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Daniel Smith Posts: 970 Joined: Sep. 2007 (Permalink) Posted: Oct. 20 2007,21:04    Found it! CNS = conserved noncoding sequences. So the pink areas in VISTA are confirmations of my hypothesis. My, there are quite a lot of them when comparing the rat and mouse genomes! -------------- "If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright "The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

JAM Posts: 517 Joined: July 2007 (Permalink) Posted: Oct. 20 2007,23:51    Quote (Daniel Smith @ Oct. 20 2007,18:35) From Wikipedia:   Quote Recent evidence suggests that "junk DNA" may in fact be employed by proteins created from coding DNA. An experiment concerning the relationship between introns and coded proteins provided evidence for a theory that "junk DNA" is just as important as coding DNA. This experiment consisted of damaging a portion of noncoding DNA in a plant which resulted in a significant change in the leaf structure because structural proteins depended on information contained in introns. That passage is bullshit, Daniel. "Junk" DNA is in no way homogeneous, and real scientists don't classify introns as "junk." The ID approach to "junk" DNA is profoundly dishonest; it ALWAYS depends on equivocating between a tiny fraction of junk and all of the junk. Every time any IDer talks about it, that dishonesty is displayed. Are you being dishonest or gullible in this case?

JAM Posts: 517 Joined: July 2007 (Permalink) Posted: Oct. 20 2007,23:59    Quote (Daniel Smith @ Oct. 20 2007,21:04) Found it! CNS = conserved noncoding sequences. So the pink areas in VISTA are confirmations of my hypothesis. No, they are conserved noncoding sequences. Your hypothesis would only be confirmed if there weren't white areas between the pink areas, remember? Quote My, there are quite a lot of them when comparing the rat and mouse genomes! Of course there are! But "quite a lot" of them doesn't fulfill your prediction that there wouldn't be any spaces (nonconserved noncoding sequences) between them at all! Here's your prediction:   Quote My prediction is that the coding and non-coding sequences (basically all sequences) will show an equal amount of evolutionary constraint. A lot isn't all, Daniel. Your hypothesis is dead meat. A hefty chunk of noncoding sequences aren't conserved. Did you find any coding sequences that weren't conserved?

JAM Posts: 517 Joined: July 2007 (Permalink) Posted: Oct. 21 2007,00:11    Quote (Daniel Smith @ Oct. 20 2007,19:09) First, thanks for making it a bit clearer. You're welcome. Why don't you reread your hypothesis and prediction before replying?   Quote Second, if the protein coding regions are dark blue and UTRs are light blue, what are the pink (CNS) regions? Are these non-coding? Yes.    Quote If so, why are they also so highly conserved between rat and mouse? By definition. The regions between those regions aren't conserved at all, which falsifies your hypothesis. QED.   Quote Sure there is.  Every kid who ever rearranged someone else's book report to try to "put it in his own words" knows about it. God's a cheating kid now? What's His motivation?   Quote BTW, giving credit to "selection" without showing the steps that were selected for is only an assumption and is not grounded in the evidence.     Assuming that there isn't evidence is dishonest, given your inability to grapple with the evidence that's been served up to you. Daniel, we have observed inversions and translocations in plants, animals, and people, in real time, and we understand how they can survive. In fact, their mere existence falsifies your hypothesis, because they demolish anything functional at the breakpoints. Quote Quote Quote I know you'll probably say that millions of years+selection can accomplish this, but where's the data to support that assumption? These *are* the data. There also are data from shorter time periods that, when extrapolated, are consistent with this. Isn't that the classic case of using the thing that must be explained as an explanation? No. For example, we use VISTA to design mouse knock-in constructs (the technology leaves small insertions behind, and we place them in between the pink areas). It makes predictions that we then test, in the process of achieving a different goal.

