Evolution vs Baraminology: the empirical showdown.
iamnotaparakeet
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Perhaps, but for a straight guy to say that to another straight guy that would seem weird, (yes related to social attitudes towards gender roles, but we won't get into that) And I assumed that was sarcasm, given that it is also used sarcastically towards the opossite sex.
From Evolution vs Baraminology to the etymology of Honey, getting off-topic is inevitable sometimes

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Not abandoned, just delayed. I've been busy at work and I had some unforeseen technical difficulties this past weekend. Thanks for reminding me though, and feel free to bump the thread if I start neglecting it again.
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iamnotaparakeet
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Not abandoned, just delayed. I've been busy at work and I had some unforeseen technical difficulties this past weekend. Thanks for reminding me though, and feel free to bump the thread if I start neglecting it again.
What kind of technical difficulties?
iamnotaparakeet
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That sucks. Hope the weather there wasn't as warm as it was here.
Probably warmer; I'm in Miami.
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iamnotaparakeet
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That sucks. Hope the weather there wasn't as warm as it was here.
Probably warmer; I'm in Miami.
Temperature in the upper 80's to mid 90's with near 100% relative humidity?
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.
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"
(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"
I've already done a little bit of this kind of analysis in another project, and I haven't seen what you claim. There are often some minor discrepancies depending on what gene is looked at, but the overall picture is usually quite consistent across the genome.
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(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"
I've already done a little bit of this kind of analysis in another project, and I haven't seen what you claim. There are often some minor discrepancies depending on what gene is looked at, but the overall picture is usually quite consistent across the genome.
In the Nature's article is said:
"One of the most pervasive challenges in molecular phylogenetics is the incongruence between phylogenies obtained using different data sets, such as individual genes"
This means that it produces unreliable results, an happens most of the time. Since I'm not able to paste the link, type in "Genome-scale approaches to resolving incongruence in molecular phylogenies" in your search engine. They did their research by mapping out the genome sequences with 8 species of yeast and said the following:
"To systematically investigate the degree of incongruence, and potential methods for resolving it, we screened the genome sequences of eight yeast species and selected 106 widely distributed orthologous genes for phylogenetic analyses, singly and by concatenation"
Basically they wanted to see how bad the incongruence results really were and wanted to fix it.
Is there any studies that you know that are consistent?
Sure, at least consistent to within the parameters laid out in this thread. There was a PNAS paper from 2008 that I spent a while reviewing on the evolution of flightless birds. Almost all the inconsistencies they found resulted from known statistical artifacts.
The incongruities that do exist are as bad or worse among closely related species (within what baraminologists call a "kind") than they are on a broader scale. This is exactly the opposite prediction that baraminology should make, and matches with evolutionary biology: broader patterns are clear, but sorting out exact relationships among closely related species can be trickier because of stochastic processes in genetic evolution.
Hm... that was a bit unclear. I'll post a better explanation later. I might need to post some pictures to demonstrate the point correctly.
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WAR IS PEACE
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The inconsistencies are because different genes evolve at different rates in different taxa. Some genes may be highly preserved in a new species, while other genes (the ones most closely associated with the changes leading to speciation, for example) will evolve faster. If you compare how closely related a group of animals are using different genes, you are necessarily going to get different results depending on which genes you focus on (note that we generally don't know in advance which ones will show the most change, outside of some that are known to be highly conserved in all or most forms of life).
iamnotaparakeet
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Actually, shouldn't evolutionary origins also have it where members of the same taxonomic branch have more similarities then those farther apart, or is this basically going to be of the same type of results as for protein sequencing in the neodarwinian paradigm which preceded genomic sequencing?
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