Hi Ashwin,
Thanks for the various references.
What I glean in reading them carefully is that biology (in general) and its major theory, evolution (in particular), are not completed works. The theory and its formulation are always being refined as biologists do their work.
So yes, the popular summaries of evolution often do not do justice to the complexities of working with the theory in real life. Some popular summaries are sloppy, and use tautological definitions. The papers you have cited are useful reminders that we have much still to learn, and much to refine even in what we have already learned.
Having cited the papers, however, you commit the non sequitur fallacy by claiming that the whole theory of evolution should be discarded. Not improved and refined, but trashed.
Actually, it is not in the least what you are saying. I draw your attention to the statement you seem to have overlooked:
Moreover, note the date of publication: 2007. Since then, Theobald et al. published a study based on a fourth kind of evidence, genomic. The only question raised about Theobald’s work is whether the nested hierarchy goes all the way back to a single first ancestor, or whether it disappears in a prokaryotic bush over a billion years ago.
Let me repeat that: none of the work you have cited disputes the ability to reliably build nested hierarchies going back hundreds of millions, if not billions, of years; and more recent genomic studies have reinforced the reliability of the nested hierarchies. The papers you cite demonstrate only that the jury is still out as to whether you can get back to a single ancestor 2 or 3 billion years ago.
So what’s the problem? In a nutshell: you seem, my friend Ashwin, inclined to leap to the unwarranted conclusion that any claim of a nested hierarchy in the animal kingdom, or among tetrapods, or among mammals, or even among primates, is just garbage non-science. But none of the evidence you have cited even begins to support this conclusion.
We can infer a more refined version of common ancestry, one in which Pan Troglodytus and H. Sapiens share a common ancestral population; in which the ape family and the canine family share a common ancestral population; in which the mammal class and reptile class share a common ancestral population; and so forth. This is the something that even the tree-detractors admit, per one of your block quotes:
I imagine that after pausing for another week or two, you will be tempted to try for a third time to find even more papers that raise the question of whether nested hierarchies can reach back to a single universal common ancestor (or not). And then you will once again be tempted to claim that the whole theory of evolution, including more modest and widely accepted corollaries such as the common ancestry of primates, is awash with hypocrisy and error. If you do succumb to the temptation, you will be wrong again.
Please prove me wrong, Ashwin. Please spare yourself and your readers the unfruitful effort of analyzing the same questions over and over again, with the only difference being a new set of papers that once again do not say what you say they say.
Surely we have better ways to redeem the time, I submit. I draw your attention to the fact that you have not yet responded to these issues
But if you prefer not to address those issues, so be it.
Grace and peace,
Chris Falter