This thread is for discussion of the test I proposed to iamnotaparakeet regarding baraminology (the prevailing view among the more serious creationists) and evolutionary biology (the prevailing view in most of the academic community). Specifically:
Orwell wrote:
If baraminology is correct, then phylogenetics should only work within a kind, whereas if evolution is correct, it should work across a much broader range of species. That is, the interspecies genetic similarities that imply that two organisms are closely related should hit some kind of wall that roughly defines a baramin. If there is some such disconnect in phylogenomic data once you hit the boundaries of a kind, then common descent has been refuted and evolution is bunk. If there is no such wall, then baraminology can be rejected for failing to provide a useful taxonomic scheme, as we can't demonstrate any divide between different "kinds."
If you agree with those testable predictions, then I propose a challenge: we will actually go through the sequenced genomic data (much of it is publicly available on the internet) and run it through standard phylogenetics software (much of which is open-source and uses publicly known algorithms so you can be sure I'm not fixing the results) in order to see which prediction is correct. I have access to a powerful Linux cluster we can use for the heavy computations, since many of the calculations could take several weeks to run on a typical home computer.
iamnotaparakeet wrote:
I accept your challenge on the term that you clearly define your terms and show your method of attaining your results.
So, the first task is to define the parameters of our experiment. I can perform the analyses using standard phylogenetics software packages such as MrBayes, GARLI, Mesquite, Clustal, and Mafft (and PAUP* if I can get access to it). Most of these programs are freely available, so I can walk any interested person through the use of them if you are interested in verifying my results. Be warned that MrBayes requires insane amounts of computing time to get any reasonable results, but I believe that any relatively modern home computer should be able to handle the others.
Now, we must decide on a group of organisms to study. We want a sample of organisms which includes some species within the same "kind" and some outgroup organisms that baraminologists would unambiguously classify as being a different kind. I would like to leave this choice up to iamnotaparakeet to ensure that the selection is a fair test of baraminology's predictions, but for the sake of computational considerations I would request that all organisms chosen be predicted to be relatively close together according to the evolutionary standpoint, eg no comparing mollusks to monkeys. Such a comparison could be made, but to do it well would require much larger datasets and several months of time on a supercomputer. Given your interest in parakeets and related species, perhaps that could be an avenue we might explore.
We also need to agree beforehand on what will constitute a disconnect in the phylogenetic data that can be regarded as separating two hypothetical "kinds." My first attempt at a definition would be that molecular genetic homology would not likely exist between two different kinds, and if it did it would not be linked to evolutionary relationships, meaning we would have no reason to expect consistent results across different genes or different techniques. So, if we examine (for instance) 20 unlinked nuclear genes and almost all produce the same proposed evolutionary relationships, and continue to do so under different phylogenetic tests (the main three are maximum parsimony, maximum likelihood, and Bayesian posterior probability) then we must conclude that there is some genome-wide link between the species being analyzed and they are related, contradicting the prediction of baraminology that different kinds are unrelated. If, on the other hand, the different genes and different tests give different or inconsistent results, then phylogenetics has failed, undermining a key prediction of evolutionary biology that we should be able to ascertain relationships among species from their genetic sequences.
Hello, I stumbled onto this site and found this thread to be interesting. I like how you broke down these two competitive theories and laid out testable observations to see which of the two hold more water. There are already results done about different genes in related species and were published in journals. If you agree with your criteria determining baraminology and evolutionary biology then the latter is completely wrong. Incongruence (conflicting results) between phylogenies is very common.
(I'm not able to post any links because of the rules of this site). But here is a quote from nature:
"One of the most pervasive challenges in molecular phylogenetics is the incongruence between phylogenies obtained using different data sets, such as individual genes"
18 Jul 2010, 2:55 am
