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| Author | Topic: molecular genetic evidence for a multipurpose genome | |||||||||||||||||||||||
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derwood Member (Idle past 1901 days) Posts: 1457 Joined: |
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mark24 Member (Idle past 5221 days)  Posts: 3857 From: UK Joined: |
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Mammuthus Member (Idle past 6501 days)  Posts: 3085 From: Munich, Germany Joined: |
quote: What is that we hear? The sound of silence  Don't hold your breathe for an answer Mark
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Fred Williams Member (Idle past 4881 days) Posts: 310 From: Broomfield Joined: |
quote: Where do you think I misrepresented you? Perhaps here:
quote: Don't you know that populations evolve, not individuals? Seriously, it sure seems you implied, and still are implying, that the cheetah population (its gene pool) has the same amount of genetic information as the pre-bottleneck parent species. If the cheetah lost a net sum of ONE useful allele from the parent population then it is patently obvious that its gene pool has LESS genetic information than the parent species. Do you agree or disagree with this?
quote: The analogy was an attempt to illustrate the impact on the gene pool after a bottleneck. Bottlenecks are a sure-fire way of producing a new sub-population whose gene pool will have less genetic information than the original parent population. Your claims regarding the cheetah clearly implied that you do not think this is the case.
quote: Your point is only valid if Peter or I had questioned the existence of random mutations. We have not done this, so your above statement is a classic strawman. You still seem to be the only one on this board who fails to recognize your "good one" was nothing of the sort.
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Fred Williams Member (Idle past 4881 days) Posts: 310 From: Broomfield Joined: |
quote: Hi Mark. LOL! Sorry. It's just that you have now given the 3rd evolutionist response to info theory, fulfilling my prediction on this board when we first started down this path. It took a couple months (hmm I guess not, it was a few months ago but I wasn't able to witness it until now). The other two that were already used BTW, were: 1) info theory doesn't apply to biology2) mistakes = new information Now you have introduced the classical 3) information was present from the beginning! I will say that #3 is the most tenable of the evolutionist information oh no excuses! For those who accept number 3, then it logically follows you reject the current evolutionary aradigm, the Neo-Darwinian Theory. Congratulations! You now are at a new fork in the road. Creation, or the Hoyle-Crick panspermia alien fantasy!
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Quetzal Member (Idle past 5897 days)  Posts: 3228 Joined: |
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mark24 Member (Idle past 5221 days) Posts: 3857 From: UK Joined: |
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peter borger Member (Idle past 7691 days) Posts: 965 From: australia Joined: |
Dear Quetzal,
Sorry for the delayed response, but I had some important things to do. My reply to your responses follow below and I will avoid capital letters: You write:Peter, the article states explicitly "low variability". You can argue semantics all you want, but your wishing something doesn't make it valid. My response:It maybe so that the article reads LOW variability, the authors demonstrate NO variability. NO is not the same as LOW (sorry for the capitals, but I have to emphasise this). So, the title of the article doesn't cover the content. You are free to focus on LOW, the authors show that the trees demonstrate NO variability on all sites tested. These sites were chosen because here variability was expected and it was performed to assess when the stands got isolated. You say:This is completely inaccurate. From the Chambers article I cited: "Pollen of Wollemia is indistinguishable from the fossil pollen form-genus Dilwynite." If we're going to continue this discussion, I think it behooves you to actually read the literature. I say:I've had a good look at figures of Dilwynite- and Wollemia pollen and it is easy to discriminate between the two. So, this argument fails. Show me the figures where they demonstrate that the pollens of dylwinites and wollemia pollen are indistinguishable. You say:This is also an inaccurate statement. Dr. Peakall points out that it's unlikely the three different stands were formed by cloning. In other words, it's unlikely due to physical separation that the three stands were formed by coppicing from a single stand. He does, however, state that each stand individually probably represents a clone from an original seeding. I say:Probably so, or probably not? Of course this the evolutionary vision and I am aware of it. It does however NOT explain the invariability in the region that are usually highly variable regions. That was my point and still is my point. It tells me that DNA sequences are stable throughout time and that difference between individual trees is not likely to be due to pointmutations, but rather through differential gene regulation. Differential regulation probably involves the histon code. You write:Looking back over your initial post, it appears to me that Woodford didn't actually make any claims you did based a on a few quotations from Woodford's book. Be that as it may, YOUR claims have not been substantiated because you're basing your assertions on either erroneous or incomplete data. My response:Demonstrate where the data are erroneous and incomplete, back it up with refernces. You write:The published information on Wollemia is not yet definitive. You are making assertions that allegedly overthrow the last century and a half of evolutionary theory based on an incomplete data set published in a popular press book written by a newspaperman. Not very likely anyones going to take you very seriously if thas all you've got. Given the fact that there ARE quite prosaic explanations, backed by numerous examples of other organisms from vertebrates to plants the case of Wollemia may be extreme but not all that unusual. My response:Of course I am not being taken seriously by evolutionists. When I registered to this site it was one of the first things