Monday, March 23, 2009

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.


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


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At 3/23/2009 09:11:00 PM, Blogger dobson said...

simply asserting over and over again that one has perceived an analogy

I see you have been reading Telic Thoughts... that's a pretty good summary of everything on the blog.

At 3/23/2009 10:40:00 PM, Anonymous Anonymous said...

Mike Gene is quite clear that the analogies within cells to human engineering are grounds for suspicion. They're not scientific proof.

At 3/23/2009 11:05:00 PM, Blogger Allen MacNeill said...

I realize that; indeed, that was my point as well. Analogies between biological objects and processes and objects and processes designed by humans could be purely "semantic", and not "real" at all. Simply observing an analogy isn't "proof" of anything, and it's difficult to determine how analogies by themselves could constitute any kind of proof.

Also, analogies between biological objects and processes and objects and processes designed by humans could just as easily be "the other way around". That is, human designers are inspired in their designs by observations of the way living systems are organized. In such a case, the analogy between the biological "model" and the engineered "mimic" would be a "real" analogy, but would say absolutely nothing about whether the biological object/process itself had been designed.

At 3/24/2009 02:54:00 AM, Anonymous Dan said...

I agree with 'dobson', having gotten tired of MikeGene et al.'s semantics since his book came out. Everything and anything is proof of design in his perspective, it seems - there's no critical introspective thinking for MikeGene when it comes to his thesis. (His followers are just impossible to have rational conversations with, for another reason I grew tired of TT.)

Anon., sure, MikeGene is clear that his view isn't science. Yet somehow, he continues to go on for years about how new discoveries fit with his views, supporting them. It's disingenuous at best.

At 3/24/2009 12:55:00 PM, Anonymous chunkdz said...

Dan wrote:

"Everything and anything is proof of design in his [Mike Gene's]perspective..."

Your assertion is shown to be false on page 279 of the book. You should read it so that you don't repeat your mistake.

At 3/26/2009 08:16:00 AM, Anonymous Dave R said...

Good post, Allen. Analogies are neither data nor arguments; suspicions are not hypotheses. And indeed, Gene goes out of his way to say that ID is not science (yet). But he wants it to be taken as scientific argument, he talks endlessly about scientific examples, and he invokes recent science papers as "evidence" for his "suspicions. Disingenuous is a pretty polite term for that kind of behavior.

For a scientist, it will take something beyond suspicions before he is worth listening to. And I don't see him, or any of his acolytes, daring to test those suspicions with any actual work. Words are all they have, and semantic weaseling is a poor substitute for actual data.

At 3/31/2009 08:43:00 AM, Anonymous Anonymous said...

Mike Gene's reply is here:


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