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Author | Topic: molecular genetic proof against random mutation (1) | |||||||||||||||||||
derwood Member (Idle past 1906 days) Posts: 1457 Joined: |
quote: Yes, of course. Because after all, the dogmatic evolutionists are afraid to discuss the falsifications of their pet theory. I rather believe that when it became clear that you were not really intereste din any rational discourse - as one can see form your TalkOrigins feedback and your posts here - that they decided to stop wasting time on you.
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derwood Member (Idle past 1906 days) Posts: 1457 Joined: |
quote: Odd - this does not even address what I wrote. YOU wrote that Kimura claimed this and that, then later admiotted that it was what YOU had in mind. I simply demonstrated the inconsistency, Mr.Borger.
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derwood Member (Idle past 1906 days) Posts: 1457 Joined: |
quote: I expect scientists to accurately represent their positions and the positions of others.
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derwood Member (Idle past 1906 days) Posts: 1457 Joined: |
PB:
quote: And the backtracking continues. You wrote in direct response to my posting of those citations that they were in fact supportive of your fantasy. Now you will 'wait and see.' Common creationist tactic- jumping to totally unwarranted conclusions.quote: Nothing you have presented even remotely does what you claim it to. Your GLO schtick has been blown out of the water. Nothing else produces an altered phenotype by 'turning on' pre-existing genes (ala NREH). So, you have done nothing at all.quote: This is in direct opposition to your earlier proclamations. But it is good to see that you are starting to try to reclaim some integrity.quote: Your metaphysical views of evolution are interesting. Common for creationists to try to 'blame' evolution for this or that, as you are implicitly doing. Irrelevant to science, of course, but interesting. You dislike evolution because of where you think it will lead philosophically or culturally or whatever. Too friggin bad.quote: I do object to the terms used by some when talking about evolution. But I wouldn't were it not for the fact that I know how creationists will interpret and twist what they say. When a paleontologist says on TV that "This fossil is one of our ancestors" or something like that, "I" know what he means. But "I" also know how cretins will spin it. That is why I object to scientists saying things like "This fossil is one of our ancestors" .Of course, I very strongly object to creationists saying thngs like "There is no evidence for evolution" or some such nonsense. And they say it all the time. because they are either totally ignorant or because they are being purposely deceptive. Which are you?[quote]
quote: Yes, that must be it. I guess looking at the whole genome beforew and after exposing these critters to strssful environments to see if changes are 'directed' just isn't the right thing to do.quote: So, proof for creation is just around the corner, right?quote: Indeed. Nor does claiming support from evidence that is in reality contrary to one's position. That is brainwashing, not science.quote: Oh, right. I forgot - one anomoly can disprove evolution, but several examples countering 'directed mutations' just don't have any effect on alternative 'hypotheses', especially those favored by creationists. Haven't done the right experiments yet, that sort of thing.quote: Was it not YOU that claimed: "ACCORDING TO EVOLUTIONARY BIOLOGISTS, GENE TREES HAVE TO BE IN AGREEMENT WITH SPECIES TREES. " It seems to me that YOU should be the one to provide documentation, since YOU are the one that claims that evolutionary biologists DO believe this. I am an evolutionary biologist (unlike you) and I know this is incorrect. I am the source.But, you seem to know Futuyma. Maybe you have his text? Well, I do, And it took me all of about 15 seconds to find this: "Coalescent theory tells us that under some circumstances, this gene tree, even if correct, may not be the same as the species tree, i.e., the phylogeny of the species form which the gene copies were taken." p. 332, "Evolutionary Biology", 3rd Ed.Emphases in original. He then goes on for some several paragrapgs explaining why this can be. Quote-mining and selective interpretations - not to mention baseless assertion - are hallmarks of cretinsm.quote: Now its at about - 10. Your 'truth', it seems, is predicated on misinterpretations, personal beliefs, shallow grasps