that came into my mind as a possible evolutionist's fallacy: O this guy doesn't understand anything about biology, so we don't have to take him seriously. I am used to that fallacy already. Furthermore, I don't know exactly how you make up your mind but I have the feeling that as long as an evolutionary vision hasn't been put forward, you simply do not know what to say about the data. For the rest you adapt to any evolutionary explanation that comes by, without objectively looking at the plausibility of the explanation. In contrast, I can immediately recognise whether molecular data are in accord with evolutionism or not. And I don't buy far-fetched evolutionary explanations anymore, since I can make up stories myself. Finally, the case of Wollemia is extreme AND unusual. Even Dr. Peakall acknowledged that. If it is so common, give me the references please that show NO variability in subpopulations of organisms. You say:lol. Okay, email him and tell him that he's wrong. He's at ANU, and quite prominently listed in the literature. As far as the quote from New Scientist, please tell me how one off-hand comment during an interview provides evidentiary support for overthrowing evolution. I guarantee you that Dr. Peakall hasn't published anything on 'all purpose genome' anywhere. It would be interesting to see the entire quote in context. I'd be willing to bet that he means something other than what you are asserting. My response:All your answers are biased by the axioma "evolution is true". You are unable to think beyond this axioma. Probably --most likely-- the axioma you live with is wrong, and I provided a different explanation, that may be wrong but --most likely-- it may as well be right. I could tell Dr Peakall about my vision, but I guess that I will have similar responses as I get from you, mammuthus, Dr Page. So, why bother.His assertion of an all-purpose genome was in response to the invariability between the two stands. Now there are even three stands. This is the context of his 'all-purpose genome': "Whatever crash-tackled the tree, one of the most conservative organisms that life has ever thrown up, must have been bordering on apocalypse. So seriously", Peakall told me, "the best genetic constitution hasn't been able to get it out of the canyon. But the flipside is, once it settled down in there its all-purpose genome has allowed it to do as well as it can. I think there's a lot of luck in this story." (The wollemi pine, J. Woodford in discussion with Dr Paekall. Page 171) So, Dr Peakall acknowledges --actually invents-- an ALL-PURPOSE genome. You write:Where'd you come up with this one? I even provided you several explanations. You also haven't shown the lack of clonality --which has been observed in Wollemia, btw. Look back at my post, toward the bottom (#1, #3, #4). You also need to read some more, your lack of understanding of population genetics is showing again. Try reading up on inbreeding depression, or topics such as habitat fragmentation and the effects of genetic drift and reduced gene flow on the genetic variability of micropopulations. There is a LOT of literature on the subject. Conservation biology depends on the understanding of these processes. My response:You didn't provide an explanation. Even Dr Paekall didn't have an explanantion. Why? Because there is NO evolutionary explanation. You are free to think that you have provided an explanation, but I know better from a molecular stance. quote:-------------------------------------------------------------------------------- Q: It's YOUR responsibility, as the claimant in this case, to provide testable, replicatable reasons why the mainstream explanations are in error. So far, all yuo've done is hand-wave away anything that contradicts you. As to your little ad hominem aside, it appears I struck a nerve. If you feel I'm unqualified to discuss the issue with you, then you are free to ignore anything I post. That won't, of course, help your case, but perhaps it will make you feel better. As a clarification, I forbore to challenge your sequence data on that one issue. Doesn't mean even someone as ignorant as I apparently am can't see the flaws in your arguments. -------------------------------------------------------------------------------- Ooops, missed responding to this one Peter. You have failed to provide a refutation of the mainstream explanations, merely re-asserted your original premise. Try again. My response:All mainstreams explanation you provided end in a dead alley. I wouldn't have had a problem with the Wollemia nobilis if there was only one stand with identical DNA. Now there are two (or three) identical populations that cannot have been cloned from each other, I --and with me Dr Peakall-- have a severe molecular evolutionary problem with the tree. I pointed this out in my previous letter, but you just don't seem to get my --and Dr Peakall's-- point. You say:You really don't see the difference between Dawkins --a scientist-- and a journalist? My response:Maybe the science writer hasn't got a university degree? So what? Besides, the socalled scientist you refer to is a zoologist who writes about genetics. The journalist writes about a newly discovered tree and interviews Dr Peakall, a scientist in the field. You say:Right, as far as it goes, except for the bit about multipurpose genomes --which as you pointed out is merely your opinion. Conservation biology is concerned with population extinction, causes and prevention. Understanding population genetics is important for this effort. Relict populations, like Wollemia, the Catalina mahogany I mentioned, etc, are highly susceptible to epidemics that can wipe out the entire species precisely because the remaining populations are genetically uniform. There are also a number of other management considerations beyond genetics, which I won't bother to go into here. My response:Your idea is that small populations are highly susceptible to diseases since they are gentcally uniform. Maybe your idea is wrong. Judging the Wollemia the are perfectly able to survive under several different conditions. Even in the city of Sydney I've encountered them. So, that is the multipurpose genome in action. Furthermore, I wonder whether you can provide evidence for your assumption that genetically uniform populations are more prone to diseases or that this observation merely reflects loss of genetic information that leads to extinction upon