What is Life?: How Chemistry Becomes Biology (Oxford Landmark Science)

by Addy Pross

we know unequivocally that there is no élan vital, that living things are made up of the same ‘dead’ molecules as non-living ones, but somehow the manner in which those molecules interact in a holistic ensemble results in something very special

Nature, if anything, pushes systems toward equilibrium, toward disorder and chaos, not toward order and function. Or does it?

Complexity science - order on the verge of chaos

Every cell is ultimately a highly organized and efficient factory for making more cells!

thanks to a newly defined area of chemistry, termed by Günter von Kiedrowski ‘Systems Chemistry’, the existing chasm separating chemistry and biology can now be bridged, and that the central biological paradigm, Darwinism, is just the biological manifestation of a broader physicochemical description of natural forces.

in the living world complexity is not arbitrary, but highly specific. Even the slightest structural change to that organized complexity may have dramatic consequences.

How is the organized complexity of the cell maintained, and how did it come into being?

all living things behave as if they have an agenda. Every living thing goes about its business of living—building nests, collecting food, protecting the young, and, of course, reproducing.

The highly complex cell structure that we have already discussed is the most explicit and profound expression of that teleonomic character. Pretty well every element within that bacterium can be associated with a particular cell function, in much the same way that the individual components of a clock—pendulum, cogs and wheels, springs, hands, cabinet, etc.—can also be associated with a particular function, except that within the cell the structural complexity and intricacy is orders of magnitude greater.

Life is defined as a material system that can acquire, store, process, and use information to organize its activities.15 Life is defined as a system of nucleic acid and protein polymerases with a constant supply of monomers, energy and protection.16 Life is defined as a system capable of 1. self-organization; 2.self-replication; 3. evolution through mutation; 4. metabolism; and 5. concentrative encapsulation.17 Life is simply a particular state of organized instability.

the NASA definition of life: Life is a self-sustained chemical system capable of undergoing Darwinian evolution.

Invariably living things are either excluded from the various definitions or non-living things are improperly included in them.

Holism contends that within complex systems in particular, unexpected emergent properties arise that cannot be derived by examining the individual components of the system

Ultimately the difference between animate and inanimate must be reduced to differences in the nature of the materials within the two worlds and, in particular, in the way those materials interact and react.

The tendency to disorder is inherent in the Second Law—ordered systems tend toward disorder, and this can be explained in statistical terms.

The discovery that self-replicating molecules exist is highly significant because, as we will see, the existence of such molecules can form the basis for understanding how life emerged, how inanimate matter began the long and arduous road from simple beginnings to the extraordinary complexity that is life.

Replicating chemical systems will tend to be transformed from (dynamically) kinetically less stable to (dynamically) kinetically more stable.

that if some convincing explanation for the availability of the key biomolecules from which all living things are composed—sugars, bases, nucleotides, amino acids, lipids, etc.—can be found, then a major step toward resolving the origin of life problem will have been taken.

The real challenge is to decipher the ahistorical principles behind the emergence of life, i.e., to understand why matter of any kind would tend to complexify in the biological direction.

if and when that ahistorical question is resolved, the problem of how life on earth emerged on the prebiotic earth would take on a totally different aspect. Being a historical question the answer might remain unknown, but the issue would no longer be a mystery in the same way that it is now.

particular event could in principle be highly contingent or effectively deterministic or anywhere in between.

biology is just chemistry, or to be more precise, a sub-branch of chemistry—replicative chemistry.

it seems logical to suggest that if life did start off simple, then life’s fundamental nature would become more understandable by examining earlier, and therefore simpler prototypes.

Over time the initially long chain RNA molecule evolved into shorter RNA chains. Shorter RNA molecules which replicated faster, out-replicated the longer ones, driving those longer ones to extinction. So what is termed natural selection within the biological world is also found to operate in the chemical world. The conclusion is highly significant. The causal sequence: replication—mutation—selection—evolution, normally associated with the biological world, in fact the sine qua non of biology, is also clearly evident at the chemical level.

what one simple replicating entity could only do inefficiently, a more complex one was able to do more efficiently.

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

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.

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.

Bottom line: in order to understand life’s essence one should focus on life’s population aspect, not its individual aspect. Life is an evolutionary phenomenon and evolution does not operate on individuals, only on populations.

Counter-intuitively, the road to a fitter population may actually pass through a ‘less fit’ individual replicator within the existing population. Population heterogeneity opens up more possibilities for evolution to carry out its magic—heterogeneous populations evolve more effectively than homogeneous ones.

The driving force for evolution is not natural selection, as is suggested from time to time. Natural selection is a rudder, not a driving force. Natural selection, as its name states, just selects. Natural selection (or its chemical equivalent, kinetic selection) helps steer the replicating population toward higher DKS by the continual elimination of those entities in the population that contribute to a lowering of its DKS. And that is true along the entire evolutionary road, from the population of simple (but unidentified) replicating entities which heralded life’s tentative beginnings, right through to complex life.

In fact, the moment some non-metabolic (downhill) replicator acquired an energy-gathering capability, could be thought of as the moment that life began.

Biology then is just a particularly complex kind of replicative chemistry and the living state can be thought of as a new state of matter, the replicative state of matter, whose properties derive from the special kind of stability that characterizes replicating entities—DKS. That leads to the following working definition of life: a self-sustaining kinetically stable dynamic reaction network derived from the replication reaction.

Life is just the resultant network of chemical reactions that emerges from the continuing cycle of replication, mutation, complexification, and selection, when it operates on particular chain-like molecules—in the case of life on Earth, the nucleic acids. It is possible that other chemical systems could also exhibit this property, but so far this question has yet to be explored experimentally. Life then is just the chemical consequences that derive from the power of exponential growth operating on certain replicating chemical systems.

DKS depends on the system continually reacting in order to replicate, to make more of itself, and that actually requires the system to be reactive, to be unstable.

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.

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.

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!

life’s morphology appears to be based on what living things require it to be, rather than some directive that comes from its underlying chemistry.

life forms that emerged from some replicating entity that did not belong to the nucleic acid family, but were able to complexify and evolve toward replicating entities of greater DKS, would likely utilize the same universal concepts that nucleic acid-based biochemistry discovered. Depending on the extent to which that other life form had evolved, it would also express network characteristics, and may have discovered the replicative value of a cell structure, in which the cell’s functional parts with its replicative and metabolic capabilities would be incorporated. The theory of life presented here is not one based on material, but one based on process, and therefore the nature of the material would be secondary, possibly even incidental, in governing life’s underlying characteristics.

Living things can consist of these single-cell entities, or they can be multicell organisms composed of blocks of individual cells. But the network perspective on life leads to an interesting and highly pertinent question: Do individual life forms actually exist? Individual living things do seem to exist, in the sense that we are surrounded by what appear to be examples of individual life forms—birds, bees, camel, humans, and, of course, unicell life, primarily bacteria, all seemingly going about their individual business. In practice, however, that individuality is not quite as clear-cut as one might think. What we classify as individual living entities may themselves be thought of as components of a network—the ever-expanding life network.

But that means that individuality is more a life strategy than a life characteristic. So-called individuality is just a technique that evolution has discovered, amongst many others, to enhance replicative ability and robustness.