More on Teleology in Evolutionary Biology

I’ve been corresponding via email with a fellow evolutionary biologist (who shall remain nameless). I thought that some of her/his comments might be useful or interesting to those who read this blog, as they have a direct bearing on the "problem" of purpose (i.e. teleology) in evolutionary biology.

My correspondent's comments and questions are in block quotes:

I’ve been following the ‘Survival of the Sickest’ thread at Uncommon Descent, and have some comments on it and on your essay on the (un)reality of adaptations.

First, a major area of agreement between us is that the original post is fatally flawed by:

1) the assumption that “Darwinism” implies “constant progress”, and

2) failure to understand that fitness is always defined relative to a particular environment, and that environments change over time.

Now, on to some points of disagreement:

You mentioned Gould and Vrba’s 1982 paper on exaptation, and wrote:

"The reason is quite simple: if (as Gould, Lewontin, and Vrba argue) adaptation isn’t legitimately part of what evolutionary theory is about, then the whole idea of “design” and “function” is read completely out of evolution, leaving only descent with modification."

I have been very strongly influenced on this topic by Warren Allman, director of the Paleontological Research Institute here in Ithaca. He asserted that all adaptations should be considered to be exaptations. His rationale for this assertion was that the term “adaptation” has built into it an assumption of teleology. Literally translated, the word "adaptation" means “toward usefulness”. It’s the “toward” part that is the problem. As you and I both understand it, evolution (including natural selection, but not artificial selection) does not tend toward anything. It has no goal as far as we can tell. Ergo, it builds on what has gone before, but without any specific goal “in mind”.

This is why “exaptation” expresses better how we understand natural selection. It builds “away from” non-functionality (or even away from previous functionality), but never really “toward” anything at all as far as we can tell. And, if Sewall Wright’s “shifting balance” theory is a reasonable model of evolution, then it never really “arrives” anywhere at all, since the “goal” is constantly shifting anyway.

I’m wondering why you think that Gould and Vrba regard adaptation as being outside the legitimate scope of evolutionary theory. My take on the paper is not that they regard the concept of adaptation as illegitimate, but just that it has been typically construed too broadly and should be broken down into the categories of true ‘adaptation’ and ‘exaptation’, where they define a true adaptation thusly:

“Following Williams, we may designate as an adaptation any feature that promotes fitness and was built by selection for its current role.”

The problem I have with this definition is the inclusion of the words “promotes” and “for”. “Promotion” means exactly what it says: “motion towards” something. Ergo, using this word immediately suggests teleology, and as I have pointed out above, teleology cannot be a valid assumption in the origin of the products of evolution at any level. This is not because including teleology allows for “a divine foot in the door” (c.f. Lewontin, 1997), but rather because it requires that the “plan” for the teleological process must exist prior to the coming into being of that process. When we do things, this assumption is perfectly valid, but when something happens in nature, such an assumption is entirely unwarranted. Where, in nature, could such a pre-existing plan exist?

As for the word “for, I always point out to my students that teleological explanations virtually always reduce to sentences that include the phrase “in order to”. This can be shortened even further to “to” (leaving out the “in order”). However, the entire phrase “in order to” can be replaced with the word “for” without changing its meaning. Ergo, the definition quoted above is still irreducibly teleological, and therefore includes an assumption that we should not make in evolutionary biology.

In my paper on the evolution of the capacity for religious experience, I began with a succinct definition of “adaptation”, from which I lay out four criteria that a characteristic (i.e. a “trait”) must meet to be considered a genuine adaptation.

An evolutionary adaptation is any heritable phenotypic character whose frequency of appearance in a population is the result of increased reproductive success relative to alternative versions of that heritable phenotypic character.

Here are the four criteria that I believe must be met for a characteristic to be considered to be an adaptation:

1) An evolutionary adaptation will be expressed by most of the members of a given population, in a pattern that approximates a normal distribution;

2) An evolutionary adaptation can be correlated with underlying anatomical and physiological structures, which constitute the efficient (or proximate) cause of the evolution of the adaptation;

3) An evolutionary adaptation can be correlated with a pre-existing evolutionary environment of adaptation (EEA), the circumstances of which can then be correlated with differential survival and reproduction; and

4) An evolutionary adaptation can be correlated with the presence and expression of an underlying gene or gene complex, which directly or indirectly causes and influences the expression of the phenotypic trait that constitutes the adaptation.

I would now modify criterion #4 to state that such genes/gene complexes must be shown to have been conserved, relative to other sequences in the genome. However, one must keep in mind that such conservation, while necessary, is not sufficient. As we know now, some sequences are conserved, but can be knocked out, with no discernible effect on phenotype. Ergo, to fully satisfy criterion #4, a characteristic must be shown to be associated with a particular gene or gene complex, the knocking out of which can be shown to have significant negative effects on fitness.

Obviously, this means that a great many characteristics that we observe in living organisms will not qualify as adaptations. I believe that this is fully justified, following Williams’ assertion that the concept of adaptation is “onerous” and should only be resorted to “in the last resort”. It is only by doing so that we may avoid the otherwise almost inevitable pitfall of appealing to teleology in our explanations.

Gould and Vrba close their paper with this:

“The argument is not anti-selectionist, and we view this paper as a contribution to Darwinism, not as a skirmish in a nihilistic vendetta. The main theme is, after all, cooptability for fitness. Exaptations are vital components of any organism’s success.”

There’s that nasty little word “for” again! Fitness is immediately measurable as relative differential reproductive success, but “adaptation” can only be legitimately inferred retrospectively. We can’t say that something is a genuine adaptation until it already is, and this seems to me the kind of logical circularity that has also plagued Herbert Spencer’s phrase “survival of the fittest”. If we stick to the four criteria listed above, we will rarely fall into the trap that teleological thinking always sets for us.

Also, you later wrote the following, which seems to acknowledge that Gould and Vrba did regard adapation as a legitimate part of evolutionary theory:

“Yes, indeed, except that I believe that Gould, Lewontin (and later, Vrba) were, like Darwin, unwilling to take their principles to their logical conclusion: that adaptations (like species) are a figment of the human imagination, and do not actually exist in nature (or, to be even more precise, do not have to exist in nature).”

What I meant by this is that the only way we can actually “detect” the presence of adaptation is by inferring it. In that sense, adaptations are not “primary” characteristics; that is, characteristics that can be directly observed (such as differential reproductive success). Rather, such “secondary” characteristics must be indirectly inferred. In that sense, they are indeed “imaginary”; we must “imagine” that they exist (as the result of our application of inferential logic), as we cannot observe them directly.

Am I missing something? Are you trying to say that although Gould and Vrba regarded adaptations as real, they nevertheless thought they should be excluded from evolutionary theory?

No, I’m saying what Williams was saying, only I’m saying it more strongly and consistently: that we should never include any hint of teleology in our explanations, as such inclusion includes the biological equivalent of that old bugaboo of physics: “action at a distance” in physics is the equivalent of “goals preceding causes” in biology.

When I reread Williams’ famous 1966 book, Adaptation and Natural Selection, which supposedly reads teleology out of evolutionary biology, I was astonished to find it shot through with the same kind of teleological reasoning that he was supposedly trying to eliminate. I think I could find all the “hidden teleology” in Williams because I have spent so much time debating with ID supporters. They are the ultimate teleologists, and can always find where we have subtly woven teleological assumptions into our biology.

Finally, you wrote:

“To be as clear as I can, I believe that asserting a position of “metaphysical materialism” is just that: a metaphysical, not a scientific assertion. Confusing metaphysics with science is nearly as pernicious as confusing “ought” and “is”. The former makes for questionable science and the latter makes for questionable ethics.”

I would agree that science has no say on metaphysical questions that don’t have observable consequences (although I would argue that even then, Ockham’s razor should cause us to prefer simpler metaphysical systems to needlessly complex ones). However, some metaphysical assertions do have observable consequences. For example, I consider the existence of the Young Earth Creationists' God to be a metaphysical assertion that has nevertheless been decisively falsified by science.

I agree, but the same cannot be said for the more subtle versions of teleology found in Michael Behe or William Dembski's works. Their books (especially Dembski’s) present a much more subtle and less easily refuted version of teleological explanation, one that is easily reinforced by our own unwitting resort to teleological explanations.

Evolutionary adaptation is where the rubber of both evolutionary theory and ID hit the road.

Now on to your essay “Are Adaptations ‘Real’?”

You wrote:

“...although there are characteristics of organisms that are correlated with relatively high reproductive success (and would therefore be considered by most evolutionary biologists to qualify as “adaptations”), it becomes problematic to decide exactly which of those characteristics are the “real” adaptations and which are merely ‘accidental’”.

