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

by Addy Pross

This miniature factory takes in raw material, and through the utilization of power from the factory’s power generator, converts those raw materials into the many functional components, which will then be assembled to produce the factory’s output. And what is that output? What does this highly elaborate nano-factory produce? More cells! Every cell is ultimately a highly organized and efficient factory for making more cells! The Nobel biologist Francois Jacob expressed it rather poetically: ‘the dream of every cell, to become two cells’.

It is not just common sense that tells us that highly organized entities don’t just spontaneously come about. Certain basic laws of physics preach the same sermon—systems tend toward chaos and disorder, not toward order and function.

Until the paradox associated with life’s emergence is resolved, we will not understand what life is.

the central biological paradigm, Darwinism, is just the biological manifestation of a broader physicochemical description of natural forces.

the principle of continuity renders it probable that the principle of life will hereafter be shown to be part, or consequence, of some general law

Ultimately, understanding life will require us to understand those special properties, both in themselves and how they came about. Some, as we will see, may be understood in Darwinian terms, though the debate about those explanations continues. Others, however, cannot be understood that way, and their very essence continues to trouble us. They certainly troubled the great physicists of the twentieth century, amongst them Bohr, Schrödinger, and Wigner, since several of life’s characteristics appear to undermine the most basic tenets of modern science.

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

The cell is not just a master chemist, but a master physicist as well. That microscopic entity uses every mechanical trick in the tradesman’s book—pumps, rotors, motors, propellers, even scissors to snip here and there, all at nano-scale, to ensure cellular functions are carried out expeditiously, as required by the cell’s ‘purpose’.

Organized complexity and one of the most fundamental laws of the universe—the Second Law of Thermodynamics—are inherently adversarial.

the highly organized state that is absolutely essential for viable biological function is somehow maintained with remarkable precision. There is even a biological term for the phenomenon whereby that organized state is maintained—homeostasis,

why we have to eat regularly to survive—to furnish the body with the necessary energy to enable the body’s regulatory mechanisms to maintain life’s organized homeostatic state.

Darwinian evolution is able to broadly explain how a simple single-cell living organism—what one might call the microbial Adam—eventually became an elephant, a whale, or a human. But Darwinian theory does not deal with the question how that primordial living thing was able to come into being.

how did a system capable of evolving come about in the first place?

Darwinian theory is a biological theory and therefore deals with biological systems, whereas the origin of lif...

life’s purposeful character. That purposeful character is so well defined and unambiguous that biologists have come up with a special name for it—teleonomy.

all living things behave as if they have an agenda.

In the non-living world, by comparison, understanding and prediction are achieved on the basis of quite different principles. No teleonomy there, just the established laws of physics and chemistry. You throw a ball into the air and you want to know where it will land? The precise landing point is not calculated by considering the ball’s purpose. The ball has no purpose. Only Newton’s laws of motion will provide the answer.

The very existence of teleonomy however, leads us to a strange, even weird, reality: in some fundamental sense we are simultaneously living in two worlds each governed by its own set of rules—the laws of physics and chemistry within the inanimate world and the teleonomic principle that dominates the biological world. Indeed, given the existence of two distinct worlds we find ourselves interacting quite differently with each of those worlds.

All of our interactions with the inanimate world are based on the recognition that there are certain laws of nature, described primarily by the physical sciences,

the essence of technology—creating systems that exploit nature’s laws in a beneficial manner.

We communicate and deal with members of our immediate family, with our work colleagues, with other members of our society in an endless series of interactions—by spoken and written word, more subtly without words, by gestures. Some of these interactions are cooperative in nature, some competitive.

Neither a physicist nor a chemist will be able to offer a useful prediction. If you want to make a prediction about some impending event in the living world, go ask a biologist, psychologist, economist, lawyer, or other teleonomic specialist, depending on the nature of the question.

It is not just multicellular cognitive beings—humans, monkeys, camels, and the like, with a brain and central nervous system that manifest this teleonomic character. That character is also clearly manifest at the level of the single cell! Put a bacterium in a glucose solution in which the glucose concentration is variable and the bacterium ‘swims’ toward the high concentration

teleonomy is as evident at the single-cell level as at the multicell level. The living world screams out teleonomy no matter where you look.

mind. We humans are a restless species, never entirely satisfied. But if we want to get to the very essence of biological purpose, we need to get away from multicellular complex beings and look at the simplest life form, that simple cell, the prokaryotic (without a nucleus) bacterium.

