An organic chemist looks at evolution
| I wrote this essay a few years ago but did not publish it. I don’t remember why. This is not written for evolutionary biologists. It is written for folks who may struggle with conversations with creationists and the like. For better or worse, here it is. On weekends I check in on C-SPAN 1 and 2 to see what folks are talking about. A couple of weekends ago on Earth Day there was a C-SPAN 1 broadcast of an April 19th, 2017, panel discussion on the ” March for Science and Threats to Science.” The segment was hosted by The Heritage Foundation and featured a number of well dressed folks who were quite authoritative and highly skilled in the rhetorical arts. Curious thing that the Heritage Foundation chose this topic to weigh in on. The discussion followed various lines of conservative analysis of the 4/22/17 March for Science and touched on the New Atheism, Neo-Darwinism, with allusions to a supposed endemic misanthropy of some March for Science participants. One of the panelists was a fellow named Stephen C. Meyer who is a senior Fellow and founder of the Discovery Institute. Meyer is a very articulate and persuasive proponent of creationism. His contribution to the discussion was a recitation of the pro-creationist argument on the weakness’s of Neo-Darwinism. The thrust of his argument centered on the alleged disagreement among scientists in the field of biological evolution and how this delegitimizes the whole concept. This line of argument is a common (dare I say standard?) rhetorical stunt used by creationists to cast doubt on the science of evolution. Creationism adherents have learned that they do not have to prove evolution is incorrect. They need only make a case for disagreement in the scientific community of its veracity or infer scientific misconduct. As a friend once quipped, they stir up a dust cloud and then complain because they can’t see anything. Darwin and the story of the expedition of the HMS Beagle is a tale of 19th century discovery that is inspirational and iconic. Too often, however, Darwin’s writings on natural selection is not portrayed in the historical context relative to modern molecular biology. When I hear creationists discuss evolution, the discussion seems to remain with the work of Darwin. I would maintain that if Darwin and Lamarck had not developed their work on natural selection, modern molecular biologists would have had to postulate evolution themselves. Public discussion of evolution in the limited context of Darwin is frequently burdened with misinterpretations and half-truths by adherents and deniers alike. It is not unusual for people to become confused by the use of imprecise language when discussing evolution-as-Darwinism. For instance, I’ve heard knowledgeable people assert “… the species evolved (such and so) in order to adapt …”. Well, yes and no. The species may well have over time evolved some adaptation. However, the words “… the species evolved …” may be misinterpreted by some as meaning that a species, when presented with some survival challenge, may have taken the chance to unsheath some mechanism to respond by rejiggering its genetics in a way that would lead to survival of subsequent generations. A more accurate description might be that fortuitous genetic mutations in the past have allowed the organism to survive challenges presented by a changing environment. There is a critical qualifier, however. A given mutation must be survivable and facilitate the continued reproduction of the critical trait to subsequent generations. Mutations occurring after the possibility of reproduction lead only to an evolutionary dead end. Evolution is blind going forward. Descriptive language must be built around that concept. Rather than consuming time and bandwidth reciting the history and elements of Darwinism, the reader is invited to pick this up elsewhere. Instead, I would like to throw an idea on the table. Perhaps writers and public figures should deemphasize Darwin’s work and emphasize the mutability of the genome. If we consider that the large scale structural morphologies of organisms are an emergent phenomenon and arise as a result of molecular and cellular scale structures, then we can begin to see evolution much like a performing symphony orchestra is comprised of many instruments, each with characteristic effects. The overall effect is the sum total of all the contributing instruments. Evolution then becomes a matter of changing the score a bit here and there to produce variants. The notion of life as an emergent phenomenon is itself evolving to a high level of theory. See: Pier Luigi Luisi, The Emergence of Life: From Chemical Origins to Synthetic Biology 2nd Edition, 2016, Cambridge University Press. With 19th century Darwinian theory, we are limited to observing evidence of change at the macroscopic level but with no credible mechanism for the manner of change or a cause for initiating a change. Without a mechanism, plausibility is a tough sell to students, teachers, and the rest of the lay public. Darwinism is a tidy package with an appealing story. However, without mention of its mechanism it resembles magic. Evolution at the molecular scale can offer mechanisms and measurements. I would offer that Darwinism could be treated in a historical context, but a transition to the level of molecules appropriate to the intended audience should happen. Evolution rests on the mutability of genes. Another troublesome aspect of explaining evolution is the plausibility of random change leading to organisms of greater complexity. The notion that the human eye or hand is the result of random change is simply too incredible for non-sciency people to accept. For them, it is an intellectual cul-de-sac that, in parallel with their religion, only validates “creation implies creator”. To folks firmly affixed in concrete reasoning, the notion of non-living, disorganized matter somehow spontaneously organizing to form elaborate life forms is beyond comprehension. This argument is often brought up as a coup de grace against evolution. Randomness as a successful driver seems so implausible. Perhaps Darwinism is better expressed as only an introduction to the story of molecular evolution. Standing in the way of a mature understanding of evolution is the plausibility of random change giving way to greater complexity. What exactly do we mean by random? Does random change imply an infinite range of categories of influence and outcome? What exactly is it that is random? This is difficult even for scientists, let alone the lay public. Let’s consider some relevant aspects of the world of the molecule. Axiom 1: The initiation of life may be a quite different chemical mechanism from the reproduction of life. The origin of life and the evolution of life are different processes. The physical conditions and available substances amenable to evolution likely diverge from those present when and where life arose. Origins and subsequent evolution must be pulled apart into separate arguments for the sake of clarity. Axiom 2: Evolution is a molecular phenomenon. In order to have macroscopic change there must be microscopic change. The DNA molecule is well established as the