Today is a little busy in the real world, but I look forward to continuing our illuminating discussion soon, and trust in your patience in the mean time.

If you have a little time today, I would still be interested in your response to my comment #54, regarding hypotheses in ID explanations.

Okay I take the blame for not communicating well, I am trying to use two different definitions at once. Let me give you some background on nested hierarchies.

Nest hierarchies were invented by Carolus Linnaeus who understood biological organisms to be designed. He wrote in the preface to a late edition of Systema Naturae:

Creationis telluris est gloria Dei ex opere Naturae per Hominem solum — The Earth’s creation is the glory of God, as seen from the works of Nature by Man alone. The study of nature would reveal the Divine Order of God’s creation, and it was the naturalist’s task to construct a “natural classification” that would reveal this Order in the universe.

Under Linneaus’ system not every feature had to fit because it was an “artificial classification.” You just needed to get things in a general groups. In this use of the term, there is no problem putting designed things into nested hierarchies.

When nested hierarchies are used in the Darwinian sense, features need to line up much more stringently. If the theory is correct, you should be able to describe the exact branching of the tree. But in fact you can’t, you can’t get any closer than an approximation, which is no better than the system Linneaus divised under the assumption of design.

The bacteria/eukaryote/archae is perfect example. It is easy to place organisms into one of the three groups, but good luck trying to find the tree from whence they came.

However, what you or I would wager is not really evidence. I think this would be a genuinely interesting and instructive exercise to try, and the results should be quite publishable. I hope that someone reading this will be inspired to try it.

In reply to Jehu, comment #45: with all due respect, I do not actually make your point, nor do I agree with it, as suggested by the subtle clue in my next sentence “This is very, very, very, very far from being the case with living organisms.” Living organisms overwhelmingly do fit into a nested hierarchy in the way that human-designed artefacts, as we both agree, do not.

Actually we do not agree. You in fact made my point originally. Let’s look at what you actually said.

On the contrary, it is not usually possible to arrange human-designed artifacts into an unambiguous nested hierarchy. Try it with cars – should you make the first level split according to engine size, country of origin, manufacturer, fuel source, transmission type, body style, passenger capacity, etc., etc.? Choosing any of these as the primary split will give you a different nested hierarchy, and there is obviously no particular reason to claim that one of these is the “right” or the “natural” one.

To begin with, this is a problem with biological organisms as well. For example, according to the Rokas article, in the elephant/sirenian/hirax clade 64% of parsimony informative mitochondrial features support and alternative tree. In the chordate/arthopod/nematode clade, in a study of over 1000 parsimony informative characters, 57% supported an alternative tree. And as we have already seen, in the bacteria/eukaryote/archae clade there is not tree to speak of.

Now with cars, I would wager that putting cars into makes, models, and years would probably create a nested hierarchy consistent with the highest percentage of parsimony informative characteristics. Many features will obviously contradict but hey – that is how it is with biology as well.

Thanks for finding a copy of the Scientific American article. I was aware the diagram was from that article but I couldn’t find it on online.

Note that from this article, Doolitte does not believe the evidence supports common descent from a single common ancestor. As the caption states,

This “tree” also lacks a single cell at the root; the three major domains
of life probably arose from a population of primitive cells that differed in their genes.

The article notes that the diagram is actually “misleadingly simple.”

Though complicated, even this revised picture would actually be misleadingly simple , a sort of shorthand cartoon, because the fusing of branches usually would not represent the joining of whole genomes, only the transfers of single or multiple genes. The full picture would have to display simultaneously the super-imposed genealogical patterns of thousands of different families of genes (the rRNA genes form just one such family).

Unless you have drunk the cool-aid, you have to realize that there is no evidence of common descent in the eukaryote/bacteria/archaea clade. You have to come up with so many hypothesis and theories to explain how the mosiac of features arose by common descent that your claim that common descent is powerful because of its “observations explained per hypothesis” completely fails.

(A) a statement like “the designer chose to provide the Asian tiger mosquito with wings” is a hypothesis.

(B) a statement like “the designer chose to provide the monarch butterfly with wings” is a different hypothesis to the one mentioned in (A)

(C ) these types of hypotheses are required by ID theory

(D) the choices made by the designer to provide different species with wings were made independently of each other

(E) there are exactly 761,600 species of living and extinct winged animals (of course there are not, but if you have a more accurate estimate of this number you are welcome to substitute it).

Regarding the eukaryote/bacteria/archaea clade, those interested can find your diagram in context (always a helpful thing to do) in a 2000 Scientific American article posted at http://shiva.msu.montana.edu/c.....ooting.pdf. The caption indicates that it is intended as a schematic or symbolic representation of the hypothesis that there was “rampant lateral gene transfer” between the various unicellular lineages that later gave rise to existing prokaryotes and eukaryotes. This is an article in a popular scientific magazine that proposes an idea of how the TOL will look when its roots are better known. To find out which of these links are currently supported by hard evidence, it is necessary to get into the primary research literature.

The design explanation requires about 761,600 hypotheses, one for each of the independent choices that the designer made to put wings on each species that has them (about 1,100 species of bats, 10,000 species of birds, maybe 750,000 species of insects, and a few hundred pterosaurs).

That is simply not true.

Just becuase the theory of common descent can wave its hand and claim a simple explanation for common feature doesn’t mean the evidence actually fits the pattern of common descent. And although your theory sounds quite simple in a High School text book, in real life, after you are done with the special pleading horizontal gene transfer, homoplasy, and convergence your theory isn’t nearly so tidy and in fact still cannot determine where the branches of the tree of life actually connect.

Have you even bothered to see what the “tree of life” looks like for the eukaryote/bacteria/archea clade? I posted the link.

http://bp0.blogger.com/_DZH2cm.....f_Life.jpg

This is an elegant theory?

However, it is interesting to know that at least some ID proponents accept common descent. I still think that ID requires far more ad-hoc hypotheses than common descent does.

Incidentally, I don’t think genotype versus phenotype is really the issue here. Both morphological and molecular data can be used in cladistic analysis and the approach is essentially similar for both types of data. For the reasons already discussed, it is possible for there to be apparent inconsistencies within either of these types of study, as well as between them. Many studies combine morphological with molecular data, the “total evidence” approach.