The Equations of Life

by Charles S. Cockell

  We are left with a general picture of what the Pauli exclusion principle does to shape life. There is a core of elements whose electron structures are sufficiently good to create stable bonds, but which can nevertheless be broken with sufficient ease to generate the huge assortment of compounds useful to life. These core elements occupy a little quintet in the periodic table—carbon, nitrogen, oxygen, phosphorus and sulfur, with little hydrogen ubiquitously hanging on whenever there is a spare electron going. These elements have just the right atomic size and the right number of spare electrons to allow for binding to each other and to some other elements to produce a molecular soup sufficient to build a self-replicating system.

  Surrounding the quintet are elements with similar chemical properties, but in which the atomic size and number of electrons make them either a little too unstable or a little too reactive to be good at producing that fine balance between stability and reactivity for making the molecules of life. Although they are not ideal for a wide miscellany of jobs, they find use when their characteristics make their chemistry just right for a particular purpose.

  Scattered through the remainder of the periodic table are the rest of the elements that, to lesser or greater degrees, find application in many places where their electrons can do something useful. Iron takes center stage in the choreography of gathering energy for life as it shifts electrons around, the core process of snatching energy from the environment with which to grow and reproduce. Elements like vanadium and molybdenum, with their dexterous electrons, pop up here and there, such as in cofactors in proteins that help speed up reactions.

  From sodium to zinc, many elements not among CHNOPS, particularly the metals, are much better at forming salts, such as common salt, sodium chloride. Although these atoms can form large macroscopic structures, as a large lump of table salt will testify, they are hugely regular and highly monotonous repeating units of atoms that seem poorly suited for producing living things. These salt-making habits explain why tin and lead Horta seem unlikely. The imaginative may well raise their hands in disdain and point out that if we add defects and faults into salt crystals, with some other elements thrown in for good measure, could we not get complexity suitable for life—self-replicating, evolving crystals?

  The conditions on Earth are just right for a vast collection of crystals and salts. Yet despite 4.5 billion years of chemical experimentation, the self-replicating, evolving crystal has yet to be reported. No good scientist would use this evidence to conclude that the phenomenon was impossible. Mineral surfaces as places for the assembly of early life have played an important part in ideas about the construction of the first self-replicating organic compounds, but many elements in the periodic table appear better suited for forming rather mundane salts in the natural environment. Life evolves to use these elements, for carrying out tasks in electron shuffling and transport, but in themselves, these elements do not seem sufficiently flexible in their bonding patterns to produce an abundance of complex molecules from which we can build a living system.

  The process of evolution rummages through the periodic table, testing elements and selecting those whose electron arrangements facilitate chemical reactions that make an organism better able to survive and reproduce.

  However, an enduring question remains: could life be something other than carbon based? Is the chemical structure of life universal? I think this question is loaded. We can say that life on Earth is carbon based if we want to categorize life according to the quality that carbon is a dominant element in the assembly of its molecules. However, life is obviously periodic table based. In some environments, organisms make use of selenium more than others do; in other circumstances, even fluorine is found in life, though this element makes no appearance elsewhere. Life is not somehow transfixed by carbon—living cells use what they can. The only principle at play here is that the elements used to construct a replicating, evolving system must have arrangements of electrons capable of yielding the chemical reactions and bonds that allow for the integrity of the living system and its continuity. In the conditions found on Earth and in many other environments in the known universe, carbon, with its binding properties to hydrogen, nitrogen, oxygen, phosphorus, and sulfur, can assemble the basic chassis of a replicating, evolving system. Other elements provide the fine-tuning to make that system work better than it might otherwise, to produce a full panoply of diverse molecules. A bountiful potpourri of elements has been (and is being) tested continuously by the process of natural selection for its uses, but no known cell has yet shown a strong selective bias to replace most of its carbon molecules with something else.

  Given what we know about the behavior of many elements at low and high temperatures, at different acidities and pressures, and at other extremes, it seems doubtful that under other physical conditions, other elements will step into the shoes of carbon and replace it with the combination of chemistry useful for a living entity.

  Ultimately, no physical conditions, at least conditions under which the atoms of the periodic table are stable, will alter the basic electron configurations of the atoms. The rate at which they undergo reactions and how they interact with other atoms will be modified by their environment. However, their core characteristics, set by the Pauli exclusion principle and its implications for electron stacking, are invariant. I would expect that on any planet in the universe, given the limited range of elements available in the periodic table, life would forage through this table in the blind process of evolution, just as it is doing on Earth, and arrive at the same set of elements. Yes indeed, the use of the elements, their applications, and their abundances in living systems will show great variance, just as they do on our planet, but the fundamental role of the major elemental players in life is likely to be the same in every galaxy in the universe.