unusual stimuli from the environment (diseases). I guess this is a chicken-egg problem, so my vision against yours. (I read somewhere that the current population of the oryx was bred from 2 individuals and the alleged extinct cape lion has been found in a Russian zoo and all descended from a couple left there by a circus in the previous century. The concept of inbreeding and enhanced susceptibility to diseases doesn't seem to account for these organisms, including Wollemia. It is a questionable concept.) You say:The only possible 'endstation of evolution' is extinction. What are you talking about 'the universe of genes of kinds'? This statement makes no sense. My response: endstations can indeed go extinct. Either endstations stay unchanged for eons or they go extinct. Could & Eldredge wrote extensively on this observation. You say:As to your comment on breeding, you are again in error. In fact, one of the main management concerns with relict populations is finding ways to preserve the existing genome of the organisms. For example, the Catalina mahogany consists of six adult trees in two karyotypes (of which one is a known hybrid). To prevent further hybridization, one recommendation I saw was to cut down the hybrid! Another example is another Australian relict, Haloragodendron lucasii, which consists of a total of 8 populations but only 7 genetic individuals. In fact, one population (of some 700 specimens), contained only 3 different genetically distinct individuals! Isolation, small population size, inbreeding depression, clonality, etc ALL contribute to homogeneity in genomes in once widely variant populations. Beyond that, speciation has nothing to do with 'loss of information' whatever that means. My response:I presume that the individuals of these organism demonstrate genetic differences? So, there is no threat to evolutionism. Why bother about hybrids, it merely demonstrates that they are of the same kind. If these organism are able to form hybrids with other organisms what is the problem? Does the hybrid have more or less distinctive genes? Does the genepool increase by cutting the hybrid down? Loss of information has nothing to do with speciation? Get familiar with contemporary biology is my advise. You say:However, if your multipurpose genome is so stable, how do you explain the vast differences observed between isolated populations of most organisms? My response:Through jumping/shuffling DNA elements that affect gene expression. Like the 10.000 generations of bacteria-reference of Mammuthus. The authors concluded that single nucleotide polymorphisms was not abundant and cannot have been a major contribution of the observed phenotypic changes. In contrast, jumping DNA elements did. You say:You're trying to argue both directions here and simply getting confused when you meet yourself in the middle. Either populations vary, or they don't, which is it under your 'multipurpose genome' scenario? Relict populations can be understood in an evolutionary ecology framework, as can their occasionally unusual genetics. Try this article for example: Disrupting evolutionary processes: The effect of habitat fragmentation on collared lizards in the Missouri Ozarks. Do some reading, Peter, you're destroying your credibility, here. My response:Please provide the reference for the lizard. I will check it on DNA analysis. I expect not to find the change at the nucleotide level (as for the bacteria), but rather on the level of gene expression. This has also been demonstrated in mice. For instance, the agouti-colour is non-mendelian inherited. It depends on a jumping DNA element (usually referred to as a retroviral element) that affect the expression of the agouti-gene. You write:Evolution predicts both variation and stasis, depending on the particular organism and the environmental factors that effect it. I write:Of course. I could have expected this. In other words evolutionism doesn't predict anything. Pretty bad for a theory. You say:Your 'theory' is both internally inconsistent and in direct opposition to observed populations. I say:Yes, and evolutionism doesn't predict anything. I will work on the inconsistencies if they are present. However, the rule on this planet is that species suddenly appear, do not change over time and then become extinct. Pretty much in accord with my hypothesis and not in accord with the gradual changes required by evolutionism. You say:To be honest, your paragraph makes very little sense; what are 'sensible sequences'? I say:Sensible-regions are regions that have a function and do therefore not change. These regions make sense, therefor sensible region. They can be protein coding regions, but also regions that code RNAs involved in regulatory mechanism, regions involved in lining up chromosomes during cell divisions, etcetera. More and more RNA consensus sequences are discovered that are required for gene expression. It will be a major part of the 'junk-DNA'. {But, as mentioned before, there is no junk in the DNA. It is an outdated evolutionary vision. Of course Dawkins still mentions it in his 1998 book that 98% is junk. But he doesn't know better-- he is a zoologists-- so he can be forgiven} You say:As for evolution not being correct, you've been given reasons why some genomes don't vary. You've been shown populations and species which DO vary when isolated. You have no argument, merely assertion and denial of evidence. I say:No, Dr Borger agrees with Dr Peakall that evolution is not sitting well here. He says: 'Wollemia is likely the exception that disproves the rule. The assumption has been made that genetic variability is good because it is the basis of natural selection. The Wollemi pine might actually proof that in some systems it is possible to have exceptionally low variability and stay reasonable happy' (page 170). In my opinion, the Wollemi pine is not an exception but the tree is the extreme of the multipurpose genome. It is proof for a multipurpose genome. quote:-------------------------------------------------------------------------------- PB: SO, IF I UNDERSTAND PROPERLY, I HAVE TO PRESENT YOU WITH EVIDENCE FOR SOMETHING THAT ISNT OBSERVED. THIS IS THE UP-SIDE-DOWN WORLD. I DO NOT HAVE TO PROOF SOMETHING THAT IS ABSENT. IN CONTRAST, YOU HAVE TO PROVE THAT THE WOLLEMIA DNA DEMONSTRATES VARIABILITY OTHERWISE IT VIOLATES MOLECULAR EVOLUTION. AS IT IS NOW, THE WOLLEMIA PINE DOESNT DEMONSTRATE ANY VARIABILITY IN ALL