In comment # 20 at http://specifiedcomplexity.freehostia.com/?p=232 PvM said:

“ID relies on the concept of analogy to infer design. Science does the hard work to provide mechanisms, pathways and provides analyses of the data to support their conclusions. That’s the big difference. How do we know an analogy really exists?”

This was precisely my point in my blogpost on identity and analogy in science (see http://evolutionlist.blogspot.com/2006/06/identity-analogy-and-logical-argument.html), and brings up a series of questions that are central to both evolutionary biology and intelligent design theory. Do we have any objective way to determine if one rock is analogous with another, for example? Or whether an anatomical feature (or a protein/substrate binding site) is analogous to another? As in the case of telology, 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/purpose are capabilities of the human mind/nervous system that have conferred enormous adaptive value on our ancestors. As in the case of our putative 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 probably the core of our “intelligence,” as demonstrated by the fact that identifying analogies has been traditionally used as one of the most sensitive guages of general intelligence (i.e. “g”) in intelligence tests (such as the Miller Analogies Test). As more than one participant in this thread has pointed out (Sal, I think you were first), doing mathematics is essentially the construction of highly compact analogies, in which numerical (and sometimes physical) relationships are expressed as abstract symbols.

Interestingly, in the case of some analogies in biological systems we have an independent double-check on our identification of analogous things. 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.

BTW, 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 systematists/taxonomists and those engaged in cladistic analysis. 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 can be insufficient to separate these two hypotheses, and lacking either fossil or genomic evidence, conclusions about actual analogy 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.

In the same comment, PvM also wrote:

“I also think that Sal 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 “anaologies 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.