How similar are phylogenetic trees?

The site you posted and the comments liked to use cars as an example. Is a blue ford four door sedan more similar to a blue chevy sedan or to a white ford pickup? The two sedans are more similar in outward appearance and function but the two fords will have far more parts in common, e. g., might have the exact same engines. This difference doesn’t mean that such comparisons are useless, just that it depends on what aspects are being considered. This difference will also be reflected in a discussion of the historical derivation of current designs (i. e., their evolution).I will also point out a common error made in the video you reference and almost all the comments. That is to not recognize the difference between an observation being evidence for a theory and that observation being proof beyond any possible doubt for that theory. The pervasiveness of both morphological and genetic trees is evidence for the theory of evolution because if these trees did not exist, if life consisted of distinct species or kinds that had no morphological similarity and totally different genetic chemistries that would firmly disprove the theory of evolution. This is not circular logic. If Mr. A is found shot to death and Mr. B is found to be standing over Mr. A and holding a smoking gun than that is evidence that Mr. B is Mr. A’s killer, because if Mr. B was miles away at the time of the murder he could not be the killer. Also, Mr. B could have found Mr. A’s dead body and instinctively picked up the gun. But his holding the gun is still evidence that he might be the killer. Most of the commenters in you reference would misrepresent this as a circular argument: If Mr.B is the killer, we might find him standing over the body holding a smoking gun. We find Mr. B standing over the body holding the smoking gun, therefore he must be the killer. Evidence is just evidence, not proof positive.Also note that neither of the two scenarios described above, 1) strong morphologic and genetic trees and 2) total lack of morphologic and genetic similarity are compatible with the ‘intelligent design’ and the ‘god-didit’ theories. In fact, any observation, positive or negative, is compatible with those two theories. This is why scientists don’t treat those theories scientifically.

I think we have to be very careful in using this phrase, particularly give the position JJ is coming from. ‘Intelligent Design’ and ‘god-didit’ both offer convenient escape hatches in this matter. It might be useful to delineate four possible categories of explanation for the diversity of life:1) an intelligent, capricious entity created all the species individually,
2) an intelligent, capricious entity created a mechanism for all species to evolve as evidenced by the fossil record, phylogenetic trees, etc.,
3) natural processes guided only by the laws of physics, chemistry, and statistics led to the evolution of all species as evidenced by the fossil record, phylogenetic trees, etc.,- 3A) Darwin’s proposed mechanism including later enhancements (the modern synthesis, genetic drift, etc.),- 3B) Lamark’s proposed mechanism,- 3C) for completeness, I’ll throw in Empedocles’ mechanism, which includes random variation but not descent with modification,4) any other scenario one can think of (I can’t think of any, but panspermia maybe).