The starting assumption is 200 separate starting points. If there is no relationship among species, there should be no nested hierarchy connecting them, and thus a star tree would be the expected result of analysis. What are your starting assumptions? What would you expect from 200 separate starting points, and why?
Millions. Millions and millions and millions of them. You know, they accumulate over time, and as each lineage splits, they do so independently in each lineage, and then that lineage splits again, and so on and so forth. They accumulate on every single branch on the tree. And since those 54 genes are present in the same genome, in each individual species, they each record the same genealogical history, which is why we get the same tree.
Not relevant to the question at hand, but yes there are equations for the fixation of mutations as a function of population size, selection coefficiency, frequency, and so on.
Because thereâs no reason for it. We donât expect things we have no reason to expect, obviously.
Since there are such an enormous number of possible trees (because thereâs an enormous number of functionally equivalent similar sequences) with 200 species, that we should get the same tree from independent loci simply as a byproduct of functional constraint is incredibly unlikely.
On the other hand, since genealogical history is recorded in genes, the consilience of independent phylogenies is straightforwardly predicted by common descent(the trees are similar because the genealogical history is similar).
So since we do have reason to expect consilience of independent phylogenies on common descent, and we do not have such a reason on independent origins (here we at most can expect mere similarity of sequence, but not similarity of trees for reasons just explained), the evidence massively supports common descent over separate origins.
Itâs like you forgot the last 7 years of exchanges weâve had on this topic before. Do I now go copy-paste the same explanations given ~200 times over the last half a decade or did that suffice? That was rhetorical of course, you will understand none of this. But here we are.
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Based on Beheâs design method and Ewertâs common design hypothesis I would expect exactly what we are seeing. A large group of common genes among species and also unique genes that help generate their differences. This appears to be part of the cause of the nested structure we are observing.
I LOVE this. It it displays all the indications we expect from evolution, then it must be designed. BRILLIANT! 
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That just shows that you donât really understand how nested hierarchies work and how they arise. In the star tree expected from separately created species, shared genes all arise at the root and unshared ones on separate branches of the star. No nested hierarchy at all. You have entirely failed to identify a reason for nested hierarchy. This conversation seems beyond your ability.
Bill, youâre showing your contempt for/lack of understanding of the scientific method again.
Scientific predictions of your hypothesis are not based on any personâs method (real or in this case, imaginary) or another hypothesis. They come from the mechanism.
Hi John
Winston appears to be using a. star as the null hypothesis when testing the tree pattern and the dependency graph.
Doesnât deal with sequences, nor consilience between trees derived from different data sets.
You are correct. And?
Why does it appear that way to you, Bill?
AND this is why I praise Ewert, because he states a testable hypothesis when no one else in ID will dare. There is nothing stopping anyone from testing Dependency Graph hypotheses in the same way as independent origin hypotheses, and no one could criticize the application of accepted methods for phylogenetic data. (As a statistician I would recommend considerations of multiple testing, but thatâs a fiddling little detail.)
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