repository of stable organizational information necessary for the construction and operation of living things. If change characteristics are to be passed along through successive generations, then DNA has to change accordingly. DNA is ordinary matter and subject to the constraints of chemistry and physics. A part of being subject to chemical change is the effect of adverse conditions to contend with in general (bio)chemical synthesis. Biochemistry is largely aqueous chemistry with all of the constraints and degrees of freedom that follow: Solubility, Gibbs free energy, transition states, polarity, acidity, concentration, catalysis, stability in an aqueous environment, reaction rates, stoichiometry, time, temperature, and reduction/oxidation potential. All of the parameters listed above represent variables with their own range of values that must be in alignment in order for life to happen. Rather than be overwhelmed by them, they could be considered as a finite number of channels in which a limited range of inputs give rise to a limited range of outputs. Axiom 3: Atoms and molecules must collide in order to react. A generalization in chemistry is that atomic and molecular interactions require the components to collide at some range of favorable trajectories. The mobility necessary for atomic and molecular interactions to occur is available in fluids but not solids. If molecules are held in place in a bulk solid phase, then they don’t have the opportunity to bump into one another just right and interact. The most abundant element in the universe is hydrogen. Water, H2O, is comprised of the most cosmically abundant element bonded to oxygen, the most abundant terrestrial heavy element. A planet that has water with a climate and pressure amenable to the liquid phase is a planet that has a start on supporting life. Life is substantially a solution phase phenomenon. Axiom 4: There is a menu of limitations in the behavior of molecules. 1. The set of atoms necessary for constructing life on earth is of limited number and variety. 2. The behavior and properties of a given atom is based on the physics of electric charges and the best description of how and where electrons spend their time. This is successfully described by quantum mechanics. 3. Because of physics and more to the point, quantum mechanics, the electrons which do the chemistry are capable of a finite variety of allowed states according to selection rules. 4. There is a limited set of ways that a given atom can attach to other atoms to make chemical bonds under ordinary terrestrial conditions. 5. Molecules are made of atoms. These atoms naturally form a set of characteristic groupings within a molecule that are energetically preferred and thus common. The groupings are called moieties or functional groups. Examples are stable 5 and 6 member rings of atoms (pentagons and hexagons), carbon chains long and short, single, double, and triple chemical bonds. The variety of connected atoms in living systems include carbon-oxygen, carbon-carbon, carbon-nitrogen, carbon-sulfur, carbon-phosphorus, oxygen-phosphorus, oxygen-hydrogen, carbon-hydrogen, nitrogen-hydrogen, sulfur-hydrogen, and maybe a few more. Atoms can connect or disconnect, but in a finite number of ways. The atoms that make up “biomolecules” have certain features that make them amenable to dissolution in water. In particular nitrogen and oxygen have non-bonding electron pairs that attract certain hydrogen groups to make something called a hydrogen bond. This behavior lends water solubility to biomolecules. 6. Certain groupings of molecules can intimately comingle indefinitely in the liquid state, but other groupings spontaneously separate into separate “phases” or layers to minimize contact. Consider oil and vinegar and how they spontaneously separate for minimum contact in salad dressing. Molecules that have a charged end and a long water insoluble end may form organized structures called micelles in water. It bears a resemblance to the cell wall. It is an example of spontaneous organization because it is energetically favorable. 7. The assembly, behavior, and disassembly of biomolecules follows finite, definable chemical interactions. Synthetic biomolecules are indistinguishable from the biological version. 8. A limited number of liquids are compatible with living systems. Life as we know it requires that molecules are mobile during certain periods. Living things reproduce and grow. This requires changes that are only possible if molecules can move within the system. Movement happens within a fluid system. The list above sketches out some limitations that atoms and molecules are subject to. It is useful to note that the atoms and molecules of life are subject to constraints that prevent them from behaving in a completely random fashion. Molecules in general will not form in every conceivable connective permutation under terrestrial conditions. Particular routes and end-states are energetically preferred. Things that have only specific behaviors are things that will always behave or react in a particular set of ways to give a limited range of products. Products from molecules that react along alternative pathways will favor the end-state of the fastest pathway. That means that there is exclusion of some molecular products. This is another loss of randomness overall. Contrary to your camp counselor’s advice, not just anything is possible. What makes the universe sensible and relatively stable is the fact that objects and events interact or unfold in ways characteristic to their building blocks. What follows from the limitations of objects and events is that many forms of behavior or channels of interaction are therefore excluded. That is, there are not an infinite number of ways that a biomolecule can behave. The interactions in which a biomolecule can behave is channeled through a limited number of pathways due to the nature of the chemical pathways that are energetically favorable. The universe is surely chaotic, but not entirely so. Organization in biomolecules, or should we say a finite number of energetically favored structures, are the result of the limited number of ways that molecules can interact under terrestrial conditions. Is is a common assertion by creationists that the odds of a hand or eyeball spontaneously forming could result from random interactions is 1 in some extremely large number. To the contrary, there is a case to be made that the hand or eyeball is the result of a series of natural molecular collisions, each constrained to a limited range of reaction possibilities over a very, very long period of time. What’s more, a small molecule at room temperature is colliding with another molecule at maybe a frequency of 10^12 or 10^14 per second*. Scale that up to 1 million years and you have a tremendous number of opportunities to produce survivable change.* These frequencies may be off a bit, but it is what I seem to remember. Genetic mutation is observable and measurable with widely available technology. The favorable mutation of the COVID virus is a recent example. This is the scale at which the gears of evolution grind forward. For macroscopic change to appear, you just wait a little longer. |