JAM Posts: 517 Joined: July 2007 (Permalink) Posted: Oct. 21 2007,00:19    Quote (Daniel Smith @ Oct. 20 2007,19:15) Another example. In this one, the pink regions outside the coding areas, are more highly conserved between rat and mouse than the coding areas. You're cherry-picking, and your hypothesis predicts that all noncoding areas will be pink, not just some of them or most of them.

jeannot Posts: 1201 Joined: Jan. 2006 (Permalink) Posted: Oct. 21 2007,03:16    Quote (JAM @ Oct. 21 2007,00:19)     Quote (Daniel Smith @ Oct. 20 2007,19:15) Another example. In this one, the pink regions outside the coding areas, are more highly conserved between rat and mouse than the coding areas. You're cherry-picking, and your hypothesis predicts that all noncoding areas will be pink, not just some of them or most of them. From your link, this random portion pretty much falsifies your hypothesis, Daniel. Why do exons tend to be more conserved as divergence time increases (from bottom to top : rat, then dog and human vs. mouse)? Anyway, your hypothesis doesn't follow your theory, if I understand it correctly. That the designer didn't add unnecessary DNA in our genomes doesn't imply similar evolution rates in coding and non coding regions. What if many non coding regions are necessary for DNA structure and stability? Surely you wouldn't expect the same selective pressure that exons undergo.

Daniel Smith Posts: 970 Joined: Sep. 2007 (Permalink) Posted: Oct. 21 2007,12:53    Quote (JAM @ Oct. 20 2007,23:59)     Quote (Daniel Smith @ Oct. 20 2007,21:04) Found it! CNS = conserved noncoding sequences. So the pink areas in VISTA are confirmations of my hypothesis. No, they are conserved noncoding sequences. Your hypothesis would only be confirmed if there weren't white areas between the pink areas, remember?     Quote My, there are quite a lot of them when comparing the rat and mouse genomes! Of course there are! But "quite a lot" of them doesn't fulfill your prediction that there wouldn't be any spaces (nonconserved noncoding sequences) between them at all! Here's your prediction:       Quote My prediction is that the coding and non-coding sequences (basically all sequences) will show an equal amount of evolutionary constraint. A lot isn't all, Daniel. Your hypothesis is dead meat. A hefty chunk of noncoding sequences aren't conserved. Did you find any coding sequences that weren't conserved? Yes!  There are also white spaces amongst the coding sequences.  If you look at the gene markers at the top, you'll see they often extend over white spaces. Like this. As I see it, there is significant constraint amongst coding and noncoding sequences - as well as significant changes. Nothing here contradicts my hypothesis. -------------- "If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright "The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

Daniel Smith Posts: 970 Joined: Sep. 2007 (Permalink) Posted: Oct. 21 2007,12:55    Quote (JAM @ Oct. 21 2007,00:19) Quote (Daniel Smith @ Oct. 20 2007,19:15) Another example. In this one, the pink regions outside the coding areas, are more highly conserved between rat and mouse than the coding areas. You're cherry-picking, and your hypothesis predicts that all noncoding areas will be pink, not just some of them or most of them. No it doesn't.  My hypothesis predicts that there will be equal amounts of constraint amongst coding and noncoding areas - not that all of it will be conserved. I never said that! -------------- "If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright "The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

Daniel Smith Posts: 970 Joined: Sep. 2007 (Permalink) Posted: Oct. 21 2007,13:29    This wide view of a random portion of the mouse/rat genome illustrates my point.  The fact that there are so many pink regions shows that the noncoding sites are generally conserved just as the coding sites are within lineages.  The question remains as to how closely mice are related to rats, but I don't see anything here that is unexpected from my point of view.  Remember, my hypothesis is that the splitting of lineages is a saltational event.  I would expect big chunks of the genome to be conserved in such an event, but I would also expect some significant changes as well. Couple this with the significant evidence in the fossil record for adaptive radiation followed by long periods of gradual evolutionary specialization, along with the mounting evidence for non-random mutation and you have the designed descent hypothesis in a nutshell: Saltational, non-random divergence of types, followed by non-random specialization within types, followed by over-specialization amongst most members of a lineage, resulting in the extinction of the overspecialized members - leaving just those members that have not (for whatever reason) become overly specialized. From my perspective therefore, concepts such as "evolutionary constraint"  - as they are generally accepted - are meaningless - since all evolutionary events are non-random. -------------- "If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright "The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

Daniel Smith Posts: 970 Joined: Sep. 2007 (Permalink) Posted: Oct. 21 2007,13:40    Quote Therefore, I predict that anytime Acromobacter guttatus Sp. K172 is subjected to an environment where it must consume nylon to survive, the same frame shift will occur, resulting in Flavobacterium Sp. KI72.             Quote Now, if these 50 labs had all started with the same pre-nylon-eating bacteria and subjected all of them to a nylon environment, I'd be surprised if a significant percentage of them didn't develop the same frame shift. I see here that the wording of my first prediction has caused some confusion.   When I said: "anytime Acromobacter guttatus Sp. K172 is subjected to... the same frame shift will occur...", I didn't mean that the frame shift would occur in every bacteria.   What I should have said was: "anytime a colony of Acromobacter guttatus Sp. K172 is subjected to an environment where it must consume nylon to survive, the same frame shift will occur within some members of that colony, resulting in Flavobacterium Sp. KI72". That would have made my intent clearer. -------------- "If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright "The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