The problem, of course, is the words “real” and “accidental”. If we are genuinely dedicated to rooting out teleology in all of our explanations of the origins of biological objects and processes, then all adaptations are “accidental”, in the sense that they are all unplanned. We perceive them as having “functions” because our naive viewpoint of reality is always teleological. We can think non-teleologically only with very great difficulty. It’s like special relativity or quantum mechanics. We have to twist our minds to be able to even begin to conceive of them, and even then we constantly slide back into our naive (and unwarranted) views of reality.

True, if by “accidental” adaptations you mean exaptations. But while it may sometimes be difficult to tell whether an adaptation is “real” or “accidental”, that is not evidence that “real” adaptations don’t exist. Indeed, the only scenario I can envision in which “real” adaptations would not exist would be one in which every fitness-enhancing feature was an exaptation.

Exactly!

But that would mean, among other things, that every incremental improvement to the eye would have to have been the accidental result of changes that were selected for some reason other than improved vision. That seems far-fetched to me. Am I misunderstanding your position?

It’s not that that every incremental improvement to the eye would have to have been the accidental result of something, it’s that every incremental change to the eye would have had to originate accidentally, but then increase in frequency as the result of differential survival and reproduction. If we think the way you worded it (and we almost always think that way), then the teleological trap is that all of the incremental changes are somehow “predestined” and that complex eyes must be the inevitable result.

But this just plays into the hands of intelligent Design supporters. When we argue that “half an eye is still adaptive” we unwittingly include the assumption that “half an eye” is just that: half of what will ultimately evolve by natural selection. But our knowledge of the natural history of vision has shown us over and over again that “half an eye” is the whole thing in many cases. We can only say that the eyes of, say, flatworms, are “half an eye” because we already know that such a thing as a “whole eye” exists in cephalopods and vertebrates. We have to disabuse ourselves of the idea that any characteristic is only partially the whole deal. All characteristics of all organisms are the whole deal for those organisms, period, end of story, that’s all She wrote. Anything else contains the beginnings of teleology, and that way lies error, endlessly compounded.

We now have the ability to selectively delete individual characteristics from many different organisms. This makes possible something that natural selection does not: the precise determination of the selective “value” of particular characteristics. This has already been done, and the surprising outcome has been that even some gene sequences that were thought to have been very important in selection (due to having been “conserved” over deep evolutionary time) are apparently insignificant or useless. We know this because knocking them out of the genome has no discernible effect on the survival or reproduction of the “knock-out” progeny.

Precisely my point, above.

That interpretation seems to depend on the hidden assumption that the environment hasn’t changed significantly in the recent history of the organism, and that the experimental environment is fully representative of the historical environment over the entire time during which the features in question evolved. In the case of knocked-out sequences that have no apparent effect on fitness, how sure are we that the experimental environment is fully representative in this way?

No, but to assume that we are making the opposite mistake - assuming that some characteristic really has some function, even if that function is entirely unobservable - is once again to fall into the “teleology trap”. This is essentially the same argument that ID people make about “junk DNA”. Just because we haven’t found any function for it, doesn’t mean that all of it has no function. They argue that all of it must have some function. They are, like the evolutionary biologists for whom Williams, Gould and Lewontin, and Gould and Vrba wrote their warnings about, assuming teleology in evolution: they are, in a word, “pan-adaptationists”.

As a hypothetical example, imagine a bacterial DNA sequence that is expressed only during the formation of spores to protect the organism during periods of extreme environmental conditions. Knock out the sequence and test the viability of the resulting variant. If the experimental environment doesn’t include the extreme conditions that induce spore formation, the organism will never attempt to express the knocked-out sequence, and so its absence will not be noticed. If the experimenter concludes that the sequence is insignificant or useless, she is mistaken.

True, but I would strongly prefer that adaptation be considered a “diagnosis by exclusion” rather than our first and most important resort. By focusing on adaptation and natural selection, we teeter on the edge of the “teleology trap” and often (maybe even usually) fall in, despite our best efforts to avoid doing so.

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As always, comments, criticisms, and suggestions are warmly welcomed!

--Allen

Analogies, Metaphors, and Inference in Science

Mike Gene, the pseudonymous founder of Telic Thoughts and the author of The Design Matrix: A Consilience of Clues has written the following about metaphors and their application to the detection of intelligent design:

Metaphors such as “fear”, “cost”, “abhor” and “angry”, commonly share the projection of consciousness onto the world. Metaphors such as these represent the human tendency to view the world through anthropomorphic glasses. However, the metaphors employed by molecular biologists are not of this type.
...
Metaphors typically break down when we begin to take them literally.
...
[but] The design terminology that is used in the language of molecular biology does not break down when interpreted literally
...
[T]here is a basic and literal truth to the use of design terminology in molecular biology–these technological concepts are just too useful. Metaphors are certainly useful when explaining concepts to other human beings, yet the design terminology often goes beyond pedagogy–it provides true insight into the molecular and cellular processes. An understanding of our own designed artifacts, along with the principles required to make them, can guide the practice of molecular biology.

Metaphors are a special case of analogies (the other being similes). I have written extensively on the subject of the use of analogies and metaphors in science, and especially in the evolution/design debate here, here, and here. The fundamental question in this ongoing debate is, how do we know an analogy really exists? For example, do we have any objective way to determine if one rock is analogous with another? Or whether an anatomical feature (or a protein/substrate binding site) is analogous to another?

As in the case of agency detection, we think we can do this very easily (just as we can easily identify what looks like design), but I would argue that this is because both "finding" analogies and "finding" design and purpose are capabilities of the human mind (and the nervous system that supports it) that have conferred enormous adaptive value on our ancestors. As in the case of our hypothesized "innate agency/design/purpose detector" (which first becomes active in very early infancy), our "analogy detector" also appears to become active at a very early age, and operates entirely in the background. That is to say, we are almost totally unaware of its operation, and concentrate only on its output.

Our ability to detect (and construct) analogies is, IMO, the core of our intelligence, as demonstrated by the fact that identifying analogies has been traditionally used as one of the most sensitive gauges of general intelligence in intelligence tests (such as the Miller Analogies Test).

In the context of Mike Gene's ideas about metaphors, doing engineering (and especially mathematics) is essentially the construction of highly compact analogies, in which numerical (and sometimes physical) relationships are expressed in the form of abstract symbols. A blueprint is simply a metaphor for a building, just as a chemical formula is a metaphor for the product of the chemical reaction, and a recipe for a cake is a metaphor for the cake. Indeed, many mathematical relationships (especially in the natural sciences) are expressed as equations, which are quite literally metaphors expressed in symbolic form. For example, Newton's equation for force:

F = ma

is a metaphor linking the concept of force with the concepts of mass and acceleration.

In molecular biology we encounter once again the concept of metaphors, for what is the genome of an organism but a highly abstract metaphor for the fully embodied and operating organism itself? I agree with those (and I expect Mike Gene would number himself among them) who assert that the encoding of "life" into a string of nucleotides is indeed the crucial difference between biological "metaphors" and physical "direct necessities". Gravity isn't "encoded" in anything, but proteins are, and so are cells, tissues, organs, organ systems, organisms, and (at least at some level) their behaviors.

So, is there a way to verify if an analogy or metaphor is "real"? In the case of some analogies in biological systems we have an independent double-check on our identification of analogies. This is based on the evolutionary concept of homology, or derivation from a common ancestor. If two structures on two different organisms (say a small bone of the jaw of a reptile and the even smaller bone in the middle ear of a mammal) appear to be analogous (on the basis of size, location, relationship to other bones, etc.) there are at least two different, though related, methods of verifying that these structures are indeed analogous (and not just accidentally similar).

One way is by means of comparative paleoanatomy, in which a series of fossils of known age are compared to determine if there is a connection between the evolutionary pathways of derivation of the structures. If such a pathway can be empirically shown to exist, this would be strong evidence for both the analogous and homologous nature of the objects.

Alternatively one could compare the nucleotide sequences that code for the structures to determine if they are sufficiently similar to warrant a conclusion of homologous derivation. In both cases, evidence for homology, combined with our intuitive "identification" of analogous structure and/or function, both point to the same conclusion: that the two structures are both analogous and homologous.

This is why structures that appear to be analogous, but for which there is no convincing evidence of homology (as in the wings of birds and insects) can present a serious problem to evolutionary biologists, and especially those engaged in biological classification. Such apparent similarities (technically called homoplasies) can either be the result of "true" (i.e. partial) analogy at the functional (and/or structural) level (and therefore assumed to be the result of convergent evolution) or they can be completely accidental. Simple inspection is often insufficient to separate these two hypotheses, and lacking either fossil or genomic evidence, conclusions about the validity of such analogies can be extremely difficult to draw. However, if there is fossil and/or genomic evidence and it points away from homology (i.e. descent from a common ancestor), then the structures can be considered to be analogous, but not homologous.

One of the dangers in invoking analogies and metaphors is overusing the concept of analogy to mean almost anything. Indeed, it is essential in discussions such as these that we be as precise as possible about our definitions, as imprecision can only lead to confusion (at best) and unsupportable conclusions (at worst).

