Saviourmachine Posted November 1, 2005 Share Posted November 1, 2005 Pseudogenes - Independent evidence Pseudogenes form a major pillar that sustains the theory of biological evolution as such. It's an independent way to order spieces. Independent of the order of fossils in the fossil record. Independent of the measured ages of the layers that contain these fossils. Independent of physiological similarities. Independent of (normal) genetic evidence. Believing that god or the devil figured out to place the errors in the genomes of all species on earth in a way that correlates with the results of these other ways of building an evolutionary tree, resembles believing in a god or satan that places the fossils in the layers to test our faith. It's the genetic equivalence of this concept. Topic borders This topic will handle only biological evolution. And it will only be about pseudogenes. Off-topic remarks shouldn't be answered. To start I'll borrow heavily from the Knowledge thread. It grew to big and I want some serious discussion overhere. I'll depersonalize my post a bit. Statistics To compare pseudogenes you have to do statistics I am afraid. ... genetic markers (such as pseudogenes and the like) should exhibit the same or at least very similar nested phylogeny.That is right. You should expect that to be the case. I obtained this study about an olfactory pseudogene comparison between human, chimp and gorilla: Human specific loss of olfactory receptor genes [pdf]. If you read with me on page 2, table 1, you see the mutations listed for human, chimp, gorilla, orang and rhesus. It's quite obvious that a mutation on a certain location that occurs simultaneously in two or more genomes does tell us something. You see e.g. on locus 11i1p a 247-stop mutation in gorilla, chimp and human. And that's the general trend throughout this tabel. And there were none emitted. Even when you consider that some locations are more easily mutated than others, due to chemical properties of the bended DNA strains, this is a remarkable result. The exact Location of the Mutations is Important Ueda S et al, “A Truncated Immunoglobulin Epsilon-pseudogene Is Found In Gorilla and Man But Not In Chimpanzee.” Proceeds of the National Academy of Sciences USA, Vol 82: pp 3712-3713, 1985. Do you understand what I mean? It’s there, then it’s gone, and then it’s back again. How do we explain that? Then, what do we do if the analysis yields a discordant (conflicting, contrary) grouping? You can see in the table in the study I referred to, that it's possible to have a pseudogene in human and in gorilla, while the chimpansee does have a normal functioning gene. Or even human and orang having pseudogenes, while the genes in chimp and gorilla have no mutations. But... what is very remarkable is that these mutations seem most often to be on different spots! It is definitely straightforward to suggest that these mutations occured parallel. To be sure you should do a statistical study measuring the amount of mutations that occur in the same spot skipping (a descendent of!) an intermediate specie and the amount of mutations that occur on different spots. Of course also this time has to be investigated that all places have really the same mutation sensitivity. Shared Point Mutations - Are they Abundant? The Alpha-1,3-GT pseudogene includes a substitution at position 726 which is uniquely shared by cows, squirrels, monkeys and gorillas, but is not in humans. Also, the rat and chimp uniquely share a C at position 55 in the GLO pseudogene. These markers are unique; wouldn’t this mean cows, squirrels and rats should be included somewhere in the primate family tree? The evidence indicates that they must have had a common ancestor somewhere. This is not exactly what I mean with a statistic study. Is there no Alpha-1,3-GT pseudogene in humans? What is the problem? Or are there other substitutions in the human equivalent? Probably the rat and the mushroom share somewhere also a mutation on their pseudogene packages. That's of course coincidence, but inevitable!Are these studies using stochastic tools? Give they a broad picture in stead of pointing out one exception? For example: maybe cows, squirrels, rats and monkeys did experience less evolutionary pressure about their colour perception or something else what is not easy to defer. Unique Mutations - Of course The CYP chimpanzee pseudogene has a deletion not shared with orangutans, gorillas or humans. Again. it’s there, then gone and then comes back again. This shows only that the person you cite, doesn't understand that the chimp genome is different from the genome of the common ancestor of human and chimp. It's certainly possible to have a mutation in the genome of one monkey, while the others don't have any. What to do with the Data? What the data appears to indicate is that we can never tell why two species share a genetic sequence, and therein lays the basic problem in using this type of evidence. It appears that we simply don’t know enough about retroviruses, pseudogenes and the like that we can be dogmatic about their interpretations. I didn't saw you cite any study that did some stochastics. One in which the investigators took a whole pseudogene package and considered all the dissimilarities with other contemporary species. I hope we can have a nice discussion having some depth. Link to comment Share on other sites More sharing options...
Saviourmachine Posted February 8, 2006 Author Share Posted February 8, 2006 Bump. To difficult? Link to comment Share on other sites More sharing options...
Ouroboros Posted February 8, 2006 Share Posted February 8, 2006 TJR left the scene, and the only one that maybe would debate you now is TxViper. Link to comment Share on other sites More sharing options...
Saviourmachine Posted February 8, 2006 Author Share Posted February 8, 2006 TJR left the scene, and the only one that maybe would debate you now is TxViper. Mmm. He's on my fundy's list. Link to comment Share on other sites More sharing options...
crazy-tiger Posted February 8, 2006 Share Posted February 8, 2006 TJR left the scene, and the only one that maybe would debate you now is TxViper. tx...? Debate? Link to comment Share on other sites More sharing options...
Zach Posted February 9, 2006 Share Posted February 9, 2006 Sometimes when presenting pseudogene evidence to creationists, the L-gulono-lactone pseudogene is brought up as a counter example. Specifically, the fact that primates as well as guniea pigs contain pseudogene GLO sequences. While this is true, what is often ignored is that the gunea pig GLO pseudogene is nonfunctional by virtue of missing exon 5, but the GLO pseudogene in primates is nonfunctional by virtue of missing exons 8 and 9. Further, sequence homology comparison of GLO in organisms which contain both the functional gene and the pseudogene clearly show that primate GLO is more closely related to human GLO than guinea pig GLO. In addition, functional GLO genes in organisms like cows and pigs are more closely related to human GLO than the guinea pig. Homology.pdf Link to comment Share on other sites More sharing options...
Saviourmachine Posted February 9, 2006 Author Share Posted February 9, 2006 ... by virtue of missing exon 5, but ... by virtue of missing exons 8 and 9Ha, thanks Zach. Yes, that's what I often point out too. I searched for a way to label these two kinds of differences. Pseudogene comparisons have been assigned no labels because of their nonfunctionality. I would like however to have different types. 1.) Pseudogenes can differ from each other, on a place that would* actually result in an identical codon. 2.) Pseudogenes can differ from each other, on a place that would* result in a different codon for each of them. 3.) Pseudogenes differ by point mutations on different places. 4.) Pseudogenes differ by different mutation type (insertion, addition, removal). No biologist could provide me with definitions from the field yet. * "would" of course: they do not code for codons anymore, because pseudogenes are defunct. Link to comment Share on other sites More sharing options...
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