Daniel Smith Posts: 970 Joined: Sep. 2007 (Permalink) Posted: Oct. 21 2007,14:09    Let me also say this: My view is that proteins are essentially the components of biological machinery - therefore I'd expect that coding for proteins would largely be similar amongst related organisms.  The (so-called)* noncoding regions, however, I believe to be instructional regions that determine how these proteins are used.  Hence, I'd expect these regions to show significant differences amongst morphologically different organisms and similarities between morphologically similar organisms. I also believe there are regions that are designed for adaptation - a kind of "working lab" cooking up non-random adaptive elements (within limits).  I'd expect these regions to change as environments change. So, to compare this to VISTA:  The dark blue / light blue regions should be similar amongst related organisms; the pink regions should be similar amongst morphologically similar, related organisms and increasingly dissimilar amongst morphologically dissimilar, related organisms; and the white regions should be dissimilar amongst all organisms. * (I say "so-called noncoding" because I believe these regions actually "code for" something - just not proteins.) -------------- "If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright "The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

oldmanintheskydidntdoit Posts: 4999 Joined: July 2006 (Permalink) Posted: Oct. 21 2007,14:20    Quote (Daniel Smith @ Oct. 21 2007,13:29) Saltational, non-random divergence of types, followed by non-random specialization within types If it is true that, as you say Quote all evolutionary events are non-random In what way are you using "non-random"? I suppose I'll find out what way you are using it if you give me your explanation of the purpose of HIV/AIDS, as per your hypothesis of non-random evolution. What purpose is evolution being directed towards Daniel? What purpose does HIV serve? -------------- I also mentioned that He'd have to give me a thorough explanation as to *why* I must "eat human babies". FTK if there are even critical flaws in Gauger’s work, the evo mat narrative cannot stand Gordon Mullings

oldmanintheskydidntdoit Posts: 4999 Joined: July 2006 (Permalink) Posted: Oct. 21 2007,14:26    Also, how are these non-random changes being made Daniel? Is it creepy Q type beings from a universe beyond our understanding playing with DNA for some reason? Can we observe it happening or is it off limits, conveniently? Or some other thing? Non-random = some thing with an plan. Odd way to communicate it! That's Q for ya! Kinda sounds like a creepy paranoia story Phillip K.Dick style to me. -------------- I also mentioned that He'd have to give me a thorough explanation as to *why* I must "eat human babies". FTK if there are even critical flaws in Gauger’s work, the evo mat narrative cannot stand Gordon Mullings

oldmanintheskydidntdoit Posts: 4999 Joined: July 2006 (Permalink) Posted: Oct. 21 2007,14:28    Quote (Daniel Smith @ Oct. 21 2007,14:09) My view is that proteins are essentially the components of biological machinery - therefore I'd expect that coding for proteins would largely be similar amongst related organisms. what are atoms called in this scheme? the components of the components of the machinery? What about gluons? Quarks? -------------- I also mentioned that He'd have to give me a thorough explanation as to *why* I must "eat human babies". FTK if there are even critical flaws in Gauger’s work, the evo mat narrative cannot stand Gordon Mullings

jeannot Posts: 1201 Joined: Jan. 2006 (Permalink) Posted: Oct. 21 2007,15:19    Quote (Daniel Smith @ Oct. 21 2007,14:09) Let me also say this: My view is that proteins are essentially the components of biological machinery - therefore I'd expect that coding for proteins would largely be similar amongst related organisms.  The (so-called)* noncoding regions, however, I believe to be instructional regions that determine how these proteins are used.  Hence, I'd expect these regions to show significant differences amongst morphologically different organisms and similarities between morphologically similar organisms. I also believe there are regions that are designed for adaptation - a kind of "working lab" cooking up non-random adaptive elements (within limits).  I'd expect these regions to change as environments change. So, to compare this to VISTA:  The dark blue / light blue regions should be similar amongst related organisms; the pink regions should be similar amongst morphologically similar, related organisms and increasingly dissimilar amongst morphologically dissimilar, related organisms; and the white regions should be dissimilar amongst all organisms. So you expect to find similarities in non coding region between eutherian and their marsupial counterparts (for instance wolf vs thylacine), and between old world vultures and new world vultures? These are examples of morphological convergence. You have to correct for relatedness between taxa you compare, as more closely related taxa tend to share a more common ancestor. EDIT : Interestingly, your view is partially right. Non-coding regions, mostly those adjacent to genes, are important in gene expression and may be the primary target for morphological novelties, according to some. But they are unlikely to represent the majority of the non-coding genome.

