What is Life?:How chemistry becomes biology (5 page)

What is remarkable, however, is that the underlying basis for life’s diversity continues to trouble biologists, beginning with Charles Darwin and through to the present day. In his
Origin of Species
text, 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 and no amount of verbal gymnastics can get around that. No wonder then that attempts to reconcile the apparently irreconcilable continues to torment modern biologists.
^5
,
6
What is clear is that the source of life’s diversity does begin with reproductive variation, though the detailed manner in which that variation leads to speciation and diversity remains controversial. In
chapter 8
, we will propose a physical approach to the problem of diversity in the living world and the cooperative nature of biological interaction that has accompanied that diversity.

Earlier we discussed how the emergence of life’s organized complexity constitutes a thermodynamic puzzle. But there is another facet of life’s nature that is related to that complexity, which is also troubling with respect to the Second Law of Thermodynamics—its far-from-equilibrium state. Consider a bird that is hovering in space, maintaining an almost stationary position by flapping its wings. Clearly that bird is in an unstable state. If it were to stop flapping its wings, it would drop to the ground. However, that bird is able to maintain its unstable state, suspended in mid-air by the continual expenditure of energy. By constantly flapping its wings the bird is essentially pushing down on the air, and so is able to overcome the earth’s gravitational pull.

The example of the hovering bird and its unstable state might seem to be a transient moment, of no general significance. But from a purely energetic point of view the hovering bird’s unstable state is actually a metaphor for all living things. Consider the energetics of the simplest life form, a bacterial cell. That cell, from a thermodynamic point of view, is also unstable and exists in what is termed a far-from-equilibrium state in that it also must continuously expend energy to maintain that state. There are many aspects to that far-from-equilibrium state but to illustrate the point we will just describe one—the existence and maintenance of ion concentration gradients in living cells. Let us describe what that means. You dissolve some table salt, sodium chloride with the chemical formula NaCl, in water, and what happens is that the crystals of salt break up into their two constituent ions, the sodium ion, Na
⁺
, and
the chloride ion, Cl
^-
. Initially the concentrations of the two ions in solution would not be uniform, but would be higher near the point of dissolution. After some time, however, the ions would, by diffusion, distribute themselves evenly throughout the solution. That is, yet again, an example of the operation of the Second Law. A situation where there is a high concentration in one part of the solution and a low concentration in another part would be unstable compared to a uniform distribution and the Second Law is quick to correct this non-uniform ion distribution.

For living cells, however, 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.

In other words, there is no thermodynamic mystery in the
ability
of cells to maintain that far-from-equilibrium state—they can do so by the continual expenditure of energy that is constantly supplied by the environment. However, there
is
a deep mystery hidden in the scheme we’ve just described, even if thermodynamically speaking the energy book-keeping has been meticulously maintained.
Just how could far-from-equilibrium chemical systems have come about in the first place?
If, as we believe, chemical processes led to the emergence of life on earth, how could chemical processes on the prebiotic earth that would be
driven
toward
their equilibrium state, meaning toward chemical systems of low energy, have led to the emergence of
complex, high-energy, far-from-equilibrium
systems? Recall, 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. In the context of the Second Law the emergence of unstable, far-from-equilibrium systems might be paraphrased:
you can’t get there from here
. But we did! The troubling question is then how did we?

Many of the molecules found in living systems are chiral, meaning that the molecule’s mirror image is not superimposable on the molecule itself. Our two hands reflect that quality—a left hand is the mirror image of a right hand, but the two hands are not superimposable on one another (Fig. 1). The term ‘handedness’ is in fact a commonly used metaphor to express this characteristic of chirality in a molecule, and in order to distinguish between these two chiral forms, different classifications are possible. One of the earlier ones, still prevalent in biology today, is the D, L classification, where one chiral molecule is labelled D (for dextro, or right-handed) and its mirror image, L (for levo, or left-handed), based on its spatial relationship to the organic substance, glyceraldehyde. The point is that 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 forms (due to slow D to L and L to D interconversion). Simply, a racemic mixture is more stable than a single chiral form—it is more disordered, and therefore will tend to be established given enough time.

Fig. 1.
Handedness associated with chiral objects. An object is chiral if its mirror image is not superimposable on itself.