Perhaps the most essential distinction to be made in this regard is between "analogies of description" (which could also be called "semantic analogies") and "analogies of function/structure" (which could also be called "natural analogies"). The former (i.e. "semantic analogies") are merely artifacts of the structure of human cognition and language, as happens whenever we describe an analogy that we have perceived.

By contrast, the latter (i.e. "natural analogies") are the actual similarities in function/structure that we are describing (i.e. that resulted in our identification and description in the first place). As in the Zen koan about the roshi and the novice in the moonlit garden, much of the confusion about which of the two types of analogies we are discussing seems to stem from confusion between the moon that illuminates the garden and the finger pointing at the moon.

In the brief example from Mike Gene's The Design Matrix posted at the head of this thread, the implication is that the analogies we perceive between biological systems and those engineered by humans are "natural analogies"; that is, they are real analogies, and not simply a form of linguistic convenience. However, there is nothing about the finding of an analogy that necessarily verifies that the analogy is "natural" (i.e. "real"), as opposed to "semantic" (i.e. "imaginary"). This would be the case even if one found repeated analogies between complex systems engineered by humans and biological systems that evolved by natural selection. To verify that an analogy is "natural" requires an independent source of validation for the assertion that the analogy is "real" and not merely "semantic". At this stage in my reasoning about this subject I am not at all sure how one would go about this.

However, one thing I am sure of is that simply asserting over and over again that one has perceived an analogy, and that this is all that is necessary to validate the analogy, is not sufficient. Even I am but mad north-north-west: when the wind is southerly I know a hawk from a handsaw.

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As always, comments, criticisms, and suggestions are warmly welcomed!

--Allen

Natural Theology, Theodicy, and The Name of the Rose

AUTHOR: Allen MacNeill

SOURCE: Original essay

COMMENTARY: That's up to you...

"Before, we used to look to heaven, deigning only a frowning glance at the mire of matter; now we look at the earth, and we believe in the heavens because of earthly testimony."
- Jorgé of Burgos, The Name of the Rose, by Umberto Eco (William Weaver, translator)

It's a new year and a new administration (in more ways than one), and over at Uncommon Descent (the former weblog of mathematician and theologian William Dembski), social epistemologist and "intelligent design" apologist Steve Fuller has begun a series of posts on the subject of theodicy.

I read his first post on the subject with some interest, as I have just finished re-reading (for the fifth time) Umberto Eco's novel, The Name of the Rose. When I was a kid, it was inconceivable to me that a person could re-read a book. That was like seeing a movie over again; it just never happened. But now I often re-read books, and any movie or television show can be viewed as many times as one can possibly stand it.

One of the reasons I re-read books is that I've found that I often discover new things in the book on re-reading. What I had never noticed before about The Name of the Rose is that one of its main themes is the relationship between empirical evidence (that is, evidence that we can observe, either directly or indirectly) and faith, as exemplified by the epigram for this blogpost.

What Jorgé of Burgos (a thinly veiled portrait of Jorgé Luis Borges) is speaking about is the relationship between empirical evidence and faith. He laments that in past times one's belief was entirely justified by faith, but now (in the 14th century) one's belief was grounded in empirical observation; that is, evidence derived from the observation of "base matter". Jorgé's theology, which could be called revealed theology, was based on scripture and religious experiences of various kinds (especially as portrayed in the Holy Bible and the biographies of the Christian saints).

The "new" way of thinking that Jorgé laments is natural theology, a branch of theology based on reason and ordinary experience, according to which the existence and intentions of God are investigated rationally, based on evidence from the observable physical world. Natural theology has a long history, reaching back to the Antiquitates rerum humanarum et divinarum of Marcus Terentius Varro (116-27 BC). However, for almost two millennia natural theology was a minority tradition in Christian theology.

The replacement of revelation theology by natural theology represents a fundamental shift in the the theological basis of belief in the existence of God, which began in the 1st century BCE, but which reached the tipping point in the early 19th century. In 1802 the Reverend William Paley published Natural Theology: or, Evidences of the Existence and Attributes of the Deity, Collected from the Appearances of Nature. Charles Darwin himself praised Paley's work, and it had a profound effect on the direction of Christian theology, especially in England and America.

Paley's argument in Natural Theology is that one can logically infer the existence and attributes of God by the empirical study of the natural world (hence the name "natural" theology). Paley's famous argument of the "watch on the heath" was based on the idea that complex entities (such as a pocketwatch) cannot come about by accident, the way simple "natural" objects such as boulders do. Rather, Paley observes that a pocketwatch clearly has a purpose (i.e. to indicate the time) and is composed of a set of designed, complex, interactive parts (the gears, springs, hands, face, case, and crystal of the watch) which we know for a fact are designed. He then argues by means of analogy that living organisms are even more clearly purposeful entities that must have a designer.

I have already pointed out the weaknesses of arguments of analogy. I have also criticized Steve Fuller's arguments vis-a-vis "intelligent design theory" (see here as well).

What I want to do in this blogpost is to analyze Fuller's first blogpost at Uncommon Descent on "ID and the Science of God". Fuller begins with a recapitulation of the definition of "intelligent design" contained in the mission statement of Uncommon Descent:

ID is the the science of design detection — how to recognize patterns arranged by an intelligent cause for a purpose [emphasis added]

Fuller takes this definition quite seriously, arguing that the "intelligence" that does the designing in ID exists "outside of matter" (i.e. outside of the natural, physical universe). He then points out that this "intelligence" is "...a deity who exists in at least a semi-transcendent state. But then he poses the crucial question: "[H]ow can you get any scientific mileage from that?"

I would extend Fuller's question by turning it around: How can one get any theological mileage out of the idea that the existence and attributes of the deity can be inferred from observations of the natural, physical universe? This is precisely the program of natural theology, and it is the reason that I believe that natural theology is both intellectually bankrupt and ultimately destructive of belief in God. And, I am apparently not alone in this second belief; several of the comments on Fuller's post express essentially the same misgivings.

The problem here is the problem of theodicy. Fuller asserts that theodicy was originally a much broader topic than it is today. According to him,

Theodicy exists today as a boutique topic in philosophy and theology, where it’s limited to asking how God could allow so much evil and suffering in the world.

However, according to Fuller, theodicy once encompassed

"...issues that are nowadays more naturally taken up by economics, engineering and systems science – and the areas of biology influenced by them: How does the deity optimise, given what it’s trying to achieve (i.e. ideas) and what it’s got to work with (i.e. matter)? This broader version moves into ID territory, a point that has not escaped the notice of theologians who nowadays talk about theodicy. [emphasis in original]

Setting aside Fuller's historical analysis of the meaning(s) of theodicy (which I believe is both incorrect and the reverse of the actual historical evolution of the idea), I believe that Fuller gives Christians who still believe in the primacy of revelation over reason good reason to be concerned about the theological implications of ID:

"[Some theists are] uneasy about concepts like ‘irreducible complexity’ for being a little too clear about how God operates in nature. The problem with such clarity, of course, is that the more we think we know the divine modus operandi, the more God’s allowance of suffering and evil looks deliberate, which seems to put divine action at odds with our moral scruples. One way out – which was the way taken by the original theodicists – is to say that to think like God is to see evil and suffering as serving a higher good, as the deity’s primary concern is with the large scale and the long term.

I have pointed out in an earlier blogpost that this line of reasoning necessarily leads to the conclusion that God (i.e. the "intelligent designer" of ID theory) is a utilitarian Whose means are justified by His ends. As I have pointed out, this conclusion is both morally abhorrent and contrary to Christian doctrine. Fuller agrees, pointing out that "...religious thinkers complained about theodicy from day one":

"...a devout person might complain that this whole way of thinking about God is blasphemous, since it presumes that we can get into the mind of God – and once we do, we find a deity who is not especially loveable, since God seems quite willing to sacrifice His creatures for some higher design principle."

This was precisely my point in my earlier post, and it parallels Darwin's feeling about the more negative attributes of the deity.

However, Fuller takes a different tack in his analysis of theodicy:

"...it’s blasphemous to suppose that God operates in what humans recognise as a ‘rational’ fashion. So how, then, could theodicy have acquired such significance among self-avowed Christians in the first place...and...how could its mode of argumentation have such long-lasting secular effects...in any field [such as evolutionary theory] concerned with optimisation?

He then goes on to make essentially the same argument as that put forth by almost all ID supporters, an argument by analogy:

We tend to presume that any evidence of design is, at best, indirect evidence for a designer. But this is not how the original theodicists thought about the matter. They thought we could have direct (albeit perhaps inconclusive) evidence of the designer, too. Why? Well, because the Bible says so. In particular, it says that we humans are created in the image and likeness of God. At the very least, this means that our own and God’s beings overlap in some sense. (For Christians, this is most vividly illustrated in the person of Jesus.)