LOCI TESTED (SEE YOUR PEAKALL REFERENCE). SO, MY ASSERTION STILL STANDS TILL PROVEN OTHERWISE. LETS AWAIT MORE STUDIES. -------------------------------------------------------------------------------- You say: No, youre changing your statement. You said that the DNA was incapable of variation. My response:No, I didn't say that. Reread my first mail, where I roughly outlined the concept of the multipurpose genome. You say:Since this is completely counter to all observations and published literature, I am more than justified in asking for evidence of YOUR claim. Show that there is a mechanism, structure, or chemical that prevents Wollemia (because that was the organism we were discussing) from varying. I say:Of course I do not have to prove an absence. The authors already showed that where variability was expected it wasn't found. In addition, I didn't say that DNA is incapable of change, but the mechanisms my be different than assumed. Change at the single nucleotide level is not a major change inducing mechanism. Rather, shuffling of DNA elements that affect gene expression will do the trick. All evidence currently present points in this direction. You may call that evolution, I know it isn't. It is variation induction through preexisting genetic elements. Probably the genome of Wollemia --and other members of the Araucariacaea-- still specifies the most optimal array of DNA repair enzymes. quote:-------------------------------------------------------------------------------- Q: 1. NONE of your claims about the tree's DNA are correct, as I have shown, using the papers referenced. Look 'em up. PB: ALL MY CLAIMS ON THE WOLLEMIA'S DNA STILL STAND. WORSE, THERE ARE NOW THREE STAND WITH THE SAME DNA SEQUENCES. -------------------------------------------------------------------------------- Feel free to keep claiming this. The published literature refutes it. My response:As demonstrated above, I will. Present the literature if you are so sure. quote:-------------------------------------------------------------------------------- Q: 2. Disinformation? Not really. Deliberate, skewed interpretation coupled with misunderstanding and a weak argument from personal incredulity, usually. PB: SCIENCE IS ABOUT INTERPRETATIONS AND I HAVE A DISTINCT INTERPRETATION THAN EVOLUTIONISM. IN MANY ASPECTS MY INTERPRETATIONS IS EQUAL TO EVOLUTIONISM AND IN SOME ASPECT SUPERIOR TO EVOLUTIONISM. -------------------------------------------------------------------------------- Lol. publish or perish, Peter. If your explanations are so superior, publish them, I'll be the first to congratulate you on your Nobel Prize. My response:Working on it. This site is a test ground. To find out what I can expect. quote:-------------------------------------------------------------------------------- Q: 3. You haven't shown a single concrete example of anything that falsifies evolution. Every example, argument, quibble, etc, that you've produced has been shown to be in error by one person or another here. Mere repeated assertion doesn't prove your case. PB: I HAVE DEMONSTRATED SEVERAL EXAMPLES FROM MOLECULAR BIOLOGY THAT CANNOT BE EXPLAINED BY EVOLUTINISM, YOU SIMPLY DENY THAT. I AM USED TO DENIAL FROM EVOLUTIONIST SO NOTHING NEW HERE. -------------------------------------------------------------------------------- Denial? You have been shown not only to be wrong in your interpretations, but woefully ignorant of the sciences and disciplines you are attempting to overthrow. If anyone's in denial, it's you. My response:Sometimes I wonder why do I still discuss with evolutionism-believers. They are so stuck in their own paradigm that they are unable to think otherwise. Even if it has been falsified over and over. Free your mind and I will show you the world how it really is. quote:-------------------------------------------------------------------------------- Q: 4. Now I insist you email him. Where in ANY his articles does Dr. Peakall talk about an all-purpose genome? {PB's restatement of the OP quote omitted for brevity.} -------------------------------------------------------------------------------- I dealt with this 'argument from quotation' above. However, if you're so absolutely certain that Dr. Peakall supports your 'multipurpose genome', ask him directly. He's a pretty nice guy, from our correspondence. I'm sure he'd be delighted to hear 1) how wrong he is on Wollemia and 2) how your miraculous multipurpose genome solves all his problems. My response:Dr Peakall was the first scientist I heard talking about an All-Purpose genome and he further opened my eyes. I think that Dr Peakall tries to get his data in accord with evolutionism since he has to 'publish or perish'. So he introduces things like the exception that proves a rule. With believers of evolutionism as the only peers for scientific journals he will have a pretty hard time to get it in if he didnt do that, dont you think so? The hypothesis of the multipurpose genome holds that stability ensuring DNA repair mechanisms (plus the redundant genetic code) keep the DNA sense-sequences from changing. The variation observed (since not all the tree are the same) is due to jumping/shuffling DNA elements that affect gene regulation. Besides, you demonstrate that you don't understand my hypothesis. The hypothesis of MP is an alternative for evolutionism and often it is superior in explanations. quote:-------------------------------------------------------------------------------- PB: Evolutionary constraints??? Come on Quetzal, don't fool yourself with these meaningless words. What are evolutinary constraints? That the 'DNA isn't plastic anymore', 'evolution ceased in this tree', 'Evolution slow-down' or other humbug. Actually this all is exactly what the multipurpose genome predicts: "endstations of 'evolutinism'" Q: Now THAT'S condescending. Meaningless words? Are you denying that organisms are constrained by their natural history (genetics, ecology, ancestry)? PB: AS FAR AS THE MULTIPURPOSE GENOME IS CONCERNED, ORGANISMS ARE CONSTRAINED TO A CERTAIN LEVEL. IT MEANS THAT THE VARIABILITY ACNNOT GO BEYOND A WELL DEFINED BORDER. THIS BORDER IS DEFINED BY THE PREEXISTING REDUNDANCIES IN THE GENOME. NEW GENES ARE NEVER ADDED TO THE GENE POOL, (UNLESS CREATONS ARE INVOLVED). -------------------------------------------------------------------------------- Once again, you're meeting yourself coming two different directions. This isn't even