Darwinists Try to Overcome Just-So Story Reputation
Try as they might, theorists cannot turn
Darwinism into a mechanistic law of science
It’s listed under “Biophysics and Computational Biology.” Both those categories appear scientifically solid, rational, and descriptive of studies involving phenomena that can be understood by laws of nature. Since the scientific revolution, much of the natural world has yielded to explanation by laws, whether they be tornadoes, volcanoes, planetary motions, auroras, lightning, and a thousand other events that arouse wonder. With natural laws incorporated into principles and equations by great scientists, we can explain and predict numerous things that older generations ascribed to mystery.
Darwinians envy the prestige of the hard sciences. Grasping “Biophysics and Computational Biology,” two of them hope to elevate the status of evolutionary theory from narrative to hard science. Ladies and gentlemen, we present (drum roll, please), a new attempt to exalt Darwinism as hard science!
Research Article: Darwinian evolution as a dynamical principle, by Charles D. Kocher and Ken A. Dill, PNAS, 7 March 2023.
Convinced of the truth of Darwinism, Kocher and Dill seem a little sheepish about its bad reputation. After the drum roll and cymbal crash, they announce to the eager crowds that they can clothe Emperor Charley with physics robes. The Abstract says,
Darwinian evolution (DE)—biology’s powerful process of adaptation—is remarkably different from other known dynamical processes. It is antithermodynamic, driving away from equilibrium; it has persisted for 3.5 billion years; and its target, fitness, can seem like “Just So” stories. For insights, we make a computational model. In the Darwinian Evolution Machine (DEM) model, resource-driven duplication and competition operate inside a cycle of search/compete/choose. We find the following: 1) DE requires multiorganism coexistence for its long-term persistence and ability to cross fitness valleys. 2) DE is driven by resource dynamics, like booms and busts, not just by mutational change. And, 3) fitness ratcheting requires a mechanistic separation between variation and selection steps, perhaps explaining biology’s use of separate polymers, DNA and proteins.
This should be rich. Darwinism like physics? Right off the bat, they use science-like acronyms to look dignified. Perhaps they can use “DE” and “SOF” in equations. Their love for DE knows no bounds, as seen in their adjectives.
Darwinian Evolution (DE) is the unrelenting drive for biological adaptation on earth. Also referred to here as Survival of the Fittest (SOF), DE is among the most resourceful, innovative, and powerful drivers in the earth’s balances of energy, matter, water, and food. Ever since the work of Charles Darwin and Herbert Spencer in the 1860’s, SOF has been invoked in narratives about biological adaptations, such as the shapes of the beaks of Darwin’s finches, the color patterning on the wings of England’s peppered moths, and many others. Its operational basics are well known: Genes encode proteins encode traits; variations are explored by mutational change; organisms compete for finite resources; and natural selection retains those genes/proteins that give the species greater fitness for its environment.
Their challenge is to turn the Stuff Happens Law into an explanatorily-rich law of science, where causation is law-like and predictable, a force driving life upward to greater heights of fitness. There’s one big problem. DE is contrary to one of the best-known laws of physics: the Second Law of Thermodynamics – and they know it.
But as a matter of basic principle, DE is not fully understood. What is the force? Why is there any force at all? What has sustained its extraordinary persistence since life began 3.5 billion years ago? SOF [survival of the fittest] resembles variational principles in physics, wherein a system explores its degrees of freedom and tends toward those states that are maxima or minima of some mathematical function, but it has its differences. Variational principles are central to physics: balls roll downhill toward states of minimum gravitational potential energy; gas molecules diffuse, tending toward states of maximum entropy. Living systems do not drive toward equilibrium. Rather, they tend toward adaptation, selfishness, and intricacy, powered by persistent inflows, in a process that has not died for billions of years. The driver of evolution is not the Second Law of Thermodynamics and is not a tendency toward equilibrium. Fitnesses in biology are unlike energies in physics. While material equilibria are tendencies toward endstates, fitnesses are tendencies across uncountably many different molecules, mechanisms of action, and degrees of freedom, toward opportunistic advantages across uncountably many environmental situations.
Kocher and Dill come up with a scheme called DEM (Darwinian Evolution Machine) to make evolution work like a physical mechanism. The model’s Malthusian roots are seen in their statement, “The heart of the DEM is ‘moms making more moms’ in competition for resources.” They treat the environment as a driver of evolution, which commits the personification fallacy that organisms are duty-bound to hop in the environmental vehicle and go where it takes them. No; they can always roll over and die.