And how, precisely, is this an argument by analogy? Here it is:

The interesting question, then, is to figure out how much of our own being is divine overlap and how much is simply the regrettable consequence of God’s having to work through material reality to embody the divine ideas ‘in’ – or, put more controversially, ‘as’ — us. Theodicy in its original full-blooded sense took this question as its starting point. [emphasis added]

By "overlap" Fuller clearly means "analogy"; that is, how analogous is the "design" of nature (presumably brought about by the "intelligent designer", i.e. God) to human (and therefore divine) "design"? This inquiry, therefore, is based on the assumption that finding such analogies is prima facie proof that "design" in nature is the result of "intelligence" (and therefore, by extension, "divine intelligence").

But, as any undergraduate in elementary logic has learned, arguments by analogy alone are not valid evidence for anything. This is because there is nothing intrinsic to analogies that can allow us to determine their validity. As I have pointed out in an earlier blogpost, all analogies are false to some degree: the only "true" analogy to a thing is the thing itself.

Fuller lists four reasons why theodicy became important at about the same time as natural theology. These are:

• that the widespread publication of the Holy Bible not only facilitated the rise of Protestantism, it also made possible "individual confirmation" of one's "overlap" (i.e. analogy) with the deity;

• that "...theodicists...read the Bible as the literal yet fallible word of God. There is scope within Christianity for this middle position because of known problems in crafting the Bible, whose human authorship is never denied...."

• that "...theodicists...claimed legitimacy from Descartes, whose ‘cogito ergo sum’ proposed an example of human-divine overlap, namely, humanity’s repetition of how the deity establishes its own existence. After all, creation is necessary only because God originally exists apart from matter, and so needs to make its presence felt in the world through matter...."; and

• that the Scientific Revolution shifted the focus of theology from revelation to empirical investigation, grounding belief in God and His intentions in observable reality via arguments by analogy.

Let's summarize all of this before going on. According to Fuller, theodicy entails that:

1) the Holy Bible illustrates the analogies between humans and God;

2) the Holy Bible is an imperfect document, written by imperfect humans (and, by extension, should not necessarily be taken literally);

3) the Cartesian cogito ergo sum provides a paradigm of the analogy between human and divine "intelligence" by pointing to the connections between "supernatural" ideas and "natural" phenomena, and

4) the scientific method, fundamentally grounded in empirical verification, provides the most valid paradigm for understanding reality.

Here is where I find the connection to The Name of the Rose. Umberto Eco has pointed out that the title of his novel has several allusions, including Dante's mystic rose, "go lovely rose", the War of the Roses, "rose thou art sick", too many rings around Rosie, "a rose by any other name", "a rose is a rose is a rose", the Rosicrucians...there are probably as many meanings as there are readers, and more. Eco asserts that the concluding Latin hexameter,

stat rosa pristina nomine, nomina nuda tenemus ("and what is left of the rose is only its name")

points to a nominalist interpretation of his novel (see "Accuracy, Precision, Nominalism, and Occam's Razor".

And I agree with his assessment; the name of the rose is not the rose. Or, as Korbzybski put it, the map is not the territory. However, this conclusion can be taken in one of two ways. According to the first (which is based on Platonic idealism), the idea of the rose is what "matters". That is, the idea of the rose pre-exists the rose, and therefore brings the rose into existence. The idea of the rose, therefore, is what is real (hence "Platonic realism"). This is the approach taken by revelation theologists, natural theologists, and ID supporters: that the "design" of the rose (i.e. the "idea" in the "mind" of the "intelligent designer") comes first, and is made manifest in the actual, physical rose.

However, an alternative interpretation is that the rose comes first; our name for the entities which exhibit "roseness" is based on our perception of the analogies between those observed entities we come to call "roses". This is the approach taken by virtually all natural scientists, especially evolutionary biologists. As I have pointed out elsewhere, the "designer" in this case is nature itself; the environment (both external and internal) of the phylogenetic lineage of the entities we call "roses". The "design" produced by this "designer" is encoded within the genome of the rose, and expressed within its phenotype, which is made manifest by an interaction between the rose's genome and its environment.

This view is perhaps most succinctly expressed by Darwin himself, in the concluding paragraph of the Origin of Species:

It is interesting to contemplate an entangled bank, clothed with many plants of many kinds, with birds singing on the bushes, with various insects flitting about, and with worms crawling through the damp earth, and to reflect that these elaborately constructed forms, so different from each other, and dependent on each other in so complex a manner, have all been produced by laws acting around us. [emphasis added]

Darwin saw the physical world as being entirely regulated by a set of natural laws, including laws which had the effect of producing the "origin of species" and evolutionary adaptations. In his published writings, he declined to attribute the authorship of such laws to a deity, and in his private correspondence he generally refused to speculate on it as well.

This is precisely the same position taken by almost all evolutionary biologists, and is echoed in the words of William of Baskerville, Umberto Eco's protagonist in The Name of the Rose, who at the conclusion of the book says:

"It's hard to accept the idea that there cannot be an order in the universe because it would offend the free will of God and His omnipotence."
- William of Baskerville, The Name of the Rose, by Umberto Eco (William Weaver, translator)

REFERENCES CITED:

Eco, U. (Weaver, W., translator) (1983) A Postscript to The Name of the Rose. Harcourt, Brace, Jovanovitch Publishers, New York, NY, ISBN #015173156X, 84 pages.

For those who are interested, I will be keeping up with Steve Fuller's later posts on this subject at Uncommon Descent. For now, have a happy new year!

As always, comments, criticisms, and suggestions are warmly welcomed!

--Allen

On the Detection of Agency and Intentionality in Nature

AUTHOR: Elena Broaddus

SOURCE: Evolution and Design

COMMENTARY: Allen MacNeill

First, many thanks to the faithful readers who have also continued to pay attention to the Evolution and Design website (the weblog of the "notorious Cornell evolution and design seminar" and the contents contained therein. I am particularly pleased that the hard work and careful thought of the students whose papers have been posted has been recognized, and even moreso that they have been given the highest praise possible: that is, critical analysis.

I would like to draw some more attention to E. Broaddus paper on the “innate” tendency to infer purpose in nature. I have long suspected that humans (and perhaps many vertebrates, especially mammals) have this tendency. As an evolutionary psychologist, I at least partially subscribe to the idea that the human mind is composed primarily of “modules” whose functions are to process particular kinds of sensory information in such a way as to yield adaptive responses to complex environmental information. This is precisely what Broaddus argues for in her paper: that the human mind (and, by extension, the vertebrate “mind” in general) has a module that is adapted specifically for the precise and rapid inference of intentionality in nature. That such an “agency detector” (to use the commonly accepted term for such a module) would have immense adaptive value is obvious. In an environment in which other entities do indeed have “intentions” (i.e. predators, competitors, potential mates, etc.), the ability to detect and infer the possible consequences of acting upon such intentions would confer immense adaptive value on any organism with such an ability.

Furthermore, as Broaddus points out (and as we discussed briefly in the seminar), to be most effective such a detector should be tuned in such a way as to detect virtually all such “intention-indicating” behaviors. This would have the effect of producing a significant number of “false positives,” as any detector that is tuned high enough to detect all actual cases would have such a side-effect.

As Broaddus points out, one of the side-effects of such an “agency detector” would be the detection of intentionality in entities that clearly had no such intentions. If, for example, one of the most important functions of such a detector in humans is to quickly “read” and assess the intentions betrayed in human facial expressions, then it would almost certainly detect human facial expressions in objects in the environment that clearly do not have such expressions, such as rocks, foliage, water stains, etc. This would explain the ability of many humans to “see” human facial expressions in such things as water stains, cinnamon buns, rocks, etc.

Clearly, there are some “natural objects” that do, indeed, have human facial expressions impressed upon them: the faces of the presidents at Mount Rushmore are an example cited ad nauseam by ID theorists. However, I am much more interested in “faces” that humans detect in rocks and other environmental objects that are clearly not produced by human agency. Indeed, the faces at Mount Rushmore constitute a kind of “control” for this ability, as they are clearly the result of intentionality, and therefore can be used to anchor that end of the “agency detection” spectrum (at the other end of which are things like “faces” in clouds, tree foliage, etc.). Somewhere in this spectrum is a cross-over point at which actual intentionality/agency disappears and facticious intentionality/agency takes over. It is the location of that cross-over point that constitutes the hinge of the argument between evolutionary biologists and ID theorists.