JAM Posts: 517 Joined: July 2007 (Permalink) Posted: Oct. 21 2007,16:45    Quote (Daniel Smith @ Oct. 21 2007,12:53)   Quote (JAM @ Oct. 20 2007,23:59)       Quote (Daniel Smith @ Oct. 20 2007,21:04) Found it! CNS = conserved noncoding sequences. So the pink areas in VISTA are confirmations of my hypothesis. No, they are conserved noncoding sequences. Your hypothesis would only be confirmed if there weren't white areas between the pink areas, remember?         Quote My, there are quite a lot of them when comparing the rat and mouse genomes! Of course there are! But "quite a lot" of them doesn't fulfill your prediction that there wouldn't be any spaces (nonconserved noncoding sequences) between them at all! Here's your prediction:           Quote My prediction is that the coding and non-coding sequences (basically all sequences) will show an equal amount of evolutionary constraint. A lot isn't all, Daniel. Your hypothesis is dead meat. A hefty chunk of noncoding sequences aren't conserved. Did you find any coding sequences that weren't conserved? Yes!  There are also white spaces amongst the coding sequences. Daniel, this is utterly, totally, completely, spectacularly false. "Genes" are in no way synonymous with "coding sequences." Only the exons (blue) are coding sequences. Not only that, but I clearly explained that the introns also were marked on the gene arrows as hash marks. The introns are NONCODING SEQUENCES.   Quote If you look at the gene markers at the top, you'll see they often extend over white spaces. Like this. Yes, those are all the noncoding parts of the genes (introns). Your hypothesis is wrong.   Quote As I see it, there is significant constraint amongst coding and noncoding sequences - as well as significant changes. Your view has no basis in reality.   Quote Nothing here contradicts my hypothesis. Your confidence and lack of humility is profoundly un-Christian, given your lack of basic knowledge. Your hypothesis is dead meat.

JAM Posts: 517 Joined: July 2007 (Permalink) Posted: Oct. 21 2007,16:57    Quote (Daniel Smith @ Oct. 21 2007,12:55)   Quote (JAM @ Oct. 21 2007,00:19)     Quote (Daniel Smith @ Oct. 20 2007,19:15) Another example. In this one, the pink regions outside the coding areas, are more highly conserved between rat and mouse than the coding areas. You're cherry-picking, and your hypothesis predicts that all noncoding areas will be pink, not just some of them or most of them. No it doesn't.  My hypothesis predicts that there will be equal amounts of constraint amongst coding and noncoding areas Daniel, any constraint at all gives you a pink area, so according to your hypothesis, everything should be well above that 50% level. That's why I very pointedly asked you the question about why the bottom of the scale is at 50%--to see if you were thinking at all. You weren't. Your hypothesis makes clear predictions.   Quote - not that all of it will be conserved. I never said that!   Quote (Daniel Smith @ Oct. 08 2007,04:27) My prediction is that the coding and non-coding sequences (basically all sequences) will show an equal amount of evolutionary constraint. What exactly does basically all sequences mean, then? Don't trip over your feet while you're backpedaling, OK? And don't forget... Quote (Daniel Smith @ Oct. 19 2007,18:14) If, after careful examination, it appears your evidence falsifies my hypothesis, I'll surely admit it.

David Holland Posts: 17 Joined: Oct. 2007 (Permalink) Posted: Oct. 22 2007,16:42    Quote (Daniel Smith @ Oct. 21 2007,13:40) What I should have said was: "anytime a colony of Acromobacter guttatus Sp. K172 is subjected to an environment where it must consume nylon to survive, the same frame shift will occur within some members of that colony, resulting in Flavobacterium Sp. KI72". Does it matter how big the colony is? If your hypothesis is correct then I don't think it should matter. If the colony size is one or one bazillion it should evolve into Flavobacterium every time. Does this apply to all bacteria? Should I get the exact same mutations every time I expose E. coli to penicillin? What about animals? Should I get the exact same mutations every time I expose mosquitoes to DDT? I know the conversation has gotten more into the genetic aspects of your hypothesis but I'm still not clear about this part of it.

