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Month: January 2012

Plantinga’s EAAN

A post now up at the Philosopher’s Carnival discusses Alvin Plantinga’s Evolutionary Argument Against Naturalism (EAAN), and comment how it is like (not exactly the same) as a global skepticism argument being self-defeating. Plantinga’s argument goes like this:

P1. If evolution is true, then we have modified monkey brains.

P2. Modified monkey brains are not evolved to find out the truth

P3. Evolutionary naturalism (the view that everything about humans, including their cognitive capacities, evolved) is the output of modified monkey brains.

C1. Therefore evolutionary theory is unreliable and should be rejected.

C2. Therefore evolutionary naturalism should be rejected.

The modified monkey brain comes directly from Darwin’s letter to William Graham, in which he wrote

Would any one trust in the convictions of a monkey’s mind, if there are any convictions in such a mind?

Plantinga directly mentions this letter, and argues that in effect if evolution is true it cannot be rational to believe that it is. The trouble with this argument is that this is exactly there opposite conclusion to the one that Darwin made. Darwin’s full argument, made in response to Graham’s book The Creed of Science, is this:

You would not probably expect anyone fully to agree with you on so many abstruse subjects; and there are some points in your book which I cannot digest. The chief one is that the existence of so-called natural laws implies purpose. I cannot see this. Not to mention that many expect that the several great laws will some day be found to follow inevitably from some one single law, yet taking the laws as we now know them, and look at the moon, what the law of gravitation — and no doubt of the conservation of energy — of the atomic theory, &c. &c. hold good, and I cannot see that there is then necessarily any purpose. Would there be purpose if the lowest organisms alone destitute of consciousness existed in the moon? But I have had no practice in abstract reasoning and I may be all astray. Nevertheless you have expressed my inward conviction, though far more vividly and clearly than I could have done, that the Universe is not the result of chance. But then with me the horrid doubt always arises whether the convictions of man’s mind, which has been developed from the mind of the lower animals, are of any value or at all trustworthy. Would any one trust in the convictions of a monkey’s mind, if there are any convictions in such a mind?

So what Darwin is arguing is that evolution gives us no confidence in metaphysical conclusions, not science. Science he takes for granted can be undertaken by modified monkey brains. They evolved to find out about the world. What evolution undercuts is the ability of monkey brains to form reasonable convictions about things like Gods and Cosmic Purpose.

Plantinga knows this, and even mentions it in a footnote but he disingenuously inverts the argument and makes it look as if Darwin was riven with doubts about his own theory. Of course he was not. This is rhetorical prevarication by omission. But the argument Darwin makes is much more interesting than a simple global skepticism. He is arguing that we can know about the world, due to our evolved faculties.

Why is that? Why can our evolved faculties make beliefs about the world reliable, but not beliefs about gods and angels? The answer is simple, according to an argument Paul Griffiths and I have made in two forthcoming book chapters: some beliefs are truth tracking because they contribute to fitness when they are true and lower fitness when they are not, while beliefs about gods and purpose in the cosmos do not in virtue of their content, but only in virtue of their being consonant with the society of the believer.

Another way to put this is that there are environmental beliefs that must be true (or at least not egregiously false) in order to improve the fitness of the belief-holder, and there are social beliefs that affect fitness in virtue of what other people also believe and how they react to the belief holder. Morality, aesthetics and most of all religion are of the latter kind. Assuming that the religious beliefs do not insist upon too many fitness lowering behaviours (like snake handling) in ways that are not balanced or exceeded by the fitness benefits of being a believer, a religious belief increases fitness only to the extent that others share it, whereas an environmental belief (like whether that food is poisonous when treated with alkaline soils, or whether the stars are reliable guides to hunting or planting seasons) increases fitness when it is true (or not too false). In other words, an environmental belief had better give not too many false positives and not too many false negatives about the way the world is, while a social belief had better give not too many false positives and negatives not about the content of the belief, but about what others around you believe also. In short, people are the environment for social beliefs, not gods, or cosmic anythings.

So if properly understood, Darwin’s argument undercuts Plantinga’s anti naturalism and in fact replaces it with a global skepticism about the non-natural, and this is not self-defeating. Plantinga’s EAAN is actually an EAAS[upernaturalism].

