==* CYTOCHROMEC PHYLOGENY MDENTON HOMOLOGY THEORYINCRISIS After all I have seen posted her

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==* CYTOCHROME_C PHYLOGENY M_DENTON HOMOLOGY THEORY_IN_CRISIS After all I have seen posted here of what I consider suspect data, I decided that I would perform some analysis of my own. The following data was generated using the NRBF protein database and the UWGCG resource. The analysises were performed using the FASTA program for sequence comparisons. Before I present the data, I would like to make it clear that amino acid comparisons in proteins allows for the most stringent analysis regarding the lattitude within which a protein may evolve. For this reason, such analyses are less than ideal. I attempted to repeat the study I present here using the genomic DNA sequences but, to be honest, I could not figure out how to make the program compare one entire gene to another. Rather, what it does is look for the region of highest homology. For instance comparing the sequence of say the cytochrome C gene of Saccharomyces cerrivisiae with that of Drosophila melanogaster, I might find a region of 780 bp that shows 65% homology. This would be fine if the gene was 780 bps in length, unfortunately the cytochrome C gene is on the order of 2 Kbs. Regardless of what I tried, I could not find a way to compare the entire 2kbs from the different organisms. I could do this manually, but considering the number of analyses involved I decline. I encourage all of you to look at this data critically. I have done nothing to doctor it, or to throw out data because it didn't seem to fit with what I might like. Chuck Maier in quoting Denton, has posted similar data, but whose analyses differ entirely from what I am posting here. The conclusions that Chuck has drawn are that there is no evidence for any evolutionary relatedeness of any organisms. When you look at what I post here, I encourage you to see if you reach the same conclusions. In order to avoid coloring the data in any way, I will refrain from discussing the data as its presented. I will be more than happy to do so at a later date. In order to keep things to a minimum, I have established a code, which will be used for the grid. It is as follows: A - Human B - Chimpanzee C - Horse D - Donkey E - Mouse F - Carp G - Lamprey H - Maize I - Neurospora J - S. pombe K - Euglena M - Tetrahymena | A | B | C | D | E | F | G | H | I | J | K | L | -+----------------------------------------------------------------------- A|XXXXX| 100 | 88.5| 89.4| 91.3| 78.6| 80.8| 66.7| 63.7| 67.3|56.6|47.5| -+----------------------------------------------------------------------- B| 100 |XXXXX| 88.5| 89.4| 91.3| 78.6| 80.8| 66.7| 63.7| 67.3|56.6|47.5| -+----------------------------------------------------------------------- C| 88.5|88.5 |XXXXX| 99.0| 94.2| 81.6| 84.6| 63.7| 65.7| 71.2|58.6|46.5| -+----------------------------------------------------------------------- D| 89.4|89.4 | 99.0|XXXXX| 95.2| 82.5| 85.6| 64.7| 65.7| 72.1|58.6|46.5| -+----------------------------------------------------------------------- E| 91.3|91.3 | 94.2|95.2 |XXXXX| 83.5| 84.6| 66.7| 65.7| 71.2|56.6|48.5| -+----------------------------------------------------------------------- F| 78.6|78.6 | 81.6|82.5 | 83.5|XXXXX| 81.6| 59.2| 57.3| 64.1|52.0|44.0| -+----------------------------------------------------------------------- G| 80.8|80.8 | 84.6|85.6 |84.6 |81.6 |XXXXX| 59.2| 59.2| 68.3|55.6|48.5| -+----------------------------------------------------------------------- H|66.7 |66.7 | 63.7|64.7 |66.7 |59.2 |59.2 |XXXXX| 58.1| 57.1|51.5|42.6| -+----------------------------------------------------------------------- I|63.7 |63.7 | 65.7|65.7 |65.7 |57.3 |59.2 | 58.1|XXXXX|70.8 |57.6|45.5| -+----------------------------------------------------------------------- J|67.3 |67.3 | 71.2|72.1 |71.2 |64.1 |68.3 | 57.1| 70.8|XXXXX|54.5|48.5| -+----------------------------------------------------------------------- K|56.6 |56.6 |58.6 |58.6 |56.6 |52.0 |55.6 |51.5 |57.6 |54.5 |XXXX|48.0| -+----------------------------------------------------------------------- L|47.5 |47.5 |46.5 |47.5 |48.5 |44.0 |48.5 |42.6 |45.5 |48.5 |48.0|XXXX| -+----------------------------------------------------------------------- All of the above data is presented in terms of percent homology, and compares amino acid sequence of the cytochrome C protein of the various organisms. =-================================================================-= From: JEFF OTTO Since that time, I have since figured out how to do this. As it turns out, I was using the wrong program of the resource. This is too