circular reasoning, your statements here and elsewhere are diametrically opposed to one another. Above you say there are no such things as constraints and the term is meaningless. Immediately afterwards you say that yes, there are constraints. Which is it? Is this one of those things where constraints are visible on Tuesday but not Thursday? As to creatons, I opened a whole new thread just for you to explain how this works. My response:What I mean is that all DNA elements required to phenotypic adaptations are already present in the multipurpose genome. For instance, the multipurpose genome has a program for sexual reproduction as well as a program for copicing. The environment simply demands which one (or both) is operative. If sexual reproduction hasn't been sensed for a while, this information is transmitted to the roots and the copicing program is initiated. Both programs can only be kept in the genome through preservation of the programs and that demand for an array of stability ensuring DNA replication mechanisms. It is an example of genetic redundancy and redundancies demand elaborate repair systems, otherwise they will be lost through entropy. You say:quote: -------------------------------------------------------------------------------- ALL ACCORDING TO YOUR AND THE CURRENTLY ACCEPTED HYPOTHESIS OF EVOLUTINISM. I DO NOT ACCEPT THIS THEORY SINCE IT DOESNT COVER ALL BIOLOGICAL OBSERVATIONS. -------------------------------------------------------------------------------- Of course it does. You certainly havent come close to showing anything that can't be explained yet. I say:That is because you don't want to see it. It would prelude the end of your current worldview. Ask Dr Page for the new-born's swim reflex in conjunction with the gag-reflex. It has no solution in the evolutionary paradigm. So, to change your reponse a bit: Of course it DOESN'T. quote:-------------------------------------------------------------------------------- YOU ASKED FOR AN ORGANISM THAT CEASED TO EVOLVE. EASY. ANY ORGANISM THAT IS NOT ABLE TO ADD GENES TO THE GENOME THAT HAVE NOT BEEN PRESENT IN THE UNIVERSE OF GENES OF THAT ORGANISM HAS CEASED TO EVOLVE. IN FACT, MOST ORGANISMS WE SEE TODAY ARE SUBJECT TO THIS CRITERION. THERE ARE NO EVOLVING ORGANISMS; THE MAJOR PART OF VARIABILITY WE SEE IS DUE TO PREEXISTING MECHANISMS OPERATING IN THE MULTIPURPOSE GENOME. I DON'T BLAME ANYBODY THAT THESE MECHANISMS ARE EASILY CONFUSED WITH EVOLUTIONISM. I USED TO DO THAT MYSELF. -------------------------------------------------------------------------------- Now we're getting somewhere. If I understand what you just wrote, any organism that can be shown to have developed any new (i.e., not transposed or whatever), completely novel gene will utterly destroy your theory? Please tell me that's the case, then we can stop these lengthy responses and all go do something useful. I say:If you can unequivocally proof that this completely novel gene came about without the interference of creatons, it would be bad for the hypothesis. For instance, the TcR gene in mammals seem to drop out of the sky (O I see, the current story is 'birth-and-death-evolution and purifying selection'). What's wrong with the idea of creatons?. Nobody ever saw birth and death evolution, and nobody ever saw a creaton. So, there is no difference (except that evolutionism is scientifically accepted). quote:-------------------------------------------------------------------------------- Q: Just for fun, how do you personally classify subspecies? How have you gone about identifying specific demes in a wild population? And why do you always put [sub] in parentheses? PB: AS MENTIONED I DO NOT SEE A POINT IN CLASSIFICATION. AS LONG AS ORGANISMS ARE ABLE TO EXCHANGE GENES/INFORMATION AND PRODUCE OFFSPRING, IN WHATEVER MANNER, THEY CAN BE CALLED RELATED, I GUESS. -------------------------------------------------------------------------------- I just had to include this section. I'm only going to cite one article out of hundreds that explains how ridiculous this assertion is, and how little you understand of population genetics, speciation, etc: Close genetic similarity between two sympatric species of tephritid fruit fly reproductively isolated by mating time. My response:Please provide the reference you cite from. That these organisms seem to be speciating can be due to loss of DNA compatibility, so I don't see a problem for my hypothesis here. Also Darwin thought he saw speciation on the Galapagos Archipelago in all the different 'species' of finches. However, we now know that they can still interbreed and are thus NO new species. It is in favour of the plasticity of the multipurpose genome (that is due to loss of genes, and differential gene regulation due to shuffling DNA elements). You say:There has been nothing remotely resembling a complete analysis (which is what Dr. Peakall is doing even as we speak). The evolutionary explanation you provided, albeit simplistic, is undoubtedly correct. You certainly haven't shown otherwise. And in fact, the coppicing after seeding from a single original organism certainly DOES explain the lack of variation. My response:The regions that are expected to change over time, and were expected to demonstrate variability, have been analysed and didn't show variability. Why would one analyse regions that are not expected to give a lot of change? Dr Peakall knows what regions to analyse in Araucaria family and he did just that. With the know results. Furthermore, coppicing could explain the invariability within the three stands NOT between the three stands. quote:-------------------------------------------------------------------------------- Q: 1. With your extensive knowledge of population genetics, I'm sure you know that inbreeding depression and mutational load can counteract each other in very small populations. Although possibly an extreme example of this, the observation that Wollemia shows negligible variation at the loci thus far compared between stands could be related to this. In other words, there may not be significant change due to mutation because, if two of the stands were originally seeded from one tree (which hasn't been shown one way or the other), under even theoretically ideal conditions, the divergence would possibly be minimal over several generations. PB: THE RESEARCHERS IN NEW SCIENTIST (NOT A PEER REVIEWED JOURNAL, I KNOW) SAY THAT PROBABLY THE TREES HAVE BEEN IN