Broaddus’s analysis of autism as a possible example of malfunctioning “agency detection” is, IMO, brilliant, and presents an immediately testable hypothesis: that autistic children lack well-tuned “agency detectors,” and that this at least partially explains their well-known indifference to intentional agents, such as other people (including their parents), animals, etc. In people with both full-blown autism and the milder Asperger’s syndrome (sometimes called Aspies”), a common attribute is an impaired ability to infer intentionality (or, in many cases, the mere existence of other minds) on the part of autistics and Aspies. As Broaddus points out, there are clear anatomical and functional differences between autistics, Aspies, and non-impaired people, and that these differences may be correlated with the etiology of these conditions. For example, it is very interesting that there appears to be more (rather than less) neurons in the brains of autistics than in non-impaired people.

This lends credence to the generally accepted hypothesis that the information processing “modules” proposed by evolutionary psychologists are the result of “pared down” neural networks that are speciallized for particular cognitive tasks. Clearly, the agency/intentionality detector in humans functions extremely well and, as the parlance goes, “in the background.” We are rarely conscious of its operation, despite the fact that it is virtually always “on.” This explains, for example, something I first noticed as a young child: that no matter how much I tried, I couldn’t NOT see faces in the patterns in the linoleum on the floor of my grandmother’s kitchen, in the foliage of trees, in rocks, and in photographs of billowing smoke, splashing water, etc. The agency/intentionality detector works extremely efficiently in people of all ages, but especially in children. Indeed, as Broaddus points out, part of becoming an adult consists in learning (usually by trial-and-error) which of the seemingly intentional entities which we perceive all the time actually are intentional agents and actually have intentions vis-a vis ourselves. We must learn, in other words, to critically analyze the constant stream of “positive” agency/intentionality detection events, and discriminate between those that affect us and those that do not. It may be that this discrimination process actually involves the neurological “re-wiring” of the parts of the sensory/nervous system that produces such detection events, and this might explain, at least in part, the decreased ability of adults to believe in the existence of intentional agents in the natural environment.

Broaddus not only presents a cogent hypothesis concerning the existence of such an agency/intentionality detector/module in humans, she proposes several possible ways of testing whether or not such a detector actually exists, and to “map” its dimensions, capabilities, biases, and limitations. I believe that this opens up a very fruitful area of empirical research into such detectors, and can ultimately lead to much more clarity about an issue that so far has generated much more heat than light. I hope that her ideas and suggestions will be followed up by others (I certainly intend to do so), and that further empirical research into this fascinating and little-known capability will add to our understanding of what makes us the peculiar creatures we are.

Update on the Cornell Evolution and Design Seminar

Things have been developing in rather interesting ways in the Cornell "Evolution and Design" seminar. We have worked our way through all of the articles/papers and books in our required reading list, along with several in the recommended list. Before I summarize our "findings", let me point out that for most of the summer our seminar has consisted almost entirely of registered students (all but one undergrads, with one employee taking the course for credit), plus invited guests (Hannah Maxson and Rabia Malik of the Cornell IDEA Club). Two other faculty members (Warren Alman and Will Provine) attended for a while, but stopped in the middle of the second week, leaving me as the only faculty member still attending (not all that surprising, as it is my course after all - however, at this point I view my job mostly as facilitator, rather than teacher).

Anyway, here is how we've evaluated the books and articles/papers we've been "deconstructing":

Dawkins/The Blind Watchmaker: The "Weasel" example is unconvincing, and parts of the book are somewhat polemical, by which we mean substituting assertion, arguments by analogy, arguments from authority, and various other forms of non-logical argument for legitimate logical argument (i.e. based on presentation and evaluation of evidence, especially empirical evidence). Dawkins' argument for non-telological adaptation (the "as if designed" argument), although intriguing, seems mostly to be supported by assertion and abstract models, rather than by empirical evidence.

Behe/Darwin's Black Box: The argument for "irreducible complexity", while interesting, appears to leave almost all of evolutionary biology untouched. Behe's argument is essentially focused on the origin of life from abiotic materials, and arguments for the "irreducible complexity" of the genetic code and a small number of biochemical pathways and processes. Therefore, generalizing his conclusions to all of evolutionary biology (and particularly to descent with modification from common ancestors, which he clearly agrees is "strongly supported by the evidence") is not logically warranted. Attempts to make such extensions are therefore merely polemics, rather than arguments supported by evidence.

Dembski/The Design Inference and "Specification: The Pattern that Signifies Intelligence": Dembski's mathematical models are intriguing, especially his recent updating of the mathematical derivation of chi, his measure for "design" in complex, specified systems. However, it is not clear if empirical evidence (i.e. counted or measured quantities) can actually be plugged into the equation to yield an unambiguous value for chi, nor is it clear what value for chi would unambiguously allow for "design detection." Dembski suggests chi equal to or greater than one, but we agreed that it would make more sense to use repeated tests, using actual designed and undesigned systems, to derive an empirically based value for chi, which could then be used to identify candidates for "design" in nature. If, as some have suggested, plugging empirically derived measurements into Dembski's formula for chi is problematic, then his equation, however interesting, carries no real epistemic weight (i.e. no more than Dawkin's "Weasel", as noted above).

Johnson/The Wedge of Truth: To my surprise, both the ID supporters and critics in the class almost immediately agreed that Johnson's book was simply a polemic, with no real intellectual (and certainly no scientific) merit. His resort to ad hominem arguments, guilt by association, and the drawing of spurious connections via arguments by analogy were universally agreed to be "outside the bounds of this course" (and to exceed in some cases Dawkins' use of similar tactics), and we simply dropped any further consideration of it as unproductive. Indeed, one ID supporter stated quite clearly that "this book isn't ID", and that the kinds of assertions and polemics that Johnson makes could damage the credibility of ID as a scientific enterprise in the long run.

Ruse/Darwin and Design (plus papers on teleology in biology by Ayala, Mayr, and Nagel): Both ID supporters and evolution supporters quickly agreed that all of these authors make a convincing case for the legitimacy of inferring teleology (or what Mayr and others call “teleonomy”) in evolutionary adaptations. That is, adaptations can legitimately be said to have “functions,” and that the genomes of organisms constitute “designs” for their actualization, which is accomplished via organisms' developmental biology interacting with their environments.

Moreover, we were able to come to some agreement that there are essentially two different types of “design”:

• Pre-existing design, in which the design for an object/process is formulated prior to the actualization of that object/process (as exemplified by Mozart’s composing of his final requiem mass); note that this corresponds to a certain extent with what ID supporters are now calling “front-loaded design”, and

• Emergent design, in which the design for an object/process arises out of a natural process similar to that by which the actualization takes place (as exemplified by Mayr’s “teleonomy”).

In addition, the ID supporters in the seminar class agreed that “emergent design” is not the kind of design they believe ID is about, as it is clearly a product of natural selection. A discussion of “pre-existing design” then ensued, going long past our scheduled closing time without resolution. We will return to a discussion of it for our last two meetings next week.

As we did not use the two days scheduled for “deconstruction” of Johnson’s Wedge of Truth, we opened the floor to members of the class to present rough drafts/outlines of their research papers for the course. It is interesting to note that both papers so presented concerned non-Western/non-Christian concepts of “design” (one focusing on Hindu/Indian and Chinese concepts of teleology in nature, and the other on Buddhist concepts of design and naturalistic causation).

Overall, the discussion taking place in our seminar classes has been both respectful and very spirited, as we tussle with difficult ideas and arguments. For my part, I have come to a much more nuanced perception of both sides of this issue, and to a much greater appreciation of the difficulties involved with coming to conclusions on what is clearly one of the core issues in all of philosophy. And, I believe we have all come to appreciate each other and our commitments to fair and logical argument, despite our differences…and even to have become friends in the process. What more could one ask for in a summer session seminar?

D'Arcy Thompson and "Front-Loaded" Intelligent Design

AUTHOR: Salvador Cordova

SOURCE: Marsupials and placentals: A case of front-loaded, pre-programmed, designed evolution?

COMMENTARY: Allen MacNeill

The concept of "front-loading" as described in Salvador Cordova's post at Telic Thoughts bears a remarkable resemblance to the ideas of the Scottish biomathematician D'Arcy Thompson (1860-1948). In his magnum opus, Growth and Form, Thompson proposed that biologists had over-emphasized evolution (and especially natural selection) and under-emphasized the constraints and parameters within which organisms develop, constraints that "channel" animal forms into particular patterns that are repeated over and over again across the phyla.

However, while Thompson's ideas strongly imply that there is a kind of teleology operating at several levels in biology (especially developmental biology), Thompson himself did not present hypotheses that were empirically testable (sound familiar?):

Thompson did not articulate his insights in the form of experimental hypotheses that can be tested. Thompson was aware of this, saying that 'This book of mine has little need of preface, for indeed it is 'all preface' from beginning to end.'

Thompson's huge book (over 1,000 heavily illustrated pages) is a veritable gold mine of ideas along the lines articulated in Sal's post. However, Thompson's underlying thesis is just as inimical to ID as is the explanation from evolutionary biology. His argument is essentially that biological form is constrained by the kind of mathematical relationships that characterize classical physics. That is, there are "built-in" laws of form that constrain the forms that biological organisms can take. And therefore, physical law provides the “front-loading”, not a supernatural “intelligent designer.”