Within the clock the components remain in place and continue to operate until one or other of them wears out and the system ceases to function. But within the living cell the situation is spectacularly different. Whereas a clock is a static system, whose parts are permanent and unchanged, every living system is dynamic. Its parts are continually being turned over. Let me explain.

intracellular protein is continually being turned over—cellular protein is constantly being degraded and resynthesized in a tightly regulated process.

Answering the ‘what is life’ question will have to come up with a good explanation for life’s dynamic and ephemeral nature.

Non-living diversity is arbitrary, while living diversity seems deliberate, coherent.

the macroscopic diversity that we see around us is just the tip of the diversity iceberg. The largely invisible microbial world is where the concept of diversity takes on new meaning.

Darwin proposed a Principle of Divergence, though from that monumental work it is not entirely clear whether the Principle of Divergence derives from his primary principle, the Principle of Natural Selection, or should be considered as an independent principle. Darwin himself seemed ambivalent on this point. The source of the conflict is clear: divergence means that many are derived from few, whereas selection (of any kind, natural or otherwise) means many are reduced to few. The two are inherently contradictory

the source of life’s diversity does begin with reproductive variation,

inherently unstable ion concentration gradients are essential for many physiological functions so a nonuniform ion distribution, termed an ion concentration gradient, exists between the cell’s interior and its exterior, despite the Second Law, and that gradient is maintained over time. How can that be? In order to maintain inherently unstable concentration gradients over time the cell has to operate ion pumps, pumping ions against the gradient—just like the bird flapping its wings to stay aloft. Of course, in order to operate those ion pumps, the cell must utilize energy, and that energy has to be supplied to the cell in some form, as discussed earlier.

how could far-from-equilibrium chemical systems have come about in the first place?

the Second Law states that all systems seek to become more stable, yet in the process of emergence exactly the opposite must have taken place.

the physical and chemical properties of two chiral molecules, D and L, are identical (though there are some exceptions that we need not concern ourselves with here). That also suggests that in an arbitrary environment the two chiral molecules should be present in equal amounts. If, however, for whatever reason we start off with a quantity of some chiral material of a single chirality, say all D, then that same Second Law of Thermodynamics discussed earlier, tells us, that given enough time, that material of single chirality will become racemic, meaning that the material will end up consisting of equal quantities of D and L

within living systems only one chiral form of the two possible chiral forms is present—biological sugars are almost invariably D-sugars, while amino acids are almost invariably L-amino acids. Living systems are universally homochiral (meaning of just one chirality). But this homochirality raises two fundamental questions. First, how did the homochirality of life emerge in the first place?

how did homochirality of living things come about from a world that is intrinsically heterochiral,

how can its maintenance be explained, given that heterochirality (an equal mixture of two chiral forms) is inherently more stable than homochirality?

nature is objective, that there is no underlying purpose to the natural order. The scientific and philosophic implications of that revolution cannot be overstated. Jacques Monod, in fact, considers that idea the single most important idea offered by man over the 150,000–200,000 years that he has inhabited the planet.

Schrödinger found himself following Bohr’s line of reasoning, and concluded, rather enigmatically, that living matter, while not eluding the established laws of physics, was likely to involve ‘other laws of physics’ hitherto unknown.

The very existence of that teleonomic character appeared to violate one of the fundamental principles of modern science—the objectivity of nature.

how could function and purpose have emerged from an objective universe devoid of function and purpose?

there is a universal energy storage facility based on the ATP molecule.

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

Cleland and Chyba claim that what is needed is not a definition of life, but a comprehensive theory of life.

At the very heart of the scientific method is the process of induction,

In fact all cognitive beings, human and non-humans alike, apply the method routinely, whether consciously or subconsciously, in a process that has been deeply engrained in us all by evolution.

Broadly speaking the wider the generalization, i.e., the greater the number of empirical observations that are embraced by the generalization, the greater its predictive power and the more significant the generalization.

Einstein’s special and general theories of relativity do—they extend and generalize the more limited Newtonian pattern.