of science, etc. Common.quote: What bullshit.. You 'stand up' for your creationism beliefs, and that is it. quote: Frankly, I don't care what an asthma researcher thinks about evolution. I don't have to convince you personally of anything, for, as has been shown on this very forum for at least 2 posters that I can easily recall, no matter what is presented, you will simply reject or twist it. That is what the adherents of supernaturalistic antimaterialsims are all about - sophism to protect their beliefs.quote: See my Futuyma ref. In addition, one would thnk that a molecular biologist - even a creationist one - would undestand that not all loci mutate with the same regularity. Though I once encountered a PhD creationist - also from Australia - that claimed to be a geneticist yet didn't know the difference between nucleotides and codons. Creationists like to append polysyllabic words to their titles/credentiasl to impress their target audiene - layfolk.Funny - when I corrected him, he, likemost cretins, actually engaged in condescension towards me - told me that I should get my "science straight" before daring to correct a PhD geneticist like him.... quote: Refs please. (who do I sound like?)quote: I see. So everyone else is wrong, and the asthma guy creationist is right.quote: I think you are - after all, what you see as an evolution disproofing anomoly is actually a fairly well understood phenomenon. Well, understood by those in the field anyway. Like the anti-non-random mutation abstracts I posted, I do have to wonder if you even read the abstact of this paper?quote: Again, I really don't care what megalomaniacs think.quote: Well, you edited out what I was responding to, and I don't want to open a new window and reread the thread to see. I think it is pretty clear that I was right. Look at the post I am responing to here, for example...quote: LOL! Yeah, it was a falsification. Read the Futuyma ref, for one. Maybe you can support your claims in a scientific way, instead of digging through the lit to find what you consider anomolies which disproof evolution.
quote: Gee, Petey - never heard of deletions before? Of course, look at what you wrote: "...GENES PRESENT IN HUMAN NOT PRSENT IN MAN. "quote: So you can't just say what you mean? Nature 2000 Dec 7;408(6813):708-13 Mitochondrial genome variation and the origin of modern humans. Ingman M, Kaessmann H, Paabo S, Gyllensten U. The analysis of mitochondrial DNA (mtDNA) has been a potent tool in our understanding of human evolution, owing to characteristics such as high copy number, apparent lack of recombination, high substitution rate and maternal mode of inheritance. However, almost all studies of human evolution based on mtDNA sequencing have been confined to the control region, which constitutes less than 7% of the mitochondrial genome. These studies are complicated by the extremevariation in substitution rate between sites, and the consequence of parallel mutations causing difficulties in the estimation of genetic distance and making phylogenetic inferences questionable. Most comprehensive studies of the human mitochondrial molecule have been carried out through restriction-fragment length polymorphism analysis, providing data that are ill suited to estimations of mutation rate and therefore the timing of evolutionary events. Here, to improve the information obtained from the mitochondrial molecule for studies of human evolution, we describe the global mtDNA diversity in humans based on analyses of the complete mtDNA sequence of 53 humans of diverse origins. Our mtDNA data, in comparison with those of a parallel study of the Xq13.3 region in the same individuals, provide a concurrent view on human evolution with respect to the age of modern humans. Subpopulations like this?quote: Oh - see above. 53 subpopulations.quote: It is fun, I agree. But there is no need to publish the obvious quote: Yes, my lack of knowledge. Maybe you heard of a paper that came out in Science a bit ago. It contained a working draft of 90% of the human genome? It showed that not only have individual genes been duplicated, but in fact much of the genome consists of huge duplicated blocks.I was talking about duplications, you now add another criterion. Good for you! quote: Yeah, ostiches and arrogant overconfident creationists, I guess.
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derwood Member (Idle past 1906 days) Posts: 1457 Joined: |
quote: Yes, but what does this have to do with what you wrote about Kimura and third codon positions, then backtracking and admitting that it was what YOU had in mind?
