixture with oxygen in what is called a combustion reaction, the resultant product is carbon dioxide and water. It doesn’t matter which hydrocarbon you start with, you always end up with carbon dioxide and water, because that is the most stable form of a mixture of C, H, and O atoms. All hydrocarbon-oxygen mixtures converge to carbon dioxide and water. That argument may be generalized to chemical systems as a whole, so one could say that the grid that connects the world of ‘regular’ chemical substances is convergent, as illustrated schematically in Fig. 7a. All roads lead to Rome and all chemical reactions are directed to what is called their thermodynamic sink—the lowest energy possibility for that combination of atoms. That’s how a chemist can frequently predict the result of a chemical reaction, that’s how he/she knows where the chemical system ‘wants to go’.

  Fig. 7. Schematic representation of branching patterns within ‘regular’ chemical space (convergent), and within replicator space (divergent).

  But let us now turn to the world of replicating systems. In contrast to a ‘regular’ chemical system, which may be thought of as contained, or closed, a replicating system must remain open at all times to allow the replicating reaction to proceed unimpeded. Being open means that building blocks for replication, as well as the energy to support the replication process, must be continually provided. In other words, in comparison to a ‘regular’ chemical reaction, which may be carried out in a closed container, a replicating reaction must remain open to the surroundings. That different situation results in the path to greater DKS being divergent, as illustrated in Fig. 7b, rather than convergent. Why? Because the path forward to greater DKS will depend on what’s available at that time and in that place, and any number of different paths toward more stable systems (in a DKS sense) are, in principle, feasible. Some replicator X might pair up with some molecule Y to create a more stable X/Y system compared to X on its own, but it also might pair up with some other molecule Z, thereby creating a stable X/Z system. The possibility of different complexification pathways leads to diversification. All stable replicating systems are continually replicating, occasionally mutating, continually complexifying, thereby exploring the world of replicating systems for increasingly effective replicators. The topology of the world of replicating systems is inherently divergent.

  This different topology for the two worlds has interesting consequences. It not only explains life’s diversity but it also explains how we are able to go back in time and seek our evolutionary roots. A divergent topology in the forward direction becomes a convergent one in the backward direction. It is that convergent topology in the reverse direction that enables us to utilize phylogenetic analysis and the fossil record to trace our evolutionary history going back in time, to deduce that all living things can be divided into three life kingdoms—Archaea, Bacteria, and Eukarya—to trace out the history of life on earth toward life’s so-called Last Universal Common Ancestor (LUCA). But that, of course, means that we can say nothing at all regarding where evolution may take us in the future. Set off on a divergent path and there’s no telling where you’ll get to. As Yogi Berra, the well-known sports celebrity, once put it: ‘If you don’t know where you are going you will wind up somewhere else.’ The different reactivity patterns of both ‘regular’ and replicative systems as a function of time—forward or backward—is simply explained.63,64

  Life’s homochirality

  We have remarked how life’s homochiral (single-handed) nature presents a puzzle at two levels. First, how did life’s single-handedness emerge from a universe that is inherently two-handed, and second, how is that homochirality maintained, given that homochirality is intrinsically less stable than heterochirality. We have seen in this book that one of the key ideas that can explain the emergence of life on earth is the enormous kinetic power of auto-catalysis. It is then remarkable to discover that the unexpected emergence of homochirality from a heterochiral environment can be explained in precisely the same terms! Normally when one carries out a chemical reaction that transforms a non-chiral substance (possessing no handedness) into a chiral one, the product is composed of equal amounts of left- and right-handed forms. But in 1995 the renowned Japanese chemist, Kenso Soai, made a remarkable discovery.65 In certain instances it is possible to obtain effectively just one homochiral product from a non-chiral starting mater
ial. Somehow the symmetry of the system is broken, which is quite extraordinary. It’s like tossing a coin a thousand times and observing 999 heads and one tail! No wonder Kenso Soai’s unexpected result caused a sensation. In other words it is possible to generate homochiral systems, starting from a non-chiral environment, even though for many years this was considered physically unreasonable. So what has this to do with the emergence of life?

  Soai’s highly unexpected result is explained by the fact that the chemical reaction he studied proceeds autocatalytically, and therefore product formation shows exponential growth. If the reaction mixture is initially seeded with a tiny excess of one of the chiral products, then the spectacular amplification that autocatalysis can generate results in that product reaching a level of purity very close to 100 per cent. In other words, just as replication is autocatalytic, so homochirality (single-handedness) can be induced in a system that shows autocatalytic behaviour. This reaction and its detailed explanation are somewhat technical but the bottom line is straightforward: the kinetic power of replication which is responsible for the emergence of life could well have been responsible for one of life’s most striking features—its homochiral character. The pieces of the life puzzle do fit together. How satisfying!

