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

This is the seventh in a series of guest posts by Arlin Stoltzfus on the role of mutation as a dispositional factor in evolution.

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Reactionary fringe meets mutation-biased adaptation. 5.1. Thinking about theories
by Arlin Stoltzfus
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 regularly 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 original Modern Synthesis, which is simply not reductionistic, 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.

"The state of the art" is a phrase that needs no modification. Nothing good can come from linking it to the name of a dead person.

Reactionary fringe meets mutation-biased adaptation
Introduction
1. The empirical case
2. Some objections addressed
3. The causes and consequences of biases in the introduction process
4. What makes this new?
5. Beyond the "Synthesis" debate
    -Thinking about theories
    -Modern Synthesis of 1959
    -How history is distorted
    -Taking neo-Darwinism
      seriously
    -Synthesis apologetics
6. What "limits" adaptation?
7. Going forwardUnfortunately, the confusion about this issue is not limited to Wikipedia and neophytes, but permeates high-level debates about evolutionary biology. Decades ago, scientists intent on defending an ongoing 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 theories. It ruins everything. How do we judge the success of a "theory" that can't fail? When theories shift in meaning to maintain the appearance of constancy, how is it possible to achieve clarity? How can we track changes in thinking if the goal-posts keep shifting?

To understand how the current state of evolutionary biology relates to the Modern Synthesis, we have to begin by understanding what theories are, how we use them, and how we recognize them.

Theory_A and Theory_C

Generations of scientific usage establish what the term "theory" means. 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) theory_C (concrete, conjectural), a grand conjecture or major hypothesis to account for some phenomenon, and (2) theory_A (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 theory_A. The title and the quotation illustrate how English speakers often denote theory_A 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 theory_A 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 theory_A and theory_C differently. The standard of validity for a theory_C is verisimilitude: how well does it match the real world? By contrast, a statement in theory_A is valid if it is correctly derived from its assumptions, even if it invokes imaginary things, e.g., infinite populations.  Once a piece of theory_A is valid (correctly derived), it is valid forever. By contrast, a theory_C takes risks, and can be refuted by contrary facts.

Opponents of the Neutral Theory_C deny its verisimilitude, but use its theoretical_A infrastructure 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 theory_C, then to theory_A.

Persons and theories

What is the possible relationship of a person P to a theory_C 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. For instance, Maynard Smith, et al. (1985) know the opposing pressures argument: they can recite it and follow the implications. Merely citing a source or naming a theory does not show knowledge.

2. P likes (dislikes) T.  P 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. At the 1959 Darwin centennial, where the architects of the Modern Synthesis declared victory, Stebbins makes a falsifiable prediction based on his commitment to a theory:

"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 new traits depends on recombination among alleles maintained in the gene pool-- one of the forgotten principles of the Modern Synthesis--, then single-celled organisms with complex adaptive structures must have evolved with recombination.

These are the relations of persons to a theory_C. For theory_A, things are simpler. If we know a theory_A, we commit to its in-principle validity, unless we suspect a problem with its derivation. In fact, theoreticians_A occasionally have lengthy disputes about the precise assumptions underlying theory_A 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 of evolution, covering all of its major causes, 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.

A personal view is typically not a cohesive theory. Scientists who write books often advocate one or more theories, but almost never claim to have a grand unified theory. The typical scientist is an explorer and an opportunistic problem-solver. 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). Few scientists are like Pearson or Fisher, dedicated to ideological purity.

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), explaining that it evolved as a counter-reaction, defined in contrast to the rejection of external heredity-modifying factors by the dominant neo-Darwinian school.

Discerning theories

A theory that is more than a mere conjecture is a mental appliance, a machine like a pasta-maker: we add some inputs and turn the crank to activate the internal logic, and the theory responds by generating hypotheses or explanations with a shape that is specific to the theory.  A theory of this kind exists to the extent that it causes different people to carry out the same kind of domain-specific reasoning. To understand the theory, we look for the reasoning it supports.

For instance, the opposing-pressures argument was used to reject variation-biased evolution, in support of the doctrine that selection is the sole source of direction in evolution. This conclusion emerges by determining the larger of two inputs, mutation rates and selection coefficients. The correctness of using this simple logic to reject variation-biased evolution depends, in turn, on the sufficiency of the theory of population-genetic "forces," which says that the causes of evolution are forces that displace allele frequencies the way that physical forces displace a particle. The pressure of mutation on an allele frequency is either aligned superfluously with selection, or against selection, in which case, selection wins.

Fisher and Haldane invoked 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 heterogeneous influences of other theories.

Because theories may be embedded in works of persuasive rhetoric, we must be careful to separate the product from the sales pitch, following the English aphorism "watch what they do, not what they say." We find the surest evidence for the content of a theory when scientists invoke the terms of the theory to conduct reasoning from premises to conclusions, exposing the inner logic. 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, e.g., Maynard Smith (1969) writes

"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 University Press)

When an author raises and then rejects absurd ideas, this is merely a ploy to convince the reader that the author is on the side of reason. Historically important ideas contrary 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., significant changes that are not made of infinitesimals. To understand historic neo-Darwinism (the dichotomy of the potter and the clay) is to understand why these ideas, in spite of being reasonable, are not included.

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