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derwood Member (Idle past 1906 days) Posts: 1457 Joined: |
Emphases mine:
Mol Biol Evol 1999 Nov;16(11):1633-40 Is selection responsible for the low level of variation in the last intron of the ZFY locus? Jaruzelska J, Zietkiewicz E, Labuda D. Institute of Human Genetics, Polish Academy of Sciences, Strzeszynska, Poland. DNA variability was investigated in the last intron of the Y-chromosome-specific zinc finger gene, ZFY, and its X homolog on Xp21.3, ZFX. No polymorphisms were found in the 676-bp ZFY segment in a sample of 205 world-wide-distributed Y chromosomes, other than a solitary nucleotide variant in one individual (nucleotide diversity pi = 0.0014%). In contrast, 10 segregating sites (pi = 0.082%) were identified within 1,089 bp of the ZFX sequence in a sample of 336 X chromosomes. Four of these polymorphisms, which contributed most of the diversity, were located within an Alu insert disrupting the ZFY-ZFX homology (pi Alu = 0.24%). The diversity in the homologous portion of the ZFX intron, although higher than that in ZFY, was lower than that found in genomic segments believed to evolve neutrally; interspecies divergence in both segments was also reduced. Although this suggests that the evolution of both ZFY and ZFX homologs may not be entirely neutral, both Tajima and HKA tests did not reject neutrality. The lack of statistical significance may be attributed to a lack of power in these tests (the low divergence and variability values reduce the power of the HKA and Tajima tests, respectively); furthermore, Homo sapiens has recently undergone a rapid population growth, and selection is more difficult to detect in an expanding population. Therefore, the failure to reject neutrality does not necessarily indicate the absence of selection. In this context, the phylogenetic argument was given more weight in out interpretations. The high level of sequence identity in ZFY and ZFX segments, in spite of their separation 80-130 MYA, reflects a lower mutation rate as compared with other segments believed to undergo unconstrained evolution. Thus, the possibility of weak selection contributing to the low level of nucleotide diversity in the last ZFY intron cannot be excluded and should be kept in mind in the population genetics studies based on Y chromosome variability. ***************************************************Mol Cells 2000 Oct 31;10(5):512-8 Evolution of the X-linked zinc finger gene and the Y-linked zinc finger gene in primates. Kim HS, Takenaka O. Division of Biological Sciences, College of Natural Sciences, Pusan National University, Korea. khs307@hyowon.cc.pusan.ac.kr We have sequenced the partial exon of the zinc finger genes (ZFX and ZFY) in 5 hominoids, 2 Old World monkeys, 1 New World monkey, and 1 prosimian. Among these primate species, the percentage similarities of the nucleotide sequence of the ZFX gene were 96-100% and 91.2-99.7% for the ZFY gene. Of 397 sites in the ZFX and ZFY gene sequences, 20 for ZFX gene and 42 for ZFY gene were found to be variable. Substitution causes 1 amino acid change in ZFX, and 5 in ZFY, among 132 amino acids. The numbers of synonymous substitutions per site (Ks) between human and the chimpanzee, gorilla and orangutan for ZFY gene were 0.026, 0.033, and 0.085, respectively. *In contrast, the Ks value between human and hominoid primates for the ZFX gene was 0.008 for each comparison. Comparison of the ZFX and ZFY genes revealed that the synonymous substitution levels were higher in hominoids than in other primates. The rates of synonymous substitution per site per year were higher in the ZFY exon than in the SRY exon, and higher in the ZFY exon than in the ZFY intron, in hominoid primates.********************************************************** *Interesting how that mirrors evolutionary hypotheses of descent.... Must be just a coincidence, I'm sure....
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derwood Member (Idle past 1906 days) Posts: 1457 Joined: |
quote: The genetic distance reflects the evidence-supported hypotheses of descent. Should have been obvious.
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derwood Member (Idle past 1906 days) Posts: 1457 Joined: |
see:
http://www2.norwich.edu/spage/zfy1a.htm It took all of about 15 minutes. There was a nucleotide link at Pubmed, I downloaded the Genbank files, and made an alignment in XESEE. All common procedures in molecular biology. Looks pretty random to me - even within species (see Ptr1 and 2, Pan troglodytes). Of course, the 'non-random' distributions are what we call synapomorphies.