For example, Thompson pointed out that the shape that droplets of viscous liquid take when dropped into water are virtually identical to the medusa forms of jellyfish, and that this "convergence of form" is therefore not accidental. Rather, it is fundamentally constrained by the physics of moving fluids, as described in the equations of fluid mechanics. Thompson's book is filled with similar examples, all pointing to the same conclusion: that biological form is constrained by the laws of physics (especially classical mechanics).

Evolutionary convergence, far from departing from Thompson's ideas, is based on essentially the same kinds of constraints. Sharks, dolphins (the fish, not the mammals), tunas, ichthyosaurs, and porpoises all appear superficially similar (despite significant anatomical differences) because their external shapes are constrained by the fluid medium through which they swim. In the language of natural selection, any ancestor of a shark, dolphin, tuna, ichthyosaur, or porpoise that (through its developmental biology) could take the shape of a torpedo could move more efficiently through the water than one that had a different (i.e. less efficient) shape, and therefore would have a selective advantage that would, over time, result in similar shapes among its proliferating ancestors. The same concept is applied to the parallel evolution of marsupial and placental mammals: similar environments and subsistence patterns place similar selective constraints on marsupial and placental mammals in different locations, resulting in strikingly similar anatomical and physiological adaptations, despite relatively non-homologous ancestry.

This evolutionary argument is now being strongly supported by findings in the field of evolutionary development ("evo-devo"), in which arguments based on "deep homology" are providing explanations for at least some of the seemingly amazing convergences we see in widely separated groups of organisms. Recent discoveries about gene regulation via hierarchical sets of regulatory genes indicate that these genes have been conserved through deep evolutionary time, from the first bilaterally symmetric metazoans to the latest placental mammals, as shown by their relative positions in the genome and relatively invariant nucleotide sequences. These genes channel the arrangement of overall anatomy and body form throughout the course of development, producing the overall shapes of organisms and the relationships between body parts that we refer to when discussing evolutionary convergence.

However, as should be obvious by now, this in no way provides evidence for the currently popular ID hypothesis of “front-loading”, except insofar that it states that the hierarchical control of overall development evolved very early among the metazoa. It provides no empirically testable way to distinguish between an evolutionary explanation and a “design” explanation. Indeed, all of the evidence to date could be explained using either theory.

And so, by the rules of empirical science, since the evolutionary explanation is both sufficient to explain the phenomena and does not require causes that are outside of nature (i.e. a supernatural designer, that is neither itself natural nor works through natural – i.e. material and efficient – causes), evolutionary biologists are fully justified in accepting the evolutionary explanation (and disregarding the “front-loaded ID” explanation.

Only in the case that the kinds of natural causes described above (especially the ability of evo-devo processes to constrain the development of overall form via purely natural means via the known biochemistry of development) can NOT explain the patterns we observe in convergent evolution should we entertain other hypotheses (especially if those other hypotheses are not empirically testable). Only then, and not before…and therefore certainly not now.

FOR FURTHER READING:

For more on Thompson and his work, see:
http://www.google.com/search?hl=en&q=D%27Arcy+Thompson&btnG=Google+Search
and especially:
http://www-history.mcs.st-andrews.ac.uk/Mathematicians/Thompson_D'Arcy.html
and follow the links at:
http://en.wikipedia.org/wiki/D'Arcy_Thompson

Also, a thread that included a discussion of Thompson's work has already appeared at Telic Thoughts http://telicthoughts.com/?p=763

--Allen

Detailed Syllabus for Cornell Evolution/Design Course

BioEE 467/B&Soc 447/Hist 415/S&TS 447: Seminar in History of Biology

Summer 2006 - Syllabus

PREREQUISITES: None (introductory course in evolutionary biology recommended, but not required)

CREDIT HOURS: 4 (does not count toward evolution distribution requirement in biological sciences)

CLASS TIMES: Tuesdays and Thursdays 6-9 PM

CLASS LOCATION: Whittaker Seminar Room, 409 Corson-Mudd Hall.

COURSE FORMAT: The format for each class will be a 90 minute interactive discussion/seminar, in which all participants present their interpretations and opinions of the concepts and readings under consideration. Participants will also have the opportunity to make presentations of their original work. Grades will be based on the quality of a term research paper, due at the end of the course, plus attendance and class participation.

GRADE BASED ON: Attendance and participation in seminar discussions, plus a letter grade on the final research paper (maximum length = 20 pages), for a total of 100 points (electronic/email submission encouraged, but not required):

Course Grade Components................Due On

Proposal for final research paper.......Fri07Jul06
Draft/outline of research paper.........Thu20Jul06
Final research Paper:= 75 points.......Thu03Aug06
Attendance..............= 10 points........overall
Participation............= 15 points........overall

COURSE TITLE: Evolution and Design: Is There Purpose in Nature?

COURSE DESCRIPTION: This seminar addresses, in historical perspective, controversies about the cultural implications of evolutionary biology. Discussions focus upon questions about gods, free will, foundations for ethics, meaning in life, and life after death. Readings range from Charles Darwin to the present (see reading list, below).

The current debate over "intelligent design theory" is only the latest phase in the perennial debate over the question of design in nature. Beginning with Aristotle's "final cause," this idea was the dominant explanation for biological adaptation in nature until the publication of Darwin's Origin of Species. Darwin's work united the biological sciences with the other natural sciences by providing a non-teleological explanation for the origin of adaptation. However, Darwin's theory has been repeatedly challenged by theories invoking design in nature.

The latest challenge to the neo-darwinian theory of evolution has come from the "intelligent design movement," spearheaded by the Discovery Institute in Seattle, WA. In this course, we will read extensively from authors on both sides of this debate, including Francisco Ayala, Michael Behe, Richard Dawkins, William Dembski, Phillip Johnson, Ernst Mayr, and Michael Ruse. Our intent will be to sort out the various issues at play, and to come to clarity on how those issues can be integrated into the perspective of the natural sciences as a whole.

In addition to in-class discussions, course participants will have the opportunity to participate in online debates and discussions via the instructor's weblog at http://evolutionlist.blogspot.com/. Students registered for the course will also have an opportunity to present their original research paper(s) to the class and to the general public via publication on the course weblog and via THE EVOLUTION LIST.

INTENDED AUDIENCE: This course is intended primarily for students in biology, biology and society, history, philosophy, and science & technology studies. The approach will be interdisciplinary, and the format will consist of in-depth readings across the disciplines and discussion of the issues raised by such readings. Although there are no prerequisites, a knowledge of evolutionary biology (equivalent to BioEE 207 and/or BioEE 278) is highly recommended. In addition to registered students, course participants will also include invited guests from the Department of Ecology & Evolutionary Biology, the Paleontological Research Institute, and the Cornell IDEA Club. Members of the general public may only attend class discussions with prior permission of the instructor.

REQUIRED TEXTS: (all texts will be available at The Cornell Store, http://www.store.cornell.edu/)

Behe, Michael (2006) Darwin's black box: The biochemical challenge to evolution. New York, NY, Free Press, 352 pages.

Dawkins, Richard (1996) The blind watchmaker: Why the evidence of evolution reveals a universe without design. New York, NY, W. W. Norton (reissue edition), 400 pages.

Dembski, William (2006) The design inference : Eliminating chance through small probabilities. Cambridge, UK, Cambridge University Press, 272 pages.

Johnson, Phillip E. (2002) The wedge of truth: Splitting the foundations of naturalism. Downers Grove, IL, InterVarsity Press, 192 pages.

Ruse, Michael (2006) Darwin and design: Does evolution have a purpose? Cambridge, MA, Harvard University Press, 384 pages.

OPTIONAL TEXTS: (all texts will be available at The Cornell Store, http://www.store.cornell.edu/)

Darwin, Charles (1859) On the origin of species by means of natural selection, or the preservation of favoured races in the struggle for life, 1st Edition (E. Mayr, ed.), Cambridge, MA, Harvard University Press, 513 pages.
Available online at: http://pages.britishlibrary.net/charles.darwin/texts/origin1859/origin_fm.html

Darwin, Charles (E. O. Wilson, ed.) (2006) From so simple a beginning: Darwin's four great books. New York, NY, W. W. Norton, 1,706 pages.
Available online at: http://pages.britishlibrary.net/charles.darwin2/texts.html#books

Dembski, William & Ruse, Michael (2004) Debating design: From darwin to DNA. Cambridge, UK, Cambridge University Press, 422 pages.

Forrest, Barbara & Gross, Paul R. (2004) Creationism's trojan horse: The wedge of intelligent design. New York, NY, Oxford University Press USA, 416 pages.