Daniel Smith Posts: 970 Joined: Sep. 2007 (Permalink) Posted: Oct. 22 2007,19:26    Quote (JAM @ Oct. 21 2007,16:57)             Quote - not that all of it will be conserved. I never said that!                 Quote (Daniel Smith @ Oct. 08 2007,04:27) My prediction is that the coding and non-coding sequences (basically all sequences) will show an equal amount of evolutionary constraint. What exactly does basically all sequences mean, then? Don't trip over your feet while you're backpedaling, OK? And don't forget...             Quote (Daniel Smith @ Oct. 19 2007,18:14) If, after careful examination, it appears your evidence falsifies my hypothesis, I'll surely admit it. First, why did you take my prediction out of context? Here's the full prediction:             Quote (Daniel Smith @ Oct. 08 2007,04:27) Take two members of the same species that have been geographically and reproductively isolated for a long period of time (the longer the better), sequence their genomes and compare them. My prediction is that the coding and non-coding sequences (basically all sequences) will show an equal amount of evolutionary constraint. I also said this:             Quote (Daniel Smith @ Oct. 06 2007,20:10) My prediction is that there are many functional sequences that are different (even radically so) amongst related lineages - this due to their being of designed, not mutational, origin. And this:             Quote (Daniel Smith @ Oct. 08 2007,02:18) 1.  Sequence comparisons between related lineages will result in a mixture of like and unlike functional sequences.   2.  Sequence comparisons within the same lineage will show evolutionary constraint across the board - even in what are presently considered neutral sites. Now, I'm not sure how closely related rats and mice are, but I think the data suggests that they're at least closely related species, within the same lineage.  The true test however, (as I've said all along) is to take samples from geographically isolated specimens of the same species and see how close they are. I've recently learned of two examples where this was done and the results are consistent with my hypothesis. The first was a study of the Ascension Island green sea turtles.  These turtles, which are notoriously faithful in returning to their breeding grounds every year, have been geographically isolated from other sea turtle populations for 60-80 million years (since the separation of South America and Africa).  A study by Brian Bowen and John Avise (abstract) found that the turtles are too genetically similar to other turtles to have been isolated for that length of time.  Their estimate - based on a sequence divergence rate of 2% per million years - was less than 1 million years.  They then go on to postulate that these sea turtles probably interbred with other populations; this despite the fact that sea turtles have never been observed to do so.  In fact, of the 28,000 females tagged over the past 30 years (at another rookery in Costa Rica), none has ever been observed at another nesting site. Another example is a study done by Scott Baker (from the abstracts on Google Scholar, I was unsure which one corresponds to this study) between Atlantic and Pacific humpback whales - which have been geographically isolated for 3 million years (since the isthmus of Panama separated the two oceans).  Again - based on a sequence divergence rate of 2% per million years - the estimated difference between these two isolated species was 6%.  The actual difference however, was found to be 0.27%.  Again, this forced the scientists to speculate about gene flows occurring between the oceans from time to time, or much slower sequence divergence rates. In any event, the results in both of these studies are consistent with, and predicted by, my hypothesis, but are not consistent with, or predicted by, the current theory of evolution.  My hypothesis accommodates the known 60-80 million year isolation of the turtles and the known 3 million year isolation of the humpbacks with no extra speculations added to make the data fit! And, I'll go out on a limb and make another prediction here: Whenever studies of this type - between geographically isolated members of the same species - are done, the results will be consistent with my hypothesis. -------------- "If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright "The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

