Posted: Feb 25, 2014 7:52 pm
by Rumraket
questioner121 wrote:
Skate wrote:Damn, Calilasseia! Nice post.


Is it correct that your argument sums up to amount to something akin to "you weren't there, so you can't know?" Others have said this, but I'd like to confirm that this is the case.

If so, I'd like to ask you how you think the Hawaiian Islands were formed.

Obviously "you weren't there, so you can't know?" applies.

No it doesn't. What part of probabilistic reasoning and building observationally falsifiable models - is escaping your comprehension here?

That's how we can convict rapists and murderers without "having been there" ourselves to witness them commit their crimes. They leave evidence behind.

questioner121 wrote:The point I'm trying to get across, with huge difficulties, is that the evidence supporting common ancestry is severely lacking data.

No it isn't.
A formal test of the theory of universal common ancestry
Universal common ancestry (UCA) is a central pillar of modern evolutionary theory1. As first suggested by Darwin2, the theory of UCA posits that all extant terrestrial organisms share a common genetic heritage, each being the genealogical descendant of a single species from the distant past3, 4, 5, 6. The classic evidence for UCA, although massive, is largely restricted to ‘local’ common ancestry—for example, of specific phyla rather than the entirety of life—and has yet to fully integrate the recent advances from modern phylogenetics and probability theory. Although UCA is widely assumed, it has rarely been subjected to formal quantitative testing7, 8, 9, 10, and this has led to critical commentary emphasizing the intrinsic technical difficulties in empirically evaluating a theory of such broad scope1, 5, 8, 9, 11, 12, 13, 14, 15. Furthermore, several researchers have proposed that early life was characterized by rampant horizontal gene transfer, leading some to question the monophyly of life11, 14, 15. Here I provide the first, to my knowledge, formal, fundamental test of UCA, without assuming that sequence similarity implies genetic kinship. I test UCA by applying model selection theory5, 16, 17 to molecular phylogenies, focusing on a set of ubiquitously conserved proteins that are proposed to be orthologous. Among a wide range of biological models involving the independent ancestry of major taxonomic groups, the model selection tests are found to overwhelmingly support UCA irrespective of the presence of horizontal gene transfer and symbiotic fusion events. These results provide powerful statistical evidence corroborating the monophyly of all known life.

In this paper, several different models are compared in their ability to reproduce the patterns we find in DNA using comparative genetics. The author does NOT just use data from "closely related species". He picks orthologous proteins shared in all of life(that's what the 'ubiquitously conserved proteins' phrase means), from bacteria to homo sapiens. Last I checked, bacteria were NOT closely related to humans.
Beyond Reasonable Doubt: Evolution from DNA Sequences

We demonstrate quantitatively that, as predicted by evolutionary theory, sequences of homologous proteins from different species converge as we go further and further back in time. The converse, a non-evolutionary model can be expressed as probabilities, and the test works for chloroplast, nuclear and mitochondrial sequences, as well as for sequences that diverged at different time depths. Even on our conservative test, the probability that chance could produce the observed levels of ancestral convergence for just one of the eight datasets of 51 proteins is ≈1×10−19 and combined over 8 datasets is ≈1×10−132. By comparison, there are about 1080 protons in the universe, hence the probability that the sequences could have been produced by a process involving unrelated ancestral sequences is about 1050 lower than picking, among all protons, the same proton at random twice in a row. A non-evolutionary control model shows no convergence, and only a small number of parameters are required to account for the observations. It is time that that researchers insisted that doubters put up testable alternatives to evolution.

This is a direct test of the prediction of evolutionary theory that sequences of homologous proteins from different species should converge as we go further and further back in time. As it says right there in the abstract. Go into the paper and read all about it.

questioner121 wrote:The abundance of data that is used to support common ancestry is based off observations from closely related species. This is then being combined with other sets of data with observations from closely related species to "confirm" common ancestry.

This has just been directly demonstrated to be false.