Graffin, Gregory W. (2004) Evolution, monism, atheism, and the naturalist world-view. Ithaca, NY, Polypterus Press (P.O. Box 4416, Ithaca, NY, 14852), 252 pages.
Can be purchased online at: http://www.cornellevolutionproject.org/obtain.html

Perakh, Mark (2003) Unintelligent design. Amherst, NY, Prometheus Books, 459 pages.

Ruse, Michael (2000): The evolution wars: A guide to the debates. New Brunswick, NJ: Rutgers University Press. 326 pages.

COURSE PACKET: (all items will be available online at the course website)

Ayala, F. (1970) Teleological explanations in evolutionary biology. Philosophy of Science, Vol. 37: pages 1-15.

Binswanger, H. (1992) Life-based teleology and the foundations of ethics. The Monist, pages 84-103.

Behe, M. (2002) Intelligent design as an alternative explanation for the existence of biomolecular machines. Unpublished manuscript.

Dembski, W. (2005) What every theologian should know about creation, evolution, and design. Orthodoxy Today. Available online at: http://www.orthodoxytoday.org/articles/DembskiDesign.php

Discovery Institute (1999) The wedge. Available online at: http://www.antievolution.org/features/wedge.html

Kitzmiller v. Dover Area School District (2005) Complete trial documents and references. Available online at:
http://en.wikipedia.org/wiki/Kitzmiller_v._Dover_Area_School_District_trial_documents

Mayr, E. (1974) Telological and teleonomic: A new analysis. Boston Studies in the Philosophy of Science, XIV, pages 91 to 117.

Nagel, E. (1977) Teleology revisited: Goal-directed processes in biology. Journal of Philosophy. Vol. 74, No. 5, pages 261-301.

COURSE SCHEDULE:
As noted in the Course Format (above), each class will be a 90 minute discussion/seminar, in which all participants will have an opportunity to present their interpretations and opinions of the concepts and readings under consideration. Only the first two classes will depart somewhat from this format. In these, the instructor will lay out the ground rules for the course and present some basic information on evolution and some of its philosophical implications. Notice that two classes have been *rescheduled* due to holidays and time conflicts. Also note that there is an optional picnic/campfire scheduled for Friday 28 July 2006 at the instructor’s home.

DAY & DATE: Tuesday 27 June 2006
6:00-7:30 Course ground rules and an introduction to evolution, "Darwin's dangerous idea"
7:30-9:00 The Natural Selection Game and discussion of the results and implications

DAY & DATE: Thursday 29 June 2006 *NO CLASS-SCHEDULING CONFLICT*

DAY & DATE: Friday 30 June 2006 *Rescheduled from Thursday 29 June*
READINGS:
Dawkins/The Blind Watchmaker
Ruse/Darwin and Design: Does Evolution Have a Purpose? chapters 1 & 2
6:00-7:30: Natural selection and scientific reasoning
7:30-9:00: Discussion of natural selection, scientific method, and philosophy of science

DAY & DATE: Tuesday 4 July 2006 *NO CLASS-INDEPENDENCE DAY*

DAY & DATE: Thursday 6 July 2006
READINGS:
Dawkins/The Blind Watchmaker
Ruse/Darwin and Design: Does Evolution Have a Purpose? chapter 3 & 4

DAY & DATE: Friday 7 July 2006 *Rescheduled due to Independence Day Holiday*
READINGS:
Dawkins/The Blind Watchmaker
Ruse/Darwin and Design: Does Evolution Have a Purpose? chapters 5 & 6

RESEARCH PROPOSAL DUE: All students must submit a tentative proposal on Friday 7 July 2006

DAY & DATE: Tuesday 11 July 2006
READINGS:
Behe/"Intelligent Design as an Alternative Explanation for the Existence of Biomolecular Machines" (provided in course packet)
Behe/Darwin’s Black Box
Ruse/Darwin and Design: Does Evolution Have a Purpose? chapter 7

DAY & DATE: Thursday 13 July 2006
READINGS:
Behe/Darwin’s Black Box
Ruse/Darwin and Design: Does Evolution Have a Purpose? chapter 8

DAY & DATE: Tuesday 18 July 2006
READINGS:
Dembski/”What Every Theologian Should Know About Creation, Evolution, and Design” (provided in course packet)
Dembski/The Design Inference
Ruse/Darwin and Design: Does Evolution Have a Purpose? chapters 9 & 10

DAY & DATE: Thursday 20 July 2006
READINGS:
Dembski/The Design Inference
Ruse/Darwin and Design: Does Evolution Have a Purpose? chapters 11 & 12

DRAFT/OUTLINE DUE: All students must submit an outline and references on Thursday 20 July 2006


DAY & DATE: Tuesday 25 July 2006
READINGS:
Discovery Institute/The wedge. Available online at: http://www.antievolution.org/features/wedge.html
Johnson/The Wedge of Truth
Ruse/Darwin and Design: Does Evolution Have a Purpose? chapter 13

DAY & DATE: Thursday 27 July 2006
READINGS: Johnson/The Wedge of Truth
Ruse/Darwin and Design: Does Evolution Have a Purpose? chapter 14

DAY & DATE: Friday 28 July 2006
Optional barbeque/picnic and campfire at professor's home, beginning at 6 PM

DAY & DATE: Tuesday 1 August 2006
READINGS:
Ayala/Teleological explanations in evolutionary biology.
Binswanger/Life-based teleology and the foundations of ethics.
Mayr/Teleological and teleonomic: A new analysis.
Nagel/Teleology revisited: Goal-directed processes in biology.

DAY & DATE: Thursday 3 August 2006
READINGS:
Kitzmiller v. Dover Area School District (2005) Judge Jones’ decision.
Ruse/Darwin and Design: Does Evolution Have a Purpose? chapter 15

RESEARCH PAPER DUE: All assigned written work due by 6:00 PM on Thursday 3 August 2006

PROFESSOR: Allen D. MacNeill
G-24 Stimson Hall
255-3357
[email protected]
http://evolutionlist.blogspot.com/

WEBSITES:
For logistical reasons, there are two course websites.

The Course Blog is located online at http://evolutionanddesign.blogsome.com/. This website is administered and moderated by the course instructor (Allen MacNeill, [email protected]), in cooperation with the blog webmaster Hannah Maxson ([email protected]), founder and president of the Cornell IDEA Club. The course blog is open to the public and contains articles, commentary, papers, etc. by students in the course and participants online. Both the moderator and the webmaster are great admirers of the traditional values of the academy: intellectual freedom, personal responsibility, and respect for others. Therefore, the course blog has several rules, which will be strictly enforced:

1. Ad hominem attacks, blasphemy, profanity, rudeness, and vulgarity will not be tolerated (although heresy will always be encouraged). However, vigorous attacks against a member's position are expected and those who cannot handle such should think twice before they post.

2. Long-running debates that are of interest only to a small number of individuals should be taken elsewhere, preferably via private email (i.e. if the moderator gets tired of reading posts concerning the population density [N] of terpsichorean demigods inhabiting ferrous microalpine environments, the posters will be encouraged to "settle it outside").

3. Pseudonyms are permitted but real names are preferred. However, if the moderator suspects that someone is posting under multiple aliases or pretending to be someone else, they will be permanently banned from the blog.

4. Mutual respect and sensitivity towards those with opposing views is essential. In particular, posts containing what the moderator feels is "creation-bashing" by evolutionists or "evolution-bashing" by creationists, will not be tolerated.

The Course Website is located online at http://www.learningrefined.com/. This website is the source for course packets and lecture notes. All students registered for the course should also register at LearningRefined.com (just follow the onscreen instructions), where they can then download the course readings packet and lecture notes (some course packet items require payment before downloading; these items will also be on free reserve).