JAM Posts: 517 Joined: July 2007 (Permalink) Posted: Oct. 22 2007,20:26    Daniel Smith,Oct. 22 2007,19:26:  "- not that all of it will be conserved. I never said that!" Daniel Smith,Oct. 08 2007,04:27 - "My prediction is that the coding and non-coding sequences (basically all sequences) will show an equal amount of evolutionary constraint." JAM: What exactly does basically all sequences mean, then? Here's a question for you. Why didn't you answer that question? You even italicized "all" for emphasis. Now, you didn't mean "all"? Quote (Daniel Smith @ Oct. 19 2007,18:14) If, after careful examination, it appears your evidence falsifies my hypothesis, I'll surely admit it.     Quote First, why did you take my prediction out of context? No, first, the evidence falsified your hypothesis and you said that you would admit it. Instead, your un-Christian pride and your inability to be objective led you to make a patently false claim--that everything within a gene was coding sequence.                     Quote (Daniel Smith @ Oct. 08 2007,04:27) Take two members of the same species that have been geographically and reproductively isolated for a long period of time (the longer the better), sequence their genomes and compare them. My prediction is that the coding and non-coding sequences (basically all sequences) will show an equal amount of evolutionary constraint. Not a problem. We have loads of sequences from mice that can be crossed with each other, despite the fact that they have been classified as different species, and we have inbred strains of house mice, which have been artificially, and completely, inbred for a century. Take your pick.     Quote I also said this:                     Quote (Daniel Smith @ Oct. 06 2007,20:10) My prediction is that there are many functional sequences that are different (even radically so) amongst related lineages - this due to their being of designed, not mutational, origin. Yes, and noting that, I asked you to make a simple prediction in response to a simple question:       Quote (JAM @ Oct. 14 2007,14:59) 2) Again, with man vs. mouse (but not synteny), each has ~30,000 genes. According to your hypothesis, how many human genes won't have a mouse ortholog and vice versa? You can make predictions for: race vs. race strain vs. strain mouse vs. man chimp vs. man, etc. Your hypothesis makes clear predictions in all those cases, doesn't it? Why did you run away from my simple question? [quote]And this:                     Quote (Daniel Smith @ Oct. 08 2007,02:18) 1.  Sequence comparisons between related lineages will result in a mixture of like and unlike functional sequences.   2.  Sequence comparisons within the same lineage will show evolutionary constraint across the board - even in what are presently considered neutral sites. Yes, and you've just seen that your hypothesis is dead wrong.     Quote Now, I'm not sure how closely related rats and mice are, but I think the data suggests that they're at least closely related species, within the same lineage. We can do the same thing for mouse strains, or mouse "species" that interbreed to yield fertile offspring. It's just not as easy as it is with VISTA, where you had to change basic facts, falsifying your promise to admit that your hypothesis was incorrect.     Quote The true test however, (as I've said all along) is to take samples from geographically isolated specimens of the same species and see how close they are. No, only if you are comparing/contrasting coding and noncoding sequences. You're fudging your hypothesis in addition to the facts now.     Quote I've recently learned of two examples where this was done and the results are consistent with my hypothesis. The first was a study of the Ascension Island green sea turtles.  These turtles, which are notoriously faithful in returning to their breeding grounds every year, have been geographically isolated from other sea turtle populations for 60-80 million years (since the separation of South America and Africa). False. That was THE HYPOTHESIS BEING TESTED, for Christ's sake.     Quote  A study by Brian Bowen and John Avise (abstract) Why would you only read/link to the abstract, when the whole paper is freely available?     Quote found that the turtles are too genetically similar to other turtles to have been isolated for that length of time.  Their estimate - based on a sequence divergence rate of 2% per million years - was less than 1 million years.  They then go on to postulate that these sea turtles probably interbred with other populations; this despite the fact that sea turtles have never been observed to do so. The BS is getting deep. 1) They looked at RFLPs in mitochondrial DNA. That's coding. Do you know what is special about mtDNA, Daniel? 2) Breeding in this species occurs offshore, so "never been observed" is nothing but pure BS to feed your ego. The authors note this clearly.     Quote In fact, of the 28,000 females tagged over the past 30 years (at another rookery in Costa Rica), none has ever been observed at another nesting site. So what? The males aren't tagged.     Quote Another example is a study done by Scott Baker (from the abstracts on Google Scholar, I was unsure which one corresponds to this study) Abstracts aren't evidence. You need to look at the DATA, not your misrepresentations of abstracts.     Quote between Atlantic and Pacific humpback whales - which have been geographically isolated for 3 million years (since the isthmus of Panama separated the two oceans). I'm sorry, Daniel, but that is just a desperate fabrication: Humpbacks hang out in Tierra del Fuego. Can you be more blatantly dishonest than that?     Quote Again - based on a sequence divergence rate of 2% per million years - the estimated difference between these two isolated species was 6%.  The actual difference however, was found to be 0.27%.  Again, this forced the scientists to speculate about gene flows occurring between the oceans from time to time, or much slower sequence divergence rates. It did, eh? The scientists weren't forced to do anything.     Quote In any event, the results in both of these studies are consistent with, and predicted by, my hypothesis, but are not consistent with, or predicted by, the current theory of evolution. False on both counts.     Quote My hypothesis accommodates the known 60-80 million year isolation of the turtles... Daniel, that is a hypothesis, it is not known.     Quote and the known 3 million year isolation of the humpbacks with no extra speculations added to make the data fit! And that's just a lie. How can humpbacks be isolated given that they are common in Tierra del Fuego?     Quote And, I'll go out on a limb and make another prediction here: Whenever studies of this type - between geographically isolated members of the same species - are done, the results will be consistent with my hypothesis. Your limb was gone with the VISTA data. You've proven that you'll fabricate rather than test your hypothesis, Daniel.