bad, because it would have made for more interesting comparisons. Oh well. WRE> look for the region of highest homology. For instance comparing the WRE> sequence of say the cytochrome C gene of Saccharomyces cerrivisiae with WRE> that of Drosophila melanogaster, I might find a region of 780 bp that WRE> shows 65% homology. This would be fine if the gene was 780 bps in This leads to the principle of functional constraints, which is contradictory to any creationist theory. That is, a given protein has regions which are not important to its function, and regions which are important to its function. Regions with little or no function are free to evolve quicker than those regions that are required for function. This is an idea full of common sense that bears up under rigorous scrutiny. WRE> I encourage all of you to look at this data critically. I have done WRE> nothing to doctor it, or to throw out data because it didn't seem to fit WRE> with what I might like. Chuck Maier in quoting Denton, has posted WRE> similar data, but whose analyses differ entirely from what I am posting WRE> here. The conclusions that Chuck has drawn are that there is no WRE> evidence for any evolutionary relatedeness of any organisms. When you WRE> look at what I post here, I encourage you to see if you reach the same WRE> conclusions. In order to avoid coloring the data in any way, I will WRE> refrain from discussing the data as its presented. I will be more than WRE> happy to do so at a later date. Since the table has already been posted, I will delete it for my reply to keep the size of the message down. What was found in that table was that there was a clear evolutionary relationship between the mammals. This demonstrates the power that exists for this sort of comparison among closely related species; irrespective of functional constraints on a given protein. It is interesting that in Denton's analysis, he neglected to use such species in his analysis. I did so as a sort of a internal control. I didn't know what to expect as we looked further and further back into time, but wanted a group of closely related organisms to serve as a control. The rest of the organisms that were used in the study were much more evolutionary diverse, some of them from ancient evolutionary lineages. The euglena and yeast species represent some of the oldest lineages whose direct ancestors are believed to be 2 billion years old. When we look at this data, and compare homologies between these diverse organisms, no clear evolutionary relationship is becomes apparent. Rather, they all seem to be roughly equidistant from one another. This was Denton's claim; there is no evidence for an evolutionary relationship and that all organisms are roughly equidistant. In a simple analysis, this would make sense. But lets look at this critically. First, in this sort of study, functional constraints are ignored. We don't know how large (or small) of a region is absolutely essential for protein function, instead we are assuming uniform evolution for the entire protein. This is clearly not the case, and will skew data. That is why, when in papers we discuss protein homology of given regions, saying a certain region from x to y shows z% homology to a similar protein from species a, b and c. A second and more subtle sort of error made is the assumption of relatedness. Intuitively, we know that we are more closely related to chimps than to a euglena. But how do we compare to say, Neurospora, when we think of a euglena? Denton says "Ha! see we are all equally distant. Neurospora shows similar homology to the euglena that we do - there is no evidence for evolutionary relationships." Well here is the thing of it. Since the time that our lineage, the Neurospora lineage, and the euglena lineage shared a common ancestor, *none of us has stopped evolving*. This is why the section dealing with the mammals alone is so powerful. In the mammal lineage, we are looking at less than a hundred million years of evolution. When we are looking at the Neurospora, human, euglena evolution we are looking at over 2 billion years - hardly an insignificant difference. From the mammal analysis, we can get an idea of the limit of sensitivity of this study, and by looking further and further out, we can see where the sensitivity falls out, and is no longer meaningful. This is specifically why scientists discuss these sorts of homologies in terms of functional constraints and discrete regions. If anyone has any questions on this, let me know. Jeff --- * Origin: Somewhere between intention and achievement (RA 1:154/32.32)

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