THE GULLY FOR THOUSAND OF YEARS AND THAT MAY ALSO IMPLICATE THAT THE TREES ARE SEPARATED FOR THOUSANDS OF YEARS. I CANT PROOF THAT AND YOU CANT PROOF THE OPPOSITE. IN MY OPINION, IT POINTS TOWARDS AN EXTREMELY STABLE GENOME, AND THUS ADVOCATES A COMPLETELY STABLE MULTIPURPOSE GENOME (OR RECENT CREATION). IT SIMPLY IS THE EXTREME OF THE NORMAL DISTRIBUTION. -------------------------------------------------------------------------------- You've managed to both contradict yourself again AND fail to answer my point. In the first place, if you admit Wollemia is at the extreme end of the normal distribution for variability, then I agree with you. My response:No, it is the extreme example of the multipurpose genome, characterised by stability of DNA sequences. You say:However, this completely contradicts your assertion that there's something special about it. Secondly, explain to me why the combination of inbreeding depression and mutational load in a highly isolated relictual micropopulation as represented by Wollemia doesn't explain the observation? My response:Inbreeding depression and mutational load counteractions sounds interesting. Could you please provide a reference for this, since I am going to look into the genetics. I mean maybe an alternative genetic program has been switched on in this situation. Next, I will explain my vision on this topic. quote:-------------------------------------------------------------------------------- Q: 2. Somatic mutations were NOT tested for V merely 18s and rcbL divergence, which would only be detectable through inheritance of different (i.e., mutated) genes. Somatic mutations are generally not considered during these types of analyses because they are usually limited to a single cell of a single individual in a single generation, and hence are useless for comparative genomics. Somatic mutations are not inherited. PB: SOMATIC MUTATIONS MIGHT BE EXPECTED IN COPICING PLANTS. -------------------------------------------------------------------------------- You have no clue what a somatic mutation is, do you? My response:No, and I don't know what a gene is and I don't know what an exon is and what an intron is. As a matter of fact, I don't know anything. A mutation not in the germ line and therefor not inherited by sexual reproduction. However, it can be expected that plants that rely on copicing will demonstrate somatic mutations --even in the 18sRNA or rcb genes. Why, since they tissue derived from rapidly dividing meristemes, and here mutations can be introduced easily. All sister cells grown from the mutated cell will also inherit the mutation. So, somatic mutations are expected. If not, the DNA is extremely stable, and in accord with the prediction done by the multipurpose genome. You write (about the dating of the trees):They were dated based on examination of one dead trunk (~350 years) and extrapolation based on observed growth pattern and comparison with trunk size of living plants. The scientists also made an assumption: the trees may be older even than that (up to 1500 years) based on the observed coppicing pattern, i.e., meaning the original trunk may have long ago rotted away while maintaining a living root system. My response:Thanks. Doesn't exclude somatic mutations in meristemes, however. quote:-------------------------------------------------------------------------------- Q: 4. All of your junk DNA, redundancies, etc, would only appear/accumulate in separated populations of multiple organisms over many generations. With Wollemia we are essentially dealing with three organisms only (although that may change with more data), not three populations. That's the implication of the coppicing growth pattern from an original seeding. PB: EVOLUTIONISM EXPECTS TO FIND THIS IN THE GENOME OF THE HORSESHOECRAB. I WAS REFERRING TO THAT. FOR CURIOSITY, HOW DO YOU DEFINE ORGANISM IN THE SENSE OF WOLLEMI NOBILIS? BY LOOKING AT THE DNA? -------------------------------------------------------------------------------- You say:No, we were talking about the tree. However, just to get rid of your horseshoe crab nonsense right from the start, the living members of this group consist of three distinct genera and five species. My response:Show me the DNA analysis and the references. I have the feeling that you still don't understand what I am trying to convey. Speciation can readily be understood from a multipurpose genome, it doesn't need evolutionism. You say:That enough variation for you? 'Living fossil'' 'lol' another 'argument from journalistic sensationalism'. Peddle it to someone who doesn't know any better. As to the designation of organism in the case of Wollemia, pending further data, I'd have to say each stand likely represents a single organism (or close enough as no matter). My response:Even if they were, the separated populations are expected to demonstrate variability. You keep denying that. Maybe you should talk to Dr Peakall about it, since you don't want to accept it from me. Best wishes,Peter [This message has been edited by peter borger, 11-05-2002]
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Mammuthus Member (Idle past 6501 days) Posts: 3085 From: Munich, Germany Joined: |
FW:
Where do you think I misrepresented you? Perhaps here: M previous post:So I questioned if Peter Borger considers all INDIVIDUAL genomes to host the variation within the population i.e. multipurpose Lamarkian adaptation. Why is it a cheetah (individual)has a "poorer" genetic content now than prior to the bottlneck? They have the SAME genes, they are diploid, the sexually reproduce, etc etc like there ancestors. However, the cheetah population as a whole has less variation. That is the consequence of a genetic bottleneck....if they do not go extinct, they do not have "poor" genetic content. They have lost alleles not genes. FW:Don't you know that populations evolve, not individuals? M: Which part or parts of these sentences from my above quote do you not understand or wish to misrepresent? "However, the cheetah population as a whole has less variation. That is the consequence of a genetic bottleneck" FW:Seriously, it sure seems you implied, and still are implying, that the cheetah population (its gene pool) has the same amount of genetic information as the pre-bottleneck parent species. M: Which is exactly why you misrepresented what I said. I specifically asked Peter if he was suggesting a Lamarkian (i.e. pre adaptive mutation