swbarnes2 Posts: 78 Joined: Mar. 2006 (Permalink) Posted: Oct. 22 2007,20:55    Quote anytime a colony of Acromobacter guttatus Sp. K172 is subjected to an environment where it must consume nylon to survive, the same frame shift will occur within some members of that colony, resulting in Flavobacterium Sp. KI72". So I take a sample of Acromobacter, I spread it on a plate.  I grow colonies from that. I replica plate those colonies onto nylon plates, and you claim that there will be a survivor in every colony? Of every plate, prepped by every lab worker in 50 labs? Now, claiming that all of the survivors (because, you suppose, there is only a single possible evolutionary solution to the problem, which is ridiculous) would have the exact same mutation, that's at least imaginable.  But what you suggest now is certifiably crazy.   So yes, you made it clear.  Clear that your understanding of biology is insane. Well, I guess you weren't interested in hearing the evidence that nylon-eating can be acquired through mutations in other genes after all.  Which makes it a lie when you said you were.  A pretty pathically transparent one at that.

Henry J Posts: 5786 Joined: Mar. 2005 (Permalink) Posted: Oct. 22 2007,22:16    Quote They then go on to postulate that these sea turtles probably interbred with other populations; this despite the fact that sea turtles have never been observed to do so. Maybe the turtles are better at doing their mating activities in private than some people think they are? Quote My prediction is that the coding and non-coding sequences (basically all sequences) will show an equal amount of evolutionary constraint. Is that when the groups are in equivalent environments, or different environments? I'm no biologist, but I'd think that in similar environments the current theory would predict similar amount of constraints as well, and that in different environments both current theory and your hypothesis would imply some differences due to the differences in needs in different surroundings. Henry

W. Kevin Vicklund Posts: 68 Joined: Oct. 2005 (Permalink) Posted: Oct. 23 2007,15:01    Quote The first was a study of the Ascension Island green sea turtles.  These turtles, which are notoriously faithful in returning to their breeding grounds every year, have been geographically isolated from other sea turtle populations for 60-80 million years (since the separation of South America and Africa).  A study by Brian Bowen and John Avise (abstract) found that the turtles are too genetically similar to other turtles to have been isolated for that length of time.  Their estimate - based on a sequence divergence rate of 2% per million years - was less than 1 million years.  They then go on to postulate that these sea turtles probably interbred with other populations; this despite the fact that sea turtles have never been observed to do so.  In fact, of the 28,000 females tagged over the past 30 years (at another rookery in Costa Rica), none has ever been observed at another nesting site. Your claims as to what Bowen and Avise wrote are rather... odd.  Let me guess: you read the abstract, but did not actually read the paper, which is freely avaible from the link you provided.  This is extremely dishonest for anyone who claims to be interested in the evidence. First, the hypothesized isolation was 40 million years or longer, rather than 60-80 million years.  While this is certainly nitpicking on my part (since 60-80 million years is longer than 40), it suggests that you didn't read the paper - very poor scholarship indeed.  But this is merely a semantic error.  Your other errors are much worse.  For example, the study included a Pacific colony as an outgroup.  The Pacific isolation only occured 3 million years ago (as you yourself noted), yet the Pacific colony showed more changes than the putative 40 million year separation!  Another major error is that you claim they postulated these populations interbred.  This is not quite true - they considered and mostly rejected it, and gave reasons for that rejection.  Rather, they postulated that it was the result of a recent colonization event, and that these events occur periodically.  