Personification is also seen in their treatment of mutations as a search for function:
Mutational search. Column (b) indicates a search over a space that we call a momsemble of all possible mutations in sequence-function polymers (proteins, DNA and RNA, and their corresponding phenotypes). Unlike equilibrium statmech, these are searches over molecular structures and functions, not over coordinates, velocities, and conformations. The mutant sequence encodes a mutant function, but at the stage of column (b), these are hypothetical, not yet realized by growth into a corresponding population.
Are they unaware of the well-known fact that functional sequences represent a minuscule fraction of sequence space? Good luck searching, mindless and aimless momsemble!
From there, Kocher and Dill do some bluffing with differential equations. But if the terms are circular, and presuppose evolutionary progress through personified searchers and debunked Malthus assumptions, then the equations are meaningless. They assume Darwinian evolution is capable of crossing fitness landscapes to fitness peaks, then show that the hypothetical entities do make it up the peaks! Well I’ll be, Goofy says. Is this even science in any sense of the word?
Their model is all fruits and nuts being consumed by mythical entities under the spell of the Stuff Happens Law.
Environments can be unruly, unstable, and undependable, even rapidly and sharply so, such as in resource booms and busts. The DEM has some memory of its history of food availability through its relative mom populations. Fig. 2 shows how an environment switching from “blue food” to “purple food” drives a transition from a coexistence of mostly green moms, with some red and orange ones, to mostly orange moms, where red has gone extinct. This environmental transition from blue to purple food drives a rebalancing of populations toward moms that can best utilize the new food and away from moms that cannot. It’s just a simple computational example of how the DEM description captures the essential feature of Darwinian adaptation to environments.
Here’s a groaner: “In short, “orange eats green’s lunch.” Why are we even giving these guys the time of day? Get real!
How to Dismiss Irreducible Complexity
The authors realize that many complex adaptations exist, and that this is often argued against Darwinian evolution by critics. Here the debate ratchets up to the breaking point. We’ll see how they handle the objection. First, they merely assume that it does (see first sentence below).
A key concept of Darwinian evolution is that biology achieves adaptations, even complex ones, through incremental random changes and opportunistic selection among those variations. Many adaptations seem clever and intricate, with many components working together with precision, like a watch. Examples are eyes, lightweight wings on birds, molecular motors, blood clotting systems, chemotaxis, and glycolysis and photosynthesis systems. Counterarguments to incremental opportunism are that complexity seems so unlikely in the absence of purposeful design, that blind watchmakers cannot make watches, and that reaching such high fitness peaks would require crossing fitness valleys. An example is the eye: To evolve an eye, opponents say, would require first creating half an eye, which is costly and would have no value. An organism that is in a local minimum of fitness would be less fit—and therefore less stable—than the wild-type organism that is already the dominant population.
Kocher and Dill refuse to cite any leading ID (intelligent design) sources for these statements. They also repeat the wrong definition for ID instead of the one from the ID leaders: complex systems, they say, “seem so unlikely” without purposeful design. The true definition is that irreducibly complex systems are best explained by intelligence instead of unguided processes like natural selection. This misrepresentation of the opposing view disqualifies Kocher and Dill from speaking for having employed the Straw Man fallacy. Debaters are required to agree on the resolution before they can participate.
In their mythical land of DE, innovations occur via Dawkins’ method of Climbing Mount Improbable, which assumes the incremental changes are additive. This commits another personification fallacy: assuming that a blind, aimless and mindless process is capable of visualizing a distant target and storing up “good” random changes to get there. Dawkins did this with his analogy of evolving Hamlet‘s phrase ‘Methinks it is like a weasel’ with random letters, assuming that the correct letters could be stored. The DEM has no way of storing correct responses. That would require foresight, and nobody is there to foresee or guide anything in the unguided world of evolution. For more on the fallacies in Dawkins’ vision of innovation by small random changes, read this.
The rest of the paper plays with imaginary “green moms” and “blue moms” in the authors’ mental fantasyland, empowered by the Driver (the Environment) to climb fitness peaks. By now, none of this matters since the referee should have sent them packing for attacking a straw man and employing multiple logical fallacies like circular reasoning and personification. It’s also sexist. They discriminate against the green dads and blue dads, who are ignored. They do, however, use the Biblical figure of Davids and Goliaths to argue that weaker players can sometimes win against stronger players: “after all, biology’s principle is survival of the fittest, not survival of the most numerous—and thus applies to populations that start out small, at the level of a single cell.”
