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These nested hierarchies don't extend beyond phyla, and attempts at phylogenetic abduction at a broader level have raised far more problems than resolved them, for example in necessary rates of HGT. To complicate the matter further, there is burgeoning evidence of non-redundancy in sequences we originally considered true pseudogenes.
Interesting. Last I heard of Koonin, he was commenting how the TOL (I think he's the only one who bothers to use that acronym) was all but dead in a peer-reviewer commentary on a review article for a post-modern Synthesis. That is, before the authors shut him up.
I can only assume Koonin wasn't aware that his comment was going to be published.
These nested hierarchies don't extend beyond phyla, and attempts at phylogenetic abduction at a broader level have raised far more problems than resolved them, for example in necessary rates of HGT. To complicate the matter further, there is burgeoning evidence of non-redundancy in sequences we originally considered true pseudogenes.
Again you are clearly misinformed and do not know how to interpret the science.
The paper you cited is only talking about the evolution of the genome in bacteria and has nothing about comparing the polymorphism of pseudo-genes in orthologous loci in other species.
The paper you cited is from 2006 and a lot has changed in the molecular world since then. But most importantly that paper has absolutely nothing to do with comparing the polymorphism of pseudo-genes in orthologous loci in other species.
That paper only discuses lateral gene transfers in bacteria. The endosymbiotic theory, is an evolutionary theory that explains the origin of eukaryotic cells from prokaryotes. This has nothing to do with Pseudogenes.
You guys are incredible at how desperate you are to try and pull the wool over peoples eyes.
Tell me how this paper has anything to do with comparing the polymorphism of pseudo-genes in orthologous loci in other species?
Interesting. Last I heard of Koonin, he was commenting how the TOL (I think he's the only one who bothers to use that acronym) was all but dead in a peer-reviewer commentary on a review article for a post-modern Synthesis. That is, before the authors shut him up.
I can only assume Koonin wasn't aware that his comment was going to be published.
Do you think rates of lateral gene transfer on that scale are plausible?
Again you are clearly misinformed and do not know how to interpret the science.
The paper you cited is only talking about the evolution of the genome in bacteria and has nothing about comparing the polymorphism of pseudo-genes in orthologous loci in other species.
The paper you cited is from 2006 and a lot has changed in the molecular world since then. But most importantly that paper has absolutely nothing to do with comparing the polymorphism of pseudo-genes in orthologous loci in other species.
That paper only discuses lateral gene transfers in bacteria. The endosymbiotic theory, is an evolutionary theory that explains the origin of eukaryotic cells from prokaryotes. This has nothing to do with Pseudogenes.
You guys are incredible at how desperate you are to try and pull the wool over peoples eyes.
Tell me how this paper has anything to do with comparing the polymorphism of pseudo-genes in orthologous loci in other species.?
You've not understood the abstract:
"Here we consider how LGT and endosymbiosis bear on contemporary views of microbial evolution, most of which stem from the days before genome sequences were available."
This means that the contemporary concept of the Tree of Life has origins from the days before genome sequences were available, and that it is now being evaluated in light of current phylogenetic data. Your interpretation of it is nonsensical.
Let's clarify another important point: This does not mean to say that limited data sets aren't available that suggest tree-like branching within phyla. It's abducing everything to a broader common origin that falls into problems.
Species phylogeny is not exclusive to coding sequences, and the concerns in question (which are still relevant today) span both prokaryotic and eukaryotic data sets, so you're also wrong on pretty much every other point.
"Here we consider how LGT and endosymbiosis bear on contemporary views of microbial evolution, most of which stem from the days before genome sequences were available."
This means that the contemporary concept of the Tree of Life has origins from the days before genome sequences were available, and that it is now being evaluated in light of current phylogenetic data. Your interpretation of it is nonsensical.
Let's clarify another important point: This does not mean to say that limited data sets aren't available that suggest tree-like branching within phyla. It's abducing everything to a broader common origin that falls into problems.
Species phylogeny is not exclusive to coding sequences, and the concerns in question (which are still relevant today) span both prokaryotic and eukaryotic data sets, so you're also wrong on pretty much every other point.
I understand the abstract of this paper. What is my interpretation of that paper that is nonsensical?
That paper has nothing to do with pseudogenes and how they are used in evolution today.
You made the claim that Pseudo genes being used to prove evolution is out of date. It is not out of date.
Yale would not be posting outdated science on their website.
Why are pseudogenes interesting?
In any study of molecular evolution, it is necessary to compare and contrast genes from a variety of organisms to gauge how the organisms have adapted to ensure their survival. Pseudogenes are vitally important since they provide a record of how the genomic DNA has been changed without such evolutionary pressure and can be used as a model for determining the underlying rates of nucleotide substitution, insertion and deletion in the greater genome
Here is a 2010 publication about the evolution of pseudogenes and how they are used written by Ondrej Podlaha, University of California, Davis, California, USA and Jianzhi Zhang, University of Michigan, Ann Arbor, Michigan, USA
Here is a 2010 publication about the evolution of pseudogenes and how they are used written by Ondrej Podlaha, University of California, Davis, California, USA and Jianzhi Zhang, University of Michigan, Ann Arbor, Michigan, USA
Your interpretation is nonsensical because you are suggesting that phylogenetic analysis stems from days before sequencing data was available. If you don't see the absurdity in that statement then nothing can help you understand the topic it's actually discussing.
Let's also reiterate this point for the hard of understanding: [These concerns] do not mean to say that limited data sets aren't available that suggest tree-like branching within phyla. It's abducing everything to a broader common origin that falls into problems.
Your interpretation is nonsensical because you are suggesting that phylogenetic analysis stems from days before sequencing data was available. If you don't see the absurdity in that statement then nothing can help you understand the topic it's actually discussing.
Let's also reiterate this point for the hard of understanding: [These concerns] do not mean to say that limited data sets aren't available that suggest tree-like branching within phyla. It's abducing everything to a broader common origin that falls into problems.
I am not suggesting that phylogenetic analysis stems from days before sequencing data was available. That is just plain absurd. Show me where I suggested this?
We are talking about 2 different subjects here.
I am talking about how Pseudogenes are used in evolution. I have posted several current papers to demonstrate this.
You made the claim that using Pseudogenes is outdated. Again I have posted current peer reviewed articles and publications that prove otherwise.
I'm talking about Pseudogenes and how they are used in science to prove evolution...what are you talking about?
Creation Mythes can twist and twist and twist the science but it never matches up with the points they are trying to prove. They are not scientists but sure like to pretend that they are.
Looks like Matadora edited his post just in time to remove the quote from the abstract.
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