Reactionary fringe meets mutation-biased adaptation. 5.1. Thinking about theories

A wikipedia page disambiguating “Modern Synthesis” defines neo-Darwinism as

“the state-of-the-art in evolutionary biology, as seen at any chosen time in history from the 1890s to the present day.”

Because “neo-Darwinism” and the “Synthesis” are conflated with whatever is widely accepted, they are now attacked on grounds that are completely unrelated to genuine neo-Darwinism or the original Modern Synthesis, e.g., as when a network of life (rather than a tree) is invoked as a contradiction of Darwinism. The attack by Noble (2015) on the

“conceptual framework of neo-Darwinism, including the concepts of ‘gene’, ‘selfish’, ‘code’, ‘program’, ‘blueprint’, ‘book of life’, ‘replicator’ and ‘vehicle’”

is entirely a critique of late-20th-century reductionism à la Dawkins, and addresses neither neo-Darwinism (selection and variation as the potter and the clay), nor the Modern Synthesis that emerged in the 1950s. The original Modern Synthesis is simply not a reductionist theory, but positively invokes emergent phenomena (population-level forces, the gene pool as dynamic buffer) in the service of selection as a high-level governing principle.

How did this confusion happen? Mayr, who died in 2005, never accepted neutral evolution. Yet, decades earlier, scientists intent on preserving a “Synthesis” began to claim that it somehow changes to accommodate new findings, making it a “moving target” (Smocovitis, 1996). This innovation defeats the purpose of falsifiable theories. What if the mutationists adopted this self-serving doctrine, claiming that mutationism is continually updated to cover new results?

Strangely, the latest defenders of orthodoxy no longer invoke “neo-Darwinism” or “Modern Synthesis,” but refer to the “Synthesis” or “Standard Evolutionary Theory” (e.g., Nature debate of 2014). What does this mean? Did the Modern Synthesis fail to update itself quickly enough? If neo-Darwinism was refuted, how precisely did that happen? What does the word “theory” even mean in these debates? What changes in evolutionary thinking have happened in the past 50 years?

To discuss such questions, we must begin with a basic understanding of what scientific theories are, and what they are not– issues established by generations of scientific usage.

TheoryA and TheoryC

Kimura’s Neutral Theory is the conjecture that the majority of changes at the molecular level result from the random fixation of selectively neutral alleles. The endosymbiotic theory holds that mitochondria and chloroplasts arose from bacterial endosymbionts. For hundreds of years, scientists have used “theory” to denote a major hypothesis or systematic conjecture. This is the primary meaning of “theory” in science.

Yet, this meaning is typically not what we have in mind when we use the word “theoretical” or “theoretician.” Population genetics theory is not the conjecture that populations have genetics, nor is music theory the conjecture that music exists.  Instead, these are bodies of abstract principles.

That is, scientists use “theory” for both (1) theoryC (concrete, conjectural), a grand conjecture or major hypothesis to account for some observed phenomena, and (2) theoryA (abstract, analytical), a body of principles relevant to some discipline, methodology or problem area (addressed at length here).

For instance, The Role of Theory in Advancing 21st Century Biology emphasizes the development of formalisms, and says that “a useful way to define theory in biology is as a collection of models,” clearly a reference to theoryA. The title and the quotation illustrate how English speakers often denote theoryA using the abstract noun, i.e., “theory” not preceded by “the” or “a.” Fisher wrote that

“No practical biologist interested in sexual reproduction would be led to work out the detailed consequences experienced by organisms having three or more sexes; yet what else should he do if he wishes to understand why the sexes are, in fact, always two?”

Familiar methods of science require theoryA statements covering imaginary, non-actual worlds, in order to support modus tollens reasoning, in which X is rejected based on the proposition if X then Y, and the observation that Y is absent. For instance, in the case of neutral models, X = neutrality, and Y is some neutral expectation about rates or patterns.  In order to have confidence in rejecting neutrality, we must be confident that, in a hypothetical world of neutrality, Y would occur.

Thus, we evaluate theoryA and theoryC differently. The standard of validity for a theoryC is verisimilitude: how well does it match the real world? By contrast, a statement in theoryA is valid if it is correctly derived from its assumptions, even if it invokes imaginary things, e.g., infinite populations.  Once a piece of theoryA is valid (correctly derived), it is valid forever. By contrast, a theoryC takes risks, and can be refuted by contrary facts.

Opponents of the Neutral TheoryC deny its verisimilitude, yet are quite happy to make use of its theoreticalA infrastructure in efforts to define and then reject neutral models, as in the review by Kreitman (1996). The paradox in Kreitman’s title “The neutral theory is dead. Long live the neutral theory” is resolved by the fact that it refers first to theoryC, then to theoryA.

Persons and theories

What is the possible relationship of a person P to a theoryC T?  In What makes it new?, we saw examples of the 3 basic types– knows, likes, loves (commits to accepting)–, each of which has positive and negative flavors:

1.  P knows (does not know) T.  That is, P expounds or applies T, revealing its inner logic. A special case is when P originates T, i.e., P expounds T for the first time. Merely citing a source or naming a theory does not show knowledge. For instance, Maynard Smith, et al. (1985) know the opposing pressures argument: they can recite it and follow the implications.

2.  P likes (dislikes) TP advocates for (against) T, arguing for (against) its likelihood on theoretical or empirical grounds. The authors of TREE’s hatchet piece dislike the theory of Yampolsky and Stoltzfus (2001), arguing against its relevance, whereas they like the correlated-selection-shapes-M theory of Box 3: they advocate this theory as being a more likely explanation for cases of an alignment between mutational and evolutionary tendencies.