Refs below the fold

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Notes on Novelty 8: Conclusion – Post evo-devo

Notes on Novelty series:
1. Introduction
2. Historical considerations – before and after evolution
3: The meaning of evolutionary novelty
4: Examples – the beetle’s horns and the turtle’s shell
5: Evolutionary radiations and individuation
6: Levels of description
7: Surprise!
8: Conclusion – Post evo-devo

With the growth of developmental genetics, it is possible to see beyond the view of homologies working at the level of whole organs. The mechanisms that define the ordinate axes of structures, the genetic circuits that pattern them, and the cell types with which organs are formed can be considered. The more that researchers look, the more they will find that the same tools have been used to build a great variety of structures long thought to have independent histories. Discerning what has been conserved and what is novel in the origins of organs and body plans will be possible only with more comparative data, experiments on non-model animals, and targeted fossil discoveries from crucial nodes in the tree of life. (Shubin et al. 2009: 822)

My conclusion is that we find novelty in a subjective sense, based upon what we think we should find in the data. Further knowledge of the underlying or overlaying mechanisms should reduce the surprisal of the trait appearing either in the paleontological record or in a distinct taxonomic group. Only when it doesn’t and in cases where it should, should we start to seek non-Darwinian mechanisms. Much of the debate over novelty in evolution has centred implicitly around what the researchers themselves find interesting, surprising or contrary to the conventional interpretations. Another factor lies in a topic I haven’t discussed here: what counts as “suitably dissimilar”, so a few words on this.

Similarity and its converse, dissimilarity, is often applied to the issues of novelty. Stephen Jay Gould attempted, for example, to apply it in the case of the Cambrian explosion (1990); some fossils’ bodyplans were too dissimilar (using the consistency index of cladistic analyses, C) to put them into existing taxonomic categories (“phyla”); subsequent work did precisely that (Briggs and Fortey 2005). Relying upon morphology – that is, description at a certain grain (indeed, the only grain available to palaeontologists most of the time; cytological data is rare and molecular data nonexistent) – Gould found some traits and overall phenotypes too weird to fit into our classifications. Briggs and Fortey showed over several decades of work summarised in their paper that they could be seen as instances of stem groups of our present clade-based phyla (that is, phyla that have been made monophyletic).

What is similarity in taxonomy? It is true that rarely does this get any kind of analytic or quantitative analysis, especially in palaeontology, but that doesn’t mean there is no analysis underlying it of which the authors are not conscious (or think it too obvious to state). The best analysis of the recognition of similarity in the literature is that of Amos Tversky, who argued that the similarity of one thing to another is the overlap of features minus the unique features to each object, out of a “feature set” (1978). This is now called “Tversky Similarity”:

Tversky Similarity  [TS]

What is crucial to understanding similarity like this, which was developed for a generic psychological account and not just for science, is that the choice of features to evaluate (which may be entirely unconscious, or a cultural convention, or even biologically imposed) determines what counts as similarity in each case. With a different feature set, different similarity indices might arise, and indeed the history of science has been one of finding the “right” feature set (for example, in the case of elements and the periodic table, Scerri 2008).

The alternative to using apparent similarity, especially at a given grain of description (the gross morphology of the organism) is to use homology. Instead of treating the relations between organisms and specimens as a matter of what they “look like”, identify homologs and organise your groupings on that basis – this is the reason for cladistics. Homologies, not similarities in the eyes of the beholders, set up a baseline for assessing how novel a trait may be, and if we can find the developmental, physiological, molecular and environmental reasons for the novelties thus uncovered, so much the better. All I am criticising is the idea that somehow, in ways we can’t even properly articulate, we need to “go beyond” or “extend” the Darwinian approach. In one sense of course we do; Darwin did not know everything. In this case, we do not; Darwin has been validated again and again regarding novelty.

I am not dismissing the idea that there can be an evolutionary explosion from some novelty or node in an evolutionary tree, although these are more often the result of subjective assessments (the Cambrian explosion has, for example, become less and less of an explosion and more and more of an evolutionary diversification of the ordinary kind, as paleontological evidence has come in). What I am dismissing is the notion that there is some objective sense in which evolutionary novelties are natural kinds. Radiations occur all the time – some clades are speciose and others are sparse. If there is a general principle why this occurs, it is not yet obvious. Maybe some kinds of developmental modularities do cause clades to be more radiative. Maybe, however, is not an explanation.

Science progresses best when it eliminates subjectivity from its categories; anthropomorphism has ever been the bugbear of good science (unless anthropoi are the objects of study, and even there we tend to project ourselves on our subjects, as any anthropologist can tell you). It has taken us over a century to begin to recognise that what Darwin started requires this in biology as in the other physical sciences. So I would like to leave the last word to somebody of a certain weight in evolutionary biology, and who seems to be on the right side of the debate on many issues, Sewall Wright:

“Creative” and “emergent” evolution

The present discussion has dealt with the problem of evolution as one depending wholly on mechanism and chance. In recent years, there has been some tendency to revert to more or less mystical conceptions revolving about such phrases as “emergent evolution” and “creative evolution.” The writer must confess to a certain sympathy with such viewpoints philosophically but feels that they can have no place in an attempt at scientific analysis of the problem. One may recognize that the only reality directly experienced is that of mind, including choice, that mechanism is merely a term for regular behavior, and that there can be no ultimate explanation in terms of mechanism—merely an analytic description. Such a description, however, is the essential task of science and because of these very considerations, objective and subjective terms cannot be used in the same description without danger of something like 100 percent duplication. Whatever incompleteness is involved in scientific analysis applies to the simplest problems of mechanics as well as to evolution. It is present in most aggravated form, perhaps, in the development and behavior of individual organisms, but even here there seems to be no necessary limit (short of quantum phenomena) to the extent to which mechanistic analysis may be carried. An organism appears to be a system, linked up in such a way, through chains of trigger mechanisms, that a high degree of freedom of behavior as a whole merely requires departures from regularity of behavior among the ultimate parts, of the order of infinitesimals raised to powers as high as the lengths of the above chains. This view implies considerable limitations in the synthetic phases of science, but in any case it seems to have reached the point of demonstration in the field of quantum physics that prediction can be expressed only in terms of probabilities, decreasing with the period of time. As to evolution, its entities, species and ecologic systems, are much less closely knit than individual organisms. One may conceive of the process as involving freedom, most readily traceable in the factor called here individual adaptability. This, however, is a subjective interpretation and can have no place in the objective scientific analysis of the problem. [Wright 1931: 159]

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Notes on novelty 7: Surprise!

Notes on Novelty series:
1. Introduction
2. Historical considerations – before and after evolution
3: The meaning of evolutionary novelty
4: Examples – the beetle’s horns and the turtle’s shell
5: Evolutionary radiations and individuation
6: Levels of description
7: Surprise!
8: Conclusion – Post evo-devo

It is now time to return to the basic argument of this series. You will recall that it went like this:

  1. Novelty is specified at some level of description based on there being a nonhomologous structure or function
  2. There is always some level of description at which there is a homology for the underlying developmental or hereditary mechanisms that develop the novel trait
  3. Novelty is therefore a function of the level or scale of description
  4. What makes it novel is therefore our lack of knowledge of the right scale or level of description of traits; when we learn the right level (say, protein or cytological), the novelty seems less novel or not novel at all.
  5. Novelty is therefore a matter of the surprisal value of the trait relative to homologies at that scale

I have made out premises one to four. Now it is time to argue for the conclusion.

There is a concept in information theory known as the surprisal value of a received message: basically it is that the information content of a message is the degree to which the sequence is surprising, which is to say, the inverse of the expectation that the sequence would be received by chance:

Surprisal

where the probability p is 0 ? p ? 1. This is also called “self-information”. Note that the key term here is expectation. The point of surprisal is that it relies upon our prior expectations of probabilities. To the extent that we have an estimation of those distributions of probabilities, the received message is surprising and informative.

An analogous case is in play here. We describe (that is, set up a sequence of symbols, either in verbal or mathematical form) some traits or characters in biological cases and estimate their likelihood under “ordinary” evolution or drift. We then are surprised (informed) when the traits concerned do not fall out as likely. This, we think, calls for a special explanation and so we start looking at “non-Darwinian” causes.

Let us consider what “Darwinian” causes might be. Darwin adduced several causes of evolution: natural selection, sexual selection, artificial selection, use and disuse, and correlation. We can lump all the selective processes together under the rubric “selection”, as all that divides them is the intent of the selective agency, or a lack of it. Use and disuse was what is often misleadingly called Darwin’s “Lamarckism”, but I have argued before that it was not. He merely thought that traits that were useful would be more strongly inherited and those that were not would be weakly inherited. As a source of novelty, use and disuse is otiose. He did not think this was a case of acquired characters as such. In any case we can dismiss this, pace epigenetics, as a case of evolutionary novelty on the basis of modern knowledge. Correlation is now known under the rubric of allometry. Some traits (like large antlers) can be due simply to regulation and moderation of growth – if body size is upregulated, antlers will grow disproportionally due to differential growth rates of parts. That leaves selection as a Darwinian mechanism for novelty. Indeed, it leaves selection as the sole mechanism for novelty.

Objections to selective accounts of novelty often rely on the argument that selection only determines the subsequent fate of a novel trait (i.e., whether it spreads to fixation or equilibrium, or is eliminated), not its origin, and there is a sense in which this is true, but we should not be so restrictive about what selection includes. Darwin and Wallace always held that selection involves prior variation; which we now refer to as mutation since the Mendelian revolution. In any sensible interpretation, selection involves random mutation (random, that is, to the selective value of the traits in that population in that environment, or any future population and environment linearly derived from it).

Another class of objections to selective accounts of novelty is that selection must occur gradually, with fitness improvement at every step. Some of these novelties are thought not to have such intermediate improvements in fitness gradients. In the case of our two exemplars, the turtle shell and the beetles’ horns, this is not the case; we can see fitness improvements (the turtles being ecological, and the beetles being sexual) at every stage. We can leave this case to one side here, then.