is what he believes in i.e. multipurpose genome) or that cheetah's somehow lost a part of their "multipurpose" genome. FW:If the cheetah lost a net sum of ONE useful allele from the parent population then it is patently obvious that its gene pool has LESS genetic information than the parent species. Do you agree or disagree with this? M: Did not say I disagree and in the paragraph above I state this though you ignored it. I disagreed with a Lamarkian mechanism where mutations occur non randomly to pre adapt an organism to novelty i.e. Borger's hypothesis. And as I said, individual cheetah's today have as many genes as each other and their ancestors give or take retrotransposition events. They have less alleles in the population. If you had actually READ what Peter and I were discussing you might not be so confused. FW:The analogy was an attempt to illustrate the impact on the gene pool after a bottleneck. Bottlenecks are a sure-fire way of producing a new sub-population whose gene pool will have less genetic information than the original parent population. Your claims regarding the cheetah clearly implied that you do not think this is the case. M: This was not your analogy. You were claiming that I believed isolating poodles would lead to generation of St. Bernards which is patently false....my question to Peter was if he believed all possible variation occurs in an individual which is Lamarkian and wrong. He claimed the cheetah has poor genetic content which is also false. It is not extinct so calling the content "poor" is an inappropriate valuation. That YOU apparently believe that isolating one dog breed leads to generation of another specific breed is your confusion, not mine. FW:Your point is only valid if Peter or I had questioned the existence of random mutations. We have not done this, so your above statement is a classic strawman. You still seem to be the only one on this board who fails to recognize your "good one" was nothing of the sort M: My point remains valid. You have yet to support your assertion of non-random mutation. Monkenstick was able to demonstrate random mutation. As to what others on this board recognize, I would not be so sure everybody is worshipping at your feet there Fred ...that evidence is also lacking.
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Mammuthus Member (Idle past 6501 days) Posts: 3085 From: Munich, Germany Joined: |
Since I am not going to get any answers to any of my questions I will jump in here in places but let Quetzal respond in full.
I say:Probably so, or probably not? Of course this the evolutionary vision and I am aware of it. It does however NOT explain the invariability in the region that are usually highly variable regions. M: So cloning does not explain invariability to you? PB:That was my point and still is my point. It tells me that DNA sequences are stable throughout time and that difference between individual trees is not likely to be due to pointmutations, but rather through differential gene regulation. Differential regulation probably involves the histon code. M: Ah so now you think that there are no differences between individuals and that the histones magically guide all development...is this an addendum to your hypothesis. All the sequences tell you is that bottlenecked species that clone have little genetic variation...wow..what a surprise! My response:Of course I am not being taken seriously by evolutionists. When I registered to this site it was one of the first things that came into my mind as a possible evolutionist's fallacy: O this guy doesn't understand anything about biology, so we don't have to take him seriously. I am used to that fallacy already. M: When you make unsupported claims or demonstrate that you don't even know about the basics of the field you are arguing against it makes it hard to take you seriously....it also does not help that you do not answer question regarding your hypothesis. PB:If it is so common, give me the references please that show NO variability in subpopulations of organisms. M: Take your pick, mice, cows, sheep and cats have been cloned...some have yielded multiple clones. PB:I could tell Dr Peakall about my vision, but I guess that I will have similar responses as I get from you, mammuthus, Dr Page. So, why bother. M: If you can't take the heat...... PB:......but I know better from a molecular stance. M: Unwarranted conclusion PB:My response: I presume that the individuals of these organism demonstrate genetic differences? So, there is no threat to evolutionism. Why bother about hybrids, it merely demonstrates that they are of the same kind. If these organism are able to form hybrids with other organisms what is the problem? Does the hybrid have more or less distinctive genes? Does the genepool increase by cutting the hybrid down? Loss of information has nothing to do with speciation? Get familiar with contemporary biology is my advise. M: That's a laugher....bottlenecks and founder events can lead to speciation i.e. restriction of genepool I see you have remained immunized against reading Hartl and Clark. PB:My response:Through jumping/shuffling DNA elements that affect gene expression. Like the 10.000 generations of bacteria-reference of Mammuthus. The authors concluded that single nucleotide polymorphisms was not abundant and cannot have been a major contribution of the observed phenotypic changes. In contrast, jumping DNA elements did. M: Patently false, the authors did not measure the contribution of point mutations as assaying mobile elements was easier. From the abstract of Lenski's paper: Molecular methods are used widely to measure genetic diversity within populations and determine relationships among species. However, it is difficult to observe genomic evolution in action because these dynamics are too slow in most organisms. To overcome this limitation, we sampled genomes from populations of Escherichia coli evolving in the laboratory for 10,000 generations. We analyzed the genomes for restriction fragment length polymorphisms (RFLP) using seven insertion sequences (IS) as probes; most polymorphisms detected by this approach reflect rearrangements (including transpositions) rather than point mutations. PB:I say: Sensible-regions are regions that have a function and do therefore not change. These regions make sense, therefor sensible region. They can be protein coding regions, but also regions that code RNAs involved in