More analogies are presented using personification and physics metaphors:
The type of signal amplification that happens in the DEM is very different from simple amplification. An amplifier makes a whole signal louder, both the quiet and the loud parts. In the DEM, only the “best” signal is amplified (i.e., “most fit”), even if that signal is very weak. To use a metaphor, the DEM takes in all the noise in a crowded room and picks out only the conversation most important to you.
But who does the picking? Who is the most fit? Time to review “Fitness for Dummies” to see what a vacuous, circular term is this word ‘fitness.’ Try out this analogy they use:
We use the metaphor of golfers on a mountainside to express how fitness valleys are crossed. Because evolution entails a driven nonequilibrium system with persistent resource availability, it is much like aimless golfers located broadly across the landscape driving golf balls uphill and downhill. The ratcheting upward on a fitness landscape happens only because those points are selected for after the fact, not targeted a priori. Since the DEM is not winner-takes-all, there are many such golfers sampling the space simultaneously. There’s power in numbers.
What’s wrong with this picture? Remember the personification fallacy. The golfers in this analogy are not like human beings trying to win a game; they can’t see where they are going, and they don’t care to win. They’re like scarecrows with golf clubs sewed onto their shaking arms in the wind. This picture would require billions of golf balls flying through the air, some of them landing on “fitness peaks” that are somehow thought to represent that nebulous term “fitness” after the fact. But nobody cares! What’s more, the mountains don’t stay put. The whole “fitness landscape” undulates randomly, because the Environment doesn’t care either. “Extinction can be avoided by innovations that arise in coexisting variants,” they say, but what’s wrong with that sentence? It assumes the DEM as evidence for DEM, and dodges the real argument for irreducible complexity. Innovations “arise” somehow? How? By evolution. How do you know evolution did it? Because they arose. Circularity again.
Watch them turn Evolution into a god or goddess selecting things, accepting things, driving organisms to higher levels of fitness nirvana.
In all fitness ratchets, such as computational Monte Carlo, the propose step is distinct from the accept step. The propose step must be as unbiased as possible and sample the space of options as uniformly and completely as possible, without prejudgment about where successes will be found. The bias and judgment are localized in the acceptance step, which selects for improved fitness. Without this separation, fitness ratchets cannot tell uphill from downhill. Without the separation of the propose step from the accept step, a machine could not discriminate a good status quo with a poor mutation from a poor status quo with a good mutation. Evolution would have no sense of fitness direction without a way to distinguish the status quo from a proposed future.
The ability to distinguish good from bad is a property of intelligent minds, not blind physical objects. Material objects don’t care. Someone might retort, ‘The way they show they care is by surviving.’ Look at the tautology in that line of thinking. How do the fittest show they are fit? By surviving. What can you tell about the survivors who survived? They must be the fittest. Sing together,
O, the fit will be survivors and survivors will be fit,
And survivors will survive to prove the fitness of the fit;
O, this natural selection, it’s so simple, isn’t it?
‘Tis ruthless marching on.
Nothing New Here
Finally, they personify all of biology. Remember that in Darwin’s mindless, material world, nobody cares. “Biology separates unbiased search and proposal from biased function and acceptance by these different physical properties of biomolecules.” Biology separates. Biology discriminates. Biology accepts. Biology rewards. Biology is like God.
We have sought insights into dynamical features of Darwinian evolution. Here are three. First, we find the importance of coexistence, rather than winner-takes-all, for evolution’s power of innovation, ability to cross fitness valleys, and resilience against extinction to the vagaries of the environment. Second, we find that environment histories are as important as fitness landscapes of mutations for understanding biological adaptations. Third, a dynamic mechanism that climbs fitness landscapes must have a division of labor, like propose and accept in Monte Carlo computer algorithms: unbiased search coupled with biased functional evaluation. Biology has performed this separation by using different polymer types—DNA for information and proteins for function.
When you extricate all the instances of rampant personification and question-begging, all their analogies and models reduce to the Stuff Happens law. The SHL is the antithesis of scientific explanation.
If any reader thinks that Kocher and Dill just whupped intelligent design, we offer you a free timeshare at the Isle of Debris, where you can evolve or perish in comfort as blind watchmakers and momsembles serve your every function, bringing you purple fruit or orange fruit that may or may not be healthy because they don’t care.
Darwinian evolution is idolatry in modern scientific guise. Instead of carving wood into a human form and bowing down to it, Darwinians construct images in their own minds that come to life, speak, and offer “understanding” to those who pray to it. It’s past time to crush this false god that has caused so much ignorance, silliness and suffering. Without their god, the Darwinists will be forced out of the trance of their Yoda Complex and, when the painful withdrawal symptoms are past, will be in a position to face reality.