We commenced this topic with the statement that many of the molecules of life are chiral. The amino acid building blocks from which all proteins are constructed, and sugars, from which nucleic acids and carbohydrates are composed, are all chiral. What is important, however, is that 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? Given the chiral nature of many objects in the world, how did homochirality of living things come about from a world that is intrinsically heterochiral, or, put differently, how did a world with its inherent
two-handedness
become
single-handed
within its biological part? And, second, once homochiral systems did emerge by some means, how can its maintenance be explained, given that heterochirality (an equal mixture of two chiral forms) is inherently more stable than homochirality? In that sense the homochiral nature of life represents yet another manifestation of life’s unstable and far-from-equilibrium character described earlier.

* * *

The above detailed description of living states and their unique characteristics should serve as a stark reminder how strikingly different living and non-living systems actually are. Actually that in itself would not be a problem. Within the inanimate world different material forms can also express very different properties. Some are solid, some liquid, some gases, some conduct electricity, some don’t. Some are coloured, some are colourless. But these differences are readily explained by basic chemical theory. Consider, for example, the three traditional states of matter of water—ice, liquid water, steam. The first is a brittle crystalline solid, the second a clear colourless liquid, and the third an invisible gas—you can’t get much more different than that! But despite the dramatically different properties of the three states, we fully ‘understand’ those three states of matter. No mystery, no confusion.

So what is the basis for that understanding? Our understanding is based on our molecular view of matter and the associated kinetic
theory which tell us that the states of matter depend on the magnitude of the forces operating between the individual molecules. The stronger those intermolecular forces, the more likely the substance will be solid. Of course the temperature of the material also has a bearing on the state of matter that is obtained. The higher the temperature, the more likely the material will be gaseous, due to the higher kinetic energy of the individual molecules. Thus the particular properties of ice, water, steam, derive directly from our molecular view of matter; the physical sciences have provided us with a pattern that enables us to convincingly relate the three states of matter to each other. Most significantly, the final and definitive confirmation that we do indeed ‘understand’ the three states of matter comes about through our ability to readily convert one state to another. Indeed, as predicted by what are termed phase diagrams, we can bring about those transformations in different ways. We can convert ice to water by either applying pressure or by heating, and we are able to convert ice to steam without having to pass through the water phase. In summary then, we say we ‘understand’ the three states of matter, solid, liquid, gas, because we can (a) explain the different properties of those different states in fundamental molecular terms, and (b) most importantly, our understanding provides us with control over the system in question—we know different ways of converting one state to another.

With respect to the biological world, however, our current understanding of material systems is unable to address life’s unique characteristics that we’ve discussed in some detail. Simply put, within the material world there exists an entire class of material systems—the biological class—that exhibits a distinct pattern of behaviour that remains unexplained in chemical terms. And,
paradoxically, that lack of understanding accompanies us
despite
the fact that the intricate mechanisms of biological function
are
increasingly understood. Somehow we know more and more of the cell’s mechanisms, yet that molecular knowledge seems to bring us no closer to understanding the essence of biological reality. We see lots and lots of trees, but a view of the forest remains frustratingly obscure. Understanding life will require that we are able to offer unambiguous explanations for life’s unique characteristics. That is one key challenge this book will attempt to address.

In the previous chapter, we highlighted life’s puzzling characteristics and described our inability to explain those characteristics in simple chemical terms. Not surprisingly, given the fundamental nature of the problem, attempts to understand life have weighed upon humankind for several millennia, so let us briefly review the central concepts that have moulded our thinking through the ages. Aristotle’s ideas, going back over 2,000 years, have been particularly influential as they stemmed directly from his extensive studies of living things—Aristotle was a dedicated biologist both in practice and in spirit. That detailed observation of living things was responsible for what might be considered his most important contribution to scientific thought—his
teleological
view of nature, a view of such powerful persuasion that it ended up dominating Western thinking for over two millennia.

Simply put, Aristotle saw in the processes by which life is generated and maintained one that indicates them to be
goal directed.
Every aspect of reproduction and embryonic development, for example,
exemplifies that purposeful and goal-directed character. Given that purpose was so clearly associated with such a wide variety of material forms (though all examples came from the biological world), it only seemed logical to conclude that an underlying purpose was associated with
all
material forms, biological
and
non-biological (Aristotle’s famous Final Cause). Indeed, that is the essence of Aristotle’s teleological view—that there is an underlying purpose to the workings of nature, that purpose governs the cosmos as a whole. Given the bountiful biological evidence for Aristotle’s teleological argument, in retrospect it is quite understandable that teleological thinking held up largely uncontested for over two millennia.