regulatory mechanism, regions involved in lining up chromosomes during cell divisions, etcetera. More and more RNA consensus sequences are discovered that are required for gene expression. It will be a major part of the 'junk-DNA'. {But, as mentioned before, there is no junk in the DNA. It is an outdated evolutionary vision. Of course Dawkins still mentions it in his 1998 book that 98% is junk. But he doesn't know better-- he is a zoologists-- so he can be forgiven} M: Too bad for your hypothesis that all of these sequences do vary even among individuals of the same species. PB:I say: Of course I do not have to prove an absence. The authors already showed that where variability was expected it wasn't found. In addition, I didn't say that DNA is incapable of change, but the mechanisms my be different than assumed. Change at the single nucleotide level is not a major change inducing mechanism. Rather, shuffling of DNA elements that affect gene expression will do the trick. All evidence currently present points in this direction. You may call that evolution, I know it isn't. It is variation induction through preexisting genetic elements. Probably the genome of Wollemia --and other members of the Araucariacaea-- still specifies the most optimal array of DNA repair enzymes. M: Please provide the citations that it is believed by ALL developmental biologists that gene expression is only changed by shuffling of DNA elements. And also please show us where all the papers showing point muations that induce major changes have been retracted. PB:My response: What I mean is that all DNA elements required to phenotypic adaptations are already present in the multipurpose genome. For instance, the multipurpose genome has a program for sexual reproduction as well as a program for copicing. The environment simply demands which one (or both) is operative. If sexual reproduction hasn't been sensed for a while, this information is transmitted to the roots and the copicing program is initiated. Both programs can only be kept in the genome through preservation of the programs and that demand for an array of stability ensuring DNA replication mechanisms. It is an example of genetic redundancy and redundancies demand elaborate repair systems, otherwise they will be lost through entropy. M: Please then demonstrate human reproduction through copicing. The program must be in there somewhere..or some left over evidence of it. PB:Please provide the reference you cite from. That these organisms seem to be speciating can be due to loss of DNA compatibility, so I don't see a problem for my hypothesis here. Also Darwin thought he saw speciation on the Galapagos Archipelago in all the different 'species' of finches. However, we now know that they can still interbreed and are thus NO new species. It is in favour of the plasticity of the multipurpose genome (that is due to loss of genes, and differential gene regulation due to shuffling DNA elements). M: Sigh...Hartl and Clark...basic evolution texts...ability to interbreed does not mean the two belong to the same species...ever hear of a hybrid zone? Obviously not. Quetzal:You say: That enough variation for you? 'Living fossil'' 'lol' another 'argument from journalistic sensationalism'. Peddle it to someone who doesn't know any better. As to the designation of organism in the case of Wollemia, pending further data, I'd have to say each stand likely represents a single organism (or close enough as no matter). PB:Even if they were, the separated populations are expected to demonstrate variability. You keep denying that. Maybe you should talk to Dr Peakall about it, since you don't want to accept it from me. M: Peakall also understands what a clone is...why don't you? Thanks for not answering any of my questions regarding your hypothesis...back to being ignored
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derwood Member (Idle past 1901 days) Posts: 1457 Joined: |
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Fred Williams Member (Idle past 4881 days) Posts: 310 From: Broomfield Joined: |
Quetzal, methinks you have been reading too much of the gobblygook at T.O. Yours is of the recent evo standard creationists are mixing definitions reply. Why don’t you just deal with the definition I gave you? If you prefer, remove the sender comment. What are you afraid of? I even offered you the simplest level of information, Shannon info. You simply cannot make a case that the cheetah has not lost genetic information from its pre-bottleneck parent population.
You must have your own idea what Genetic information is. Do you think the cheetah has lost information, yes or no. If no, explain why.
quote: MEGAROTFL!  Q, I can’t count the times I’ve been down this road. If it isn’t sand patterns on a beach, or pee messages in snow, or rings in a tree, or arrows shot across a battlefield, or tiles heading for one’s dome. Blah blah blah. These are simply diversions and invariably a big waste of time. Stick to the debate. I again ask, Do you think the cheetah has less genetic information from its pre-bottleneck parent population, yes or no. If no, give us your definition of genetic information that leads you to reach such an amazing conclusion.
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Fred Williams Member (Idle past 4881 days) Posts: 310 From: Broomfield Joined: |
Mark, we’ve already been down this road, and IMO you are just playing games. I don’t blame you, you are arguing from a losing position. I already answered you here, and don’t want to keep repeating myself: http://EvC Forum: Information and Genetics
It’s important for the reader to note that Mark still refuses to give an example he would consider as a loss of information. Apparently in his world any change to a genetic sequence is a gain in information. If not, then he needs to explain himself. Please provide what you would consider a loss of genetic information. Perhaps the following should be added to my list: #4: claim that all amino-acid-altering mutations add information. PS. I guess you really didn’t pick #3. You ruined my prediction and now everyone knows.
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peter borger Member (Idle past 7691 days) Posts: 965 From: australia Joined: |
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Fred Williams Member (Idle past 4881 days) Posts: 310 From: Broomfield Joined: |
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