In addition to the course blog and website, the following websites are recommended as sources of information:

Access Research Network (information & research/intelligent design): http://www.arn.org/
Adventures in Ethics & Science (blog/evolutionist): http://scienceblogs.com/ethicsandscience/
Answers in Genesis (news & commentary digest/young-Earth creationist) http://www.answersingenesis.org/
Anthro-L list at SUNY Buffalo (anthropology listserve/evolutionist): http://listserv.buffalo.edu/user/sub.shtml
Austringer, The (blog/evolutionist): http://austringer.net/wp/
Concerned Scientist (blog/evolutionist): http://danielrhoads.blogspot.com/
Cornell Idea Club (information/intelligent design): http://www.rso.cornell.edu/idea/
Creation News (news & commentary digest/young-Earth creationist): http://www.nwcreation.net/news.html
Darwinian Conservatism (blog/politics/evolutionist): http://darwinianconservatism.blogspot.com/
Design Paradigm (blog/intelligent design): http://designparadigm.blogsome.com/
Discovery Institute (news & commentary digest/intelligent design): http://www.discovery.org/
Dispatches from the Culture Wars (blog/evolutionist): http://scienceblogs.com/dispatches/
Evolgen (blog/evolutionist): http://scienceblogs.com/evolgen/
Evolution at PBS (TV series/evolutionist): http://www.pbs.org/wgbh/evolution/index.html
Evolution at Wikipedia.com (encyclopedia-wiki): http://en.wikipedia.org/wiki/Evolution
EvolutionBlog (blog/evolutionist): http://www.scienceblogs.com/evolutionblog/
Evolution List (blog/evolutionist): http://evolutionlist.blogspot.com/
Evolution News (news & commentary digest/intelligent design): http://www.evolutionnews.org/
Evolution Update (links & sources/evolutionist): http://users.mstar2.net/spencersa/evolutus/
Evolutionary Psychology (listserve/evolutionist): http://groups.yahoo.com/group/evolutionary-psychology/
Evolving Thoughts (blog/evolutionist): http://evolvethought.blogspot.com/
EvoWiki (encyclopedia-wiki/evolutionist): http://www.evowiki.org/index.php/Main_Page
Hpb. Etc/ (blog/history & philosophy of biology): http://drrob.typepad.com/hpb_etc/
ID in the United Kingdom (Blog/intelligent design): http://www.idintheuk.blogspot.com/
iDesign at UCI (blog/intelligent design): http://www.ics.uci.edu/~aasuncio/idesign.htm
Indian Cowboy (blog/evolutionist): http://www.indiancowboy.net/blog/
Intelligent Design at Wikipedia (encyclopedia-wiki): http://en.wikipedia.org/wiki/Intelligent_design
Intelligent Design The Future (blog/intelligent design): http://www.idthefuture.com/
International Society for Complexity, Information, & Design (info/intelligent design): http://www.iscid.org/
Intersection, The (blog/evolutionist): http://scienceblogs.com/intersection/
Loom, The (blog/evolutionist): http://www.corante.com/loom/
National Center for Science Education (news & commentary digest/evolutionist): http://www.ncseweb.org/
Nature (news, commentary, original research/scientist): http://www.nature.com/nature/index.html
New York Times/Science Online (commentary digest): http://nytimes.com/pages/science/index.html
Panda's Thumb, The (blog/evolutionist): http://www.pandasthumb.org/
Pew Forum on Religion and Public Life (links & sources) http://pewforum.org/docs/?DocID=114
Pharyngula (blog/evolutionist): http://scienceblogs.com/pharyngula/
ResearchID.org (online research/intelligent design): http://www.researchintelligentdesign.org/wiki/Main_Page
Science (news, commentary, original research/scientist): http://www.sciencemag.org/
Science & Technology Daily News (news & commentary digest): http://www.scitechdaily.com/
Science & Theology Daily (news digest): http://www.stnews.org/articles.php?category=commentary
Scientific American (news, commentary, original research/scientist): http://www.sciam.com/
Society for the Study of Evolution (information & links/evolutionist): http://www.evolutionsociety.org/
Stranger Fruit (blog/evolutionist): http://scienceblogs.com/strangerfruit/
Talk.Origins (online FAQs/evolutionist): http://www.talkorigins.org/origins/faqs.html
Telic Thoughts (blog/intelligent design): http://telicthoughts.com/
Terra Daily News (news digest): http://www.terradaily.com/
Understanding Evolution (museum website/evolutionist): http://evolution.berkeley.edu/

Genetics and the Explanatory Filter

AUTHOR: Salvador Cordova

SOURCE: An Instance of Design Detection?

COMMENTARY: Allen MacNeill

There is a thread at Uncommon Descent in which the development of a commercial service for identifying Genetically Modified Objects (GMOs) is given as an example of industry use of William Dembski's "explanatory filter." Dembski claims that the "explanatory filter" can unambiguously identify "intelligently designed" entities, especially entitities in which information is encoded in a sequences of digital bits (as in the genetic code in DNA).

As one of the comments on the thread suggested that I would have a difficult time refuting this argument, my interest was piqued, and so here is my reply:

As has already been pointed out numerous times (not the least by William Dembski himself), Dr. Dembski has asserted that all biological entities are designed, as indicated by the fact that their nucleotide sequences are highly improbable, yet tied to a necessary biological function. However, if this is truly the case, then it should be literally impossible to separate GMO sequences from naturally evolved sequences using Dembski's "explanatory filter", since both types of sequences conform to his definition of "complex specified information."

However, since companies are able to distinguish between "natural" and GMO sequences at a level of reliability that real-world companies will pay them handsomely for their services, it is therefore clear that there is something fundamentally different between GMO sequences (i.e. sequences that really are designed by intelligent entities) and "natural" sequences (i.e. sequences that have evolved by natural selection and/or genetic drift). Therefore, I must conclude that, rather than providing evidence for the efficacy of the "explanatory filter," the ability to distinguish between genuinely "intelligently designed" and "natural" nucleotide sequences provides powerful evidence for the assertion that the difference between the two is the result of fundamentally different processes: "design" in the case of the former, and "natural selection/genetic drift" in the case of the latter.

(2) The idea that an "explanatory filter" can clearly and unambiguously distinguish between "intelligently designed" and "naturallly evolved" nucleotide sequences is directly contradicted by our experience with the structure and function of most adaptive genetic sequences. As just one example, consider the following nucleotide sequence: TTGACA-17 base pairs-TATAAT. Those of you with some knowledge of molecular genetics should immediately recognize this sequence as the "core" of a typical promoter; that is, a nucleotide sequence that is "recognized" (i.e. provides a binding site for) RNA polymerase during gene transcription. According to Dr. Dembski's model of "CSI", this sequence can only have come about via "intelligent design", because it has such a low probability of existing that for it to have arisen by chance is negligable.

However, as some of you may know, this sequence is actually the "consensus sequence" for the promoter. There are others, including (but not necessarily limited to) TAGACA-17 base pairs-TATAAT, TACACA-17 base pairs-TATAAT, ACCACA-17 base pairs-TATAAT, and TTCACA-17 base pairs-TATAAT. The probability of RNA polymerase binding to one of these alternative sequences is purely a function of how much the sequence deviates from the consensus sequence (i.e. it will bind least often to ACCACA-17 base pairs-TATAAT, as this sequence differs from the consensus sequence by three base pairs, whereas the other sequences differ by only one or two base pairs). The biological significance of this variability in base sequence in gene promoters is this: the regulation of gene expression is at least partly a function of the frequency at which such promoter sequences are bound to by RNA polymerase.

This means that deviations from the consensus sequence, rather than being "mistakes" which the "explanatory filter" should be able to identify as such, deviations from the consensus sequence are actually tied to the rate of gene transcription, which are in turn tied to rates of gene product function in the cell. For example, a gene product (i.e. protein) that is used very often in the cell would be coded for by a gene for which the promoter is very close to the consensus sequence, thereby causing the gene product to be synthesized more often. By contrast, a gene product used less often by the cell would be coded for by a gene with a promoter sequence that deviated more from the consensus sequence, and therefore would be transcribed and translated less often.

This means that deviations from the consensus sequence, rather than having less biological significance (and therefore more likelihood of existing by chance, and therefore less likelihood of being identified by Dembski's "explanatory filter"), would actually be just as biologically significant as the consensus sequence. In other words, if the "explanatory filter" is to be of any use at all, it must explain why random deviations from the consensus sequence (i.e. the "designed" sequence) are in reality just as important to cellular function as the consensus sequence itself, until suddenly (when none of the base pairs match the consensus sequence) the promoter stops functioning as a promoter at all. You can't have it both ways: either the functions of "deviant" promoter sequences are just as "designed" as the consensus sequences, or they aren't. But this means that essentially all nucleotide sequences are "intelligently designed", making the "explanatory filter totally useless for any meaningful investigation of genetic processes. Philosophically intriguing to a few theologically inclined non-scientists perhaps, but totally irrelevant to biology.

From the standpoint of natural selection, however, functions arising from deviations from the consensus sequence are exactly what one would expect, as natural selection is just as capable of exploiting random deviations as it is of exploiting "designed" (i.e. adaptive) sequences. Indeed, from the standpoint of natural selection, there are no such things as "designed" sequences; nucleotide sequences are only more or less adaptive, as reflected in their frequencies in populations. Some sequences are apparently not adaptive at all (i.e. they are not conserved as the result of natural selection) - we sometimes refer to such sequences as "junk DNA", although that term carries implications that do not reflect what we currently understand about non-adaptive DNA sequences. Other sequences (the ones that the "explanatory filter" is supposed to be able to distinguish) are adaptive at some level. However, the only way to tell if a sequence is actually adaptive is to be able to show, from the level of nucleotide sequence all the way up to phenotypic differences, that there is a statistically significant difference between the reproductive success (i.e. "fitness") associated with one sequence as compared with another. Until this is possible (and we are a long way from it), any attempt to rule out selection as the efficient cause of nucleotide sequences is pointless (as is the "explanatory filter").

--Allen