3.  P commits to accepting (rejecting) T, possibly with some limits, as if compelled inescapably by logic or evidence. That is, P reasons about the world as if T (or not-T) is not merely conjectural, but a solid foundation for further reasoning. For instance, in the following passage from the 1959 Darwin centennial (when the victory of the Modern Synthesis was declared), Stebbins makes a falsifiable prediction based on his commitment to a theoryC:

“One very important point here is this: if we say that genetic recombination is necessary to generate new adaptive systems and then say that such highly adaptive and complex systems as the cell of an amoeba, or a euglena with its nucleus, chloroplasts, eyespots, flagella, etc., evolved without the aid of genetic recombination, we are contradicting ourselves. Even though we don’t know that genetic recombination exists in these one-celled organisms, we must postulate its existence at the time they evolved”

Stebbins, p. 115 to 116 of Vol 2, Tax and Calendar, Evolution After Darwin: Issues in Evolution

That is, if the ability of selection to create complex traits depends on recombination among alleles maintained in the gene pool– a defunct principle of the Modern Synthesis–, then single-celled organisms with complex adaptive structures must have evolved with recombination.

These are relations of persons to a theoryC. For theoryA, things are simpler. If we know a theoryA, we commit to its in-principle validity, unless we suspect a problem with its derivation. In fact, theoreticiansA occasionally have lengthy disputes about the precise assumptions underlying theoryA statements, e.g., Hamilton’s rule or Fisher’s fundamental theorem. 

Views and schools of thought

In the Origin of Species, Darwin invokes 3 major means of evolutionary modification, which we can denote with A (natural selection), B (use and disuse) and C (direct effects of environment), in a ratio of roughly 25:5:1. On this basis, we could define Darwin’s view as D ::= A > B > C

In this way, we could define a view for every scientist. 

We could cluster these views into schools of thought or research programs based on similarity, or based on a social network. Each cluster would have a spectrum of know-like-love relationships to various ideas.

However, these person-based concepts usually do not correspond to cohesive theories, e.g., most single-author books about evolution do not present grand unified theories. The typical scientist is an explorer and an opportunistic problem-solver. A scientist may value conflicting theories. Why not? Few scientists are like Pearson or Fisher, dedicated to ideological purity.  Before Kimura turned his vaulting ambition to neutral evolution, it was directed at the antithetical goal of unifying theoretical population genetics with a deterministic maximization principle (see Grodwohl, 2017).

Likewise, schools or traditions can be inconsistent or arbitrary.  DeLage and Goldsmith (1913) write that ”The truth is that [neo-]Lamarckism was never a real system” (p. 244) because it evolved as a counter-reaction, defined in contrast to the complete rejection of external heredity-modifying factors by the dominant neo-Darwinian school. 

Discerning theories

A theory exists to the extent that it causes different people to carry out the same kind of domain-specific reasoning. The way to understand a theory is to look for the reasoning it supports, going from inputs to outputs based on some internal logic.

For instance, the opposing-pressures argument was used to reject the general idea of variation-biased evolution, and to support the doctrine that selection is the sole source of direction in evolution. This conclusion emerges by comparing the magnitudes of two inputs, mutation rates and selection coefficients. The internal logic depends on the “forces” theory, which says that evolutionary causation can be understood in terms of mass-action pressures on allelic frequencies. Under this theory, the direction of mutation, when not aligned with the direction of selection, must be opposed to selection, and the mutation-selection balance equation tells us what happens in this case.

Fisher, Haldane, and others expressed the opposing-pressures theory in similar ways. By contrast, expressions of neo-Darwinism or the Modern Synthesis are quite diverse. We can think of them as the diverse phenotypic expressions of an underlying genotype. If the expressions are too diverse, it may mean that there is no common theory, or that the common theory is only a weak determining factor due to the influence of other theories.

Finally, because theories are often embedded in works of persuasive rhetoric, we must be careful to separate the product from the sales pitch, following the English aphorism to watch what they do, not what they say. We find the surest evidence for the content of a theory, not when scientists present an explicit description, but when they invoke the terms of the theory to conduct reasoning from premises to conclusions, exposing the inner logic.

In particular, scientists with the “love” relationship to a theory may exaggerate strengths, ignore weaknesses, and set up false comparisons to flatter the object of their affection.  Fisher’s Ch. 1 argues that, once the discrete basis of heredity is recognized, then neo-Darwinism follows and all other views must be cast aside. Yet, we do not define neo-Darwinism as the view that follows from genetics, because Fisher’s assertion is clearly false, e.g., neutrality, mutation-biased evolution, and saltations are all compatible with Mendelian population genetics.

Likewise, consider the following from Maynard Smith (1969)

”If one invents counter-examples, they seem absurd.  Thus if someone discovers a deep-sea fish with varying numbers of luminous dots on its tail, the number at any one time having the property of being always a prime number, I should regard this as rather strong evidence against neo-Darwinism.  And if the dots took up in turn the exact configuration of the various heavenly constellations, I should regard it as an adequate disproof.  The apparent absurdity of these examples only shows that what we know about existing organisms is consistent with neo-Darwinism.”

(p. 86 of “The Status of Neo-Darwinism” in  Waddington CH, editor. Towards a Theoretical Biology 2. Sketches. Edinburgh: Edinburgh Universeity Press)

This passage tells us nothing important about neo-Darwinism, because the counter-examples are absurd.  Actual historic counter-examples to neo-Darwinism include (1) one-step speciation by de Vriesian macromutations, (2) parallelism or trends due to biases in variation per Vavilov (1922) or Eimer (1898), (3) evolutionary change dependent on the timing or character of individual mutations, (4) rampant neutral evolution, and (5) saltations, i.e., changes that are not composed of infinitesimals.

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