  We have explained the emergence of homochirality from a non-chiral environment, but how is that homochirality maintained if homochirality is intrinsically less stable than heterochirality. Like several previous life dilemmas, this issue is also resolved through the DKS concept. Yes, systems that are of one chiral form are less stable than heterochiral mixtures, but that is only true in a thermodynamic sense. We have already seen that in the context of replicating systems, the stability that counts is DKS, and for this stability kind it turns out that homochiral systems are more stable than heterochiral ones. Life’s reactions require high specificity, meaning precise lock-and-key type interactions between reacting molecules and that can only be obtained in homochiral systems. Introduce heterochirality into such systems and you will end up with half the keys not fitting into their locks! Homochiral systems are therefore more effective replicators than heterochiral ones, and as a consequence homochiral systems exhibit greater stability in the crucial DKS sense.

  Life’s teleonomic character

  We discussed this most amazing of life’s properties in some detail in chapter 1. To reiterate, both the structure and the behaviour of all living things lead to an unambiguous and unavoidable conclusion—living things have an ‘agenda’. Living things act on their own behalf. But how can that be? How can matter, when organized in the manner we classify as biological, seemingly follow different rules from those of inanimate systems? How can matter of any kind appear to have an agenda? Let us see how the DKS concept can help resolve this puzzle. Recall that the reactions of simple replicating systems—say, replicating molecules—would follow the thermodynamic directive, much like a car without an engine follows the gravitational directive—it can only roll downhill. But once a replicating entity has taken on an energy-gathering capability, the replicating entity is now ‘freed’ of thermodynamic constraints and can follow the kinetic directive—the drive toward greater DKS. As we discussed earlier, a replicating entity with an energy-gathering capability is now like a car with an engine—it can go uphill too. That means that a replicating system with an energy-gathering capability would appear to have an agenda. It would seem to be acting purposefully, as it would no longer need to be confined to the downhill thermodynamic path, which we interpret as objective behaviour, but rather the path toward systems of greater DKS, which could involve the equivalent of rolling some way uphill. In other words, once a replicator has taken on an energy-gathering capability (as part of the general process of complexification toward more complex and more stable replicating systems), we would interpret and understand its subsequent replicative behaviour as purposeful.66 Monod’s paradox—how a purposeful system can emerge from an objective universe, is seen to result from the interplay of kinetic and thermodynamic directives in chemical reactions. In the ‘regular’ chemical world, thermodynamics is the dominant directive and results in so-called objective behaviour. In the replicating world, kinetics is the dominant directive and so actions in that world appear purposeful.

  Consciousness

  There are other profound life issues that we have not touched upon—consciousness, for example. While consciousness is certainly a characteristic of life, it is not an essential one, as it is only associated with advanced life forms. Accordingly, we have not dealt with it. Nonetheless, the issue of consciousness should be mentioned, if only to demonstrate how limited our understanding of some life characteristics remains. Having said that, the phenomenon of consciousness can be explored through its evolutionary context. Evolution is the process by which all properties of matter are exploited in the evolutionary drive toward more effective replicating systems. Evolution exploits matter’s propensity for hardness when that is useful, as in bones. It exploits matter’s ability to be flexibly firm when that is needed, as in cartilage; matter’s ability to be liquid when that is needed, as in blood; matter’s ability to be transparent as in crystallin, the protein from which the lens of the eye is made; matter’s ability to conduct electric charge, and so on. But it turns out that matter in some particular organization has an even more remarkable characteristic—the remarkable property of consciousness. Indeed, an extraordinary characteristic—matter can be self-aware. Evolution has discovered that capability of matter, like all others that it has come across, and utilized it in the ongoing search for stable replicating entities. If we want to understand consciousness and its basis, we should study its source—neural activity at its most rudimentary level, and then track the phenomenon, step by step, through to its more advanced manifestations, ultimately to us humans. So the approach would be the same as the one we have taken in addressing the problem of abiogenesis—start simple. A fascinating scientific journey awaits us.

  How would alien life look?

  Having explained life’s global characteristics in chemical terms, we can now pose the question: how would alien life look? Since we believe that life on Earth emerged from inanimate matter, it naturally follows that under appropriate conditions life could also emerge elsewhere in the universe. And while that life could also be based on the same molecular foundation—the nucleic acid–protein duo—other replicative combinations cannot be ruled out. We now understand that the basis of life consists of long-chain molecules capable of catalysing their own replication, which together with other chain-like molecules possessing catalytic capabilities would undergo a continual process of replication, mutation, and complexification. However, there is no reason at all to believe that in principle there would not be chemical combinations, other than that nucleic acid-protein duo, that could lead to that same general result. In fact, all of our experience in chemistry tells us that chemical characteristics are related to groups of substances, not to individual ones, so the expectation would be that, in principle at least, there would be a group of materials on which the processes of life could be based. So, if life did emerge on some other planet, one based on a different biochemistry from that on earth, can our theory of life offer some insight into how such life would appear? I believe so. My short answer: life on other planets would look exactly like that on our own!