So taking selection to be blind variation and selective retention, in Donald Campbell’s felicitous phrasing (Campbell 1965), the mechanism that produces novelty in a Darwinian fashion is some random variation to an existing trait, and selection on it when it has fitness differences. Obvious enough. However, it needs a bit of filling out. Fortunately, Thornhill and Ussery have done this already (2000). The pathways or routes to novel traits posited by the most general Darwinian view, and I think properly assigned to Darwin himself, are: serial direct evolution, parallel direct evolution, elimination of functional redundancy, and adoption from a different function. I will paraphrase and extend these (which were originally written to deal with the rather uninteresting claims of intelligent design).

Serial direct evolution occurs when some trait is modified along the lineage (the ancestor-descendent sequence), so that the trait at the end is distinct from the trait at the beginning. The sequence in seriatim has to occur at what I am calling the same grain of description. Changing the grain (upwardly or downwardly) would no long count as a series. I would call this sequential evolution of novelty.

Parallel direct evolution occurs when more than one functionally connected component is modified simultaneously to form a complex structure. The example Thornhill and Ussery give is a table where all the legs need to be extended in concert for the table to function (and the biological example here is the complex vertebrate eye). This is clearly compositional in nature.

How parallel and serial evolution can actually differ, as opposed to being merely conceptually different, is unclear. Any trait in a living system, because it is a system, must involve more than one part. Suppose a serial evolutionary process modifies a rib. That will change all attachments and integuments connected to the rib. It will change the shape of the body, and hence the locomotory subsystems. Internal organs and functions will shift, subtly or greatly. Organisms are not evolved by adding a single new part, and given that organisms develop as a system, any change in any part will affect many others, which will have to evolutionary adjust over time.

So I think that we can bring these two forms of Darwinian evolutionary routes into one: some part or parts are modified lineally and in sequence. This is not necessarily gradualism, though. Changes at one grain of resolution and description can be abrupt, so long as the descriptions at some grain allow us to identify homology over time. [A change without homological relations would indeed be non-Darwinian.]

The elimination of functional redundancy occurs when a part that had a now-redundant or unnecessary function loses that function enabling it to form the seed for another function. This leads to adoption from another function. Functional descriptions, however, are relative to the choice of functions that matter to the observer; it is inevitable that a part of almost any function of any complexity will also play a functional role in several or many other functional processes. So while the bones of the jaw that became those of the middle ear (Thornhill and Ussery’s example) lost their functional role as “jaw bones” (as stress-supporting biomechanics structs for mastication), they undoubtedly retained their functional role as skull supporting, facial muscles supporting bones, while they evolved. They “lost” one function (or better, lowered it gradually, more or less) and gained another “gradually, more or less) but retained many others and these, too, evolved. Our choice of what to describe here remains the key issue. Again, also, I think we can collapse these two.

Darwinian selection occurs on variation, so the real question is how variation occurs. As far as I can tell, there are four ways this can happen:

  1. Deletion of a part.
  2. Duplication of a part.
  3. Rearrangement of a part.
  4. Insertion of a part.

Consider genes in the traditional four letter code. A letter can be deleted, given a “novel” sequence (especially if the deletion is in the start or stop region of an open reading frame), or a sequence or letter can be duplicated to the same effect. When duplication occurs, one copy can be retained under the old function, while the new copy evolves through the other three ordinary Darwinian processes. A sequence can be inverted or chopped up and distributed through other sequences, forming all kinds of novelties of products downstream. Or a sequence can have an atomistic part (a “mer”) at that grain of description (here: the nucleotide “letters”) inserted.

Once these novel variants occur, and they may occur through deterministic processes at the grain of description but remain “random” relative to the selective pressures that obtain at the trait or organismic level, selection takes over and explains why so many of the population, or all of them, have the trait concerned.

In no way is an explanation other than a Darwinian selective account required to explain novelty unless it could be shown that a part arose without any kind of precursors whatsoever. In other words, there is no prior sequence of parts at any grain. When arguments are put that Darwinian selection is insufficient to account for a novel trait, usually on the basis of some kind of systems theory, it is because the descriptions do not permit a change of grain. And this is a matter of surprisal only when grain is fixed. Suppose, to return to our information theoretic example, you had a full description of all parts of the sender, and what is fed into it, along with a full description of the channel and the receiver. What might be surprising then would be some noisy interference, not that you had received the same or very similar sequence as was sent. What matters is what your grain of description is – an engineer’s or an operator’s.

It may be that there are indeed properties of systems that are surprising (at least, until we have worked them out) and which have, at some grain of description, explanatory weight in evolutionary contexts; but I suspect and hold that, like selection itself, these will always be promissory notes for a full and physical description to come, just like a mathematical equation is not explanatory until we can fill out the denotation and interpretation of the variables.

 

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