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derwood Member (Idle past 1906 days) Posts: 1457 Joined: |
quote: It seems that the term is ubiquitous. Basically, for those that do no tknow, a synapomorphy is what is also referred to as a 'shared deerived trait' in cladistics. In other words, a trait (in this case, a mutation at a specific locus/site) that is due to common descent. quote: My pleasure. I don't know if the term has been 'recently' adopted by molecular ststematists or not - I think rather not, as I have several publications form the 80s that use the term. Perhaps it was limited to 'specialists' until relatively recently?
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derwood Member (Idle past 1906 days) Posts: 1457 Joined: |
Interesting how science actually tries to solve problems, while pseudoscience tries to use them to support pet beliefs....
J Mol Evol 1994 Dec;39(6):569-78 Contrasting rates of nucleotide substitution in the X-linked and Y-linked zinc finger genes. Shimmin LC, Chang BH, Li WH. Human Genetics Center, University of Texas Houston Health Science Center, 77225. We have sequenced the entire exon (approximately 1.180 bp) encoding the zinc finger domain of the X-linked and Y-linked zinc finger genes (ZFX and ZFY, respectively) in the orangutan, the baboon, the squirrel monkey, and the rat; a total of 9,442 bp were sequenced. The ratio of the rates of synonymous substitution in the ZFY and ZFX genes is estimated to be 2.1 in primates. This is close to the ratio of 2.3 estimated from primate ZFY and ZFX intron sequences and supports the view that the male-to-female ratio of mutation rate in humans in considerably higher than 1 but not extremely large. The ratio of synonymous substitution rates in ZFY and ZFX is estimated to be 1.3 in the rat lineage but 4.2 in the mouse lineage. The former is close to the estimate (1.4) from introns. The much higher ratio in the mouse lineage (not statistically significant) might have arisen from relaxation of selective constraints. The synonymous divergence between mouse and rat ZFX is considerably lower than that between mouse and rat autosomal genes, agreeing with previous observations and providing some evidence for stronger selective constraints on synonymous changes in X-linked genes than in autosomal genes. At the protein level ZFX has been highly conserved in all placental mammals studied while ZFY has been well conserved in primates and foxes but has evolved rapidly in mice and rats, possibly due to relaxation of functional constraints as a result of the development of X-inactivation of ZFX in rodents. The long persistence of the ZFY-ZFX gene pair in mammals provides some insight into the process of degeneration of Y-linked genes. So, yes, common descent.
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derwood Member (Idle past 1906 days) Posts: 1457 Joined: |
quote: Yes, of course I have. I own a collection of Kimura's works and have read his book. What about it?
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derwood Member (Idle past 1906 days) Posts: 1457 Joined: |
quote: Lets watch out word choice, shall we? I "admitted" nothing - I knew this all along and never said otherwise. the region Kim et al. analyzed was a little over 300 bp in length. Is it a little odd that no changes occurred? Perhaps. Then, there is no requirement that any changes - neutral or otherwise - should have occurred. Unless you have some documentable 'rules' that state as much?
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derwood Member (Idle past 1906 days) Posts: 1457 Joined: |
quote: So Peter B. thinks that evolution is overturned becasue about 80 nucleotides in 'neutral' positions did not exhibit substitution in 20 million years. Of course, where is Borger's evidence that there were no back mutations? Not that it matters, really. No, if there were an intergenic locus of 5kb that showed no change between species in 20 million years, I would be a bit suspicious. But nothing in 300+ bps? Chance alone can probably explain that... But.... That is about 0.0000025 % of the genome. I guess we should ignore the fact that most of the remaining 99.9999975% doesn't show anything out of the ordinary (at least according to asthma guy creationist Borger).
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derwood Member (Idle past 1906 days) Posts: 1457 Joined: |
quote: Because you are RIGHT, right? And all those thousands of others in relevant fields are all just wrong, right? I have to agree with Monken....
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derwood Member (Idle past 1906 days) Posts: 1457 Joined: |
quote: I think I see the problem - Peter B - Do you know the difference between a gene and an exon? It is an honest question. After all, a PhD-holding creationist once appeared on a discussion board, claiming that his doctorate was in microbiology and genetics, and launched into a diatribe about the human genome having 3 billion codons...
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