Joined: May 2002
You argue that designed objects will not produce nested hierarchies. I already gave the aircraft example, let's consider the example a bit further. Consider all machines that use gasoline as a fuel. Within that set you have various subsets, such as those that move and do not move. Of those that move, some fly, others move along the surface of the earth. In the latter, you have various numbers of wheels, such as 2, 4, 6, 8, …, and a few outliers with odd number of wheels. Of those with 4 wheels, you have different ratios of interior volume to overall size (eg, vans have a higher ratio). Of those with lower ratios you have different carburetors (fuel injection for sports cars), and so forth. I am contriving this example off the top of my head, but perhaps you can explain why this cannot be a case of a nested hierarchy. In support of your claim you pasted a few paragraphs from a web document which does not support your claim. The web document is discussing the relationships, across designed objects, of characters which have no influence on performance or are constant over the entire set. What we have called in this thread "arbitrary design decisions."
Did you even read the quote? The very first sentence pointed out that anything can be subjectively classified into a nested hierarchy if you arbitrarily pick characters. This is exactly what you do above. The point is that your "tree" would not be produced by an analysis of other subsystems of gasoline-driven machines, e.g. tires, liscense plates, GPS units, radios, onboard computers, whatever. On the other hand, in biology there are a large number of systems (genes, limbs, skulls, etc.) that produce highly-congruent nested trees. Other fairly similar examples are things like languages and scribe-copied documents, both of which are produced by a process of copying and gradual modification (although in these cases the possibility of lateral transfer is somewhat higher than it is in eukaryote biology).
As for web references, if they cite the primary literature then you either have to show they are mis-using the literature, or that the literature itself is wrong. Theobald cites a large number of papers discussing the difference between arbitrary and natural hierarchies -- designed objects like cars and planes produce the former, copied & gradually modified objects (like languages, scribe-copied documents, and...organisms) produce the latter.
I'll include some of Theobald's refs so that interested parties can look them up:
Archie, J. W. (1989) "A randomization test for phylogenetic information in systematic data." Systematic Zoology 38: 219-252.
Faith, D. P., and Cranston, P. S. (1991) "Could a cladogram this short have arisen by chance alone?: on permutation tests for cladistic structure." Cladistics 7: 1-28.
Farris, J. S. (1989) "The retention index and the rescaled consistency index." Cladistics 5:417-419.
Felsenstein, J. (1985) "Confidence limits on phylogenies: an approach using the bootstrap." Evolution 39: 783-791.
Hillis, D. M. (1991) "Discriminating between phylogenetic signal and random noise in DNA sequences." In Phylogenetic analysis of DNA sequences. pp. 278-294 M. M. Miyamoto and J. Cracraft, eds. New York: Oxford University Press.
Hillis, D. M., and Huelsenbeck, J. P. (1992) "Signal, noise, and reliability in molecular phylogenetic analyses." Journal of Heredity 83: 189-195. PubMed
Ringe, D. (1999) "Language classification: scientific and unscientific methods." in The Human Inheritance, ed. B. Sykes. Oxford: Oxford University Press, pp. 45-74.
You seem to be extrapolating from the discussion given there on arbitrary design decisions to conclude that designed objects cannot produce nested hierarchies. Perhaps I am misunderstanding you.
Of course designed objects can produce just about anything, because a hypothetical designer can always be invented who wants to produce X for goodness-knows-what reason. This is a major problem for ID "theory", no predictions are made unless some specifications are put on the hypothetical IDer, and no one wants to even hypothesize any such specifications (you don't have to have foreknowledge of the designer, just a hypothesis...this is how science proceeds).
But you said that ID predicts congruent phylogenies. I am arguing that this is not established or even likely based on what we know about designed objects.
Is there more than one cost function?
This section seems like you are trying to say something about how the designer would design things so that congruent phylogenies resulted due to functional constraints, or something. But what you have to explain, in order to explain things as well as current theory, is how all of those arbitrary characters (many of them, such as DNA degeneracy, absolutely known to be functionless differences) produce statistically the same nested hierarchical trees! If you can't do that then there's no reason to switch from the current explanation.
Can homologies arise from different genes?
You next go on to discuss homologies, but I'm not sure what the point is. You state that paleontologists can easily distinguish between the placental wolf and marsupial wolf skulls, as though I had stated otherwise. Of course they can, they can also easily distinguish between the bat's wing and human hand, but this does not prevent the pentadactyl pattern from being claimed as evidence for evolution. You pasted a figure of the two skulls which appear highly similar yet are supposed to have evolved independently. You say the similarities are "superficial." I have heard this said many times before, but how is it that these similarities are superficial whereas homologies such as the pentadactyl pattern, which exhibit a large degree of variance (compare the porpoise, bat and horse) are significant?
Because the homologies all correlate with each other to a high degree of statistical confidence, producing a Linnean-type classification, whereas those features that you would expect would be the important features (as revealed by you example of classification of gas-driven machines based on function, or John Bracht's imaginings that amino acid sequence won't turn out to be largely degenerate with respect to structure and function after all) in fact don't correlate with the Linnean-type classification.
If the genes and proteins of penguins, sharks, dolphins, seals, etc. grouped together, and bats and birds grouped together, etc., then you'd have an argument, but they don't. This is a massive mystery from an ID perspective but easily explained by evolution.
We should also note that homologies can develop from different genes, or otherwise follow different development patterns.
This is an argument of Wellsian origin and depends largely on obfuscatory use of quotes and words like "different" (and Wells' unique views about the unimportance of DNA, which are rebutted in detail this ISCID thread). Similar genes perform similar developmental functions a very long ways back, e.g. Hox genes and front-to-back patterning:
An interesting challenge?
Finally, you issued a challenge which sounded interesting but, forgive me if I am slow this morning, I had trouble following. You wrote:
If the hypothesized IDer decided that there needed to be some carnivorous canine-type critters in Australia, why bother with all the genetic engineering that would be required, when a simple aboriginal boat sufficed to bring dingos to Australia only ~15,000 years ago? -- Yersinia
Can you elaborate a bit?
You and Cre8tionist have proposed that convergences like the placental/marsupial wolf are better explained by intelligent design for the same function.
I pointed out that rather than the "same" design being transplanted, it looks more like it was independently invented by modification of different starting points, and that the convergence is superficial in that the true relationships of the organisms remain clear based on homologies.
But, if you are going to maintain the hypothesis that ID accounts for the complex carnivory specializations of wolves and thylacines, you have to explain why it appears that the design wasn't transplanted, but rather re-invented. If a designer wanted carnivores in Australia, it would have been much easier just to put some dogs on a boat, as the stone-age Aborigines did, rather than do all of that complex creative genetic engineering twice in two different ways.
Ditto for carnivorous marsupial "cats" in isolated south America, cacti vs. south African succulents, lemurs in Madagascar, Hawaiian honeycreepers, and of course Darwin's finches. Why should independent design correlate so well with geographical isolation? Did the IDer not know of boats?