  The idea that physical principles explain why carbon is the central atom in life’s construction and water the milieu in which life operates brings me to one final and essential point. There are two possible directions for our conviction that carbon- and water-based life is universal, that physical principles narrow the possible chemical architecture of life. The first I will call the soft view. In this view, alien biochemistries, be they silicon-based life forms in liquid nitrogen or acid-resistant life in sulfuric acid clouds, are possible but rare. The unusual conditions required for these alien life forms and the relative cosmic abundance of carbon chemistry and water make them unlikely types of life. We might also call this the abundance-based view of carbon-water bias.

  The second view is the hard view, what we might call the chemistry-based view of carbon-water bias. According to this view, no other forms of life are possible and the chemical properties of other elements such as silicon or alternative solvents such as ammonia are inadequate in their diversity to drive the formation of life, regardless of their cosmic abundance.

  My view on life is minimally the soft view and leaning strongly on the hard view. The abundance of carbon compounds and water makes it likely that life elsewhere, if it comes into existence, is carbon and water based. As we have seen, the sheer universal distribution of carbon chemistry and water and the propensity of these two substances to collect on planetary bodies of all kinds suggests that they provide the most likely ingredients for life.

  However, why do I only “lean strongly” on the hard view, the view that carbon- and water-based life is the only possibility? Simply because it would be poor science to be dogmatic.

  Can we rule out that in some planetary system somewhere, there is a body on which ammonia oceans have formed because of an unusually high abundance of this liquid in that area of space, where the geochemical conditions have allowed for self-replicating simple organisms to emerge? Can we rule out that in some planetary crust somewhere, a low abundance of oxygen or the right physical and chemical conditions have frustrated the formation of silicates and in some little pocket, a self-replicating set of silicon compounds has come into existence?

  In the absence of mu
ch greater knowledge of the chemistry of the elements, it would be foolish to dismiss these possibilities, even though a dogmatic support for hard carbon-water bias is rhetorically appealing. Our still-incomplete understanding of both chemistry and the full diversity of conditions under which planetary systems form requires that we keep an open mind. Nevertheless, even soft carbon-water bias leaves us with a view of something universal about life on Earth, the simple physical principles that nudge and narrow the atomic structure of living things.

  CHAPTER 11

  UNIVERSAL BIOLOGY?

  WHATEVER OBSERVATIONS ABOUT THE preponderance of carbon-based chemistry and water in the universe might entice us into drawing strong conclusions about the structure of life and its potential atomic similarity elsewhere, there remains an inescapable fact, an ineluctable limit to our current knowledge—we have only one planet from which to draw our conclusions. Using terrestrial life to draw inferences about whether universal physical principles operating on life would result in similar or identical outcomes, if indeed life has occurred elsewhere, necessarily pens us in. Sometimes this is referred to as the N = 1 problem. Any scientist with even the most meager self-respect feels uncomfortable drawing conclusions from a sample size of one. For this reason, many people feel that a discussion about the extent to which the characteristics of life are universal or inevitable is a flawed enterprise.

  The effort to find what is common in all life on Earth and, hypothetically, elsewhere is sometimes referred to as an attempt to discover if there is a universal biology. It is easy to get trapped into an argument about whether biology is autonomous and has laws distinctive to physics, but naming conventions are uninteresting. The term universal biology is simply shorthand for asking “What aspects of a self-replicating lump of matter that evolves in response to its environment are common to all examples of such material?” I have assumed that self-replicating matter that evolves is my general working definition of life.

  We create a problem for ourselves when we sharply define biology and physics as two separate areas of science since we are led, by our own mental slavery to human language, to start asking meaningless questions about whether some “laws of biology” are universal. In truth, there are no laws of biology or even physics; there are only laws that determine how the universe works. Those laws are inseparably operational on all forms of matter. Calling ourselves physicists or biologists is an unfortunate tribalism. Biologists just happen to focus their efforts on particular lumps of matter that do some interesting things, and we often call those things “life,” but biologists and physicists share a common interest in matter in the same universe and in the potentially universal principles they can draw about the ordering of this universe.

  Although many people think that the N = 1 problem makes the question of what characteristics of biology might be universal impossible to answer, we are probably on less shaky ground than we might assume. Many of the characteristics of life that we have explored in this book seem aligned to physical rules that we infer would work on any life anywhere.

  We have seen the reasons for carbon as a major element of life and the preponderance of complex carbon chemistry through the universe over other elements. Water seems like a very good candidate for a universal biological solvent, in light of its physical properties and its abundance across the cosmos. But we have seen other contenders for universal features of life. The tendency of protein chains to fold together toward their lowest energy state results in a few predictable folding types. We might predict, from these observations, that any chain of compounds that makes up a life form would fold together in a limited number of ways in which universal thermodynamic considerations at least play some part. Cellularity, the physical process of concentrating molecules against environments that naturally tend to disperse and diffuse, is a good contender for a universal characteristic of self-replicating systems of matter.

  At the scale of whole organisms, evolution has explored many millions of experiments in form, not merely one. Convergent evolution offers us a vast menagerie of animals whose shapes and structures have been molded independently into similar forms by physical principles, such as our friends the moles. The scaling laws that define the interrelationship between animal size and properties as diverse as metabolic rate and life span across a vast range of creatures, from cats to whales, suggest principles applicable to any type of life. These observations show us that within our one biosphere, we have a collection of experiments from which to examine how physical principles drive common forms of life at its different scales. A single biosphere does not mean we cannot fathom general principles on how evolutionary products are fashioned by physical laws, with the implication that we might use these principles to predict the nature of life elsewhere. The argument that because all life on Earth shares, as a common heritage, a so-called last universal common ancestor, any discussion about universal biology is flawed certainly does caution us to be careful about similarities caused by common biochemical and developmental heritage. But even with this caveat, we can still discern why the successful origin of life that led to our particular evolutionary experiment has the atomic characteristics it has. We can still observe organisms converging into forms that reflect physical principles, even given certain ancestral similarities and channels of developmental biology.

  However, we often find it less easy to discover where contingency might have a powerful role to play. We might wonder about the genetic code. That the code employs particular bases and is optimal with four may well be a predictable outcome of using the class of molecules with which we are familiar. Although our genetic code looks much less of a freak accident than we once thought, we are still left with the question of how many radically alternative chemical systems of hereditary information could exist in living things. Is it zero, ten, a hundred, or some other number? Other questions about our genetic code abound. Do we need an intermediary, a messenger such as RNA, between the code and functional molecules?

  Even if we cannot define exact molecular combinations that are universal, we might be able to say something about the expected universal features of their general chemistry. Perhaps, like DNA with its negatively charged phosphate backbone, we can at least predict that the molecular stuff of other life would be made of long chains with repeated negative or positive charges along its length. Synthetic biology and our continued adventures in chemistry may well allow us to answer these questions, eventually enabling us to further describe the characteristics universal to life.

  Perhaps it is a mistake to focus on particular structures of life, but instead we should direct our attention to life processes or products that we can show are inextricably linked to inescapable physical principles. These processes and products may be a more likely path to discover what is universal about life.

  For living things to reproduce and evolve, generating the panoply of creatures we observe on the planet, they must contain a code that passes from one generation to the next and contains within it the information needed to produce new living things. That code must not be perfectly reproduced, or there will be no variation on which the environment can act to generate new forms. However, the reproduction of the code must not be so imperfect that each generation contains many errors, causing life to degenerate into an amorphous organic mess caused by an “error catastrophe.” Perhaps this feature of life, which inextricably links it to the evolutionary process, is universal. That life is a “system of reproducing matter containing a code whose reproduction lies between perfection and error catastrophe” might be a contender for a universal physical characteristic of matter that makes life. Here, then, we might seek universality in life by identifying those characteristics required for matter to undergo evolution, one of features we have decided circumscribes the matter we call life.

  That life is a system of matter that dissipates energy and uses energy to reproduce and evolve leads us to look toward its energetics and thermodynamics as a potential source of defining universal characteri
stics. For example, if we think that electron transfer might be a universal way to gather energy, then we might single out a few elements or molecules that any living thing can use to gather energy. We know that life could use hydrogen and carbon dioxide as a source of energy (and make methane in the process) anywhere in the universe with a suitable biochemical machinery because these two compounds produce a thermodynamically favorable, energy-yielding reaction in many environments. This is a fact set by physical laws, not by contingent evolution. Thus, tabulating the universal electron donors and acceptors that life can use to gather free energy from the environment is a rather trivial matter, and this exercise allows for universal observations about the energetic potentialities of life.

  Energetic considerations might yield other predictions. If alien life forms eat each other, we could also predict food chains with fewer larger predators at the top of these links, where energy is limited, and a larger number of small creatures in the lower levels of the food chain, as we see in life on Earth. From the electron transfer chains at the subatomic scale to food webs at the population scale, these facets of life are driven by thermodynamics. Moreover, an exploration of the biological consequences of laws that instantiate the movement of energy, such as the basic laws of thermodynamics, might well allow us to define the universal forms of life.

  When it comes to predicting the forms of living things, we might look at inviolable equations such as P = F/A and explore likely universal outcomes of the imposition of this equation on organic forms—moles and wormlike entities at the scale of whole organisms. Many of the equations we have explored in this book, unexceptional and universal in their applicability, provide a framework for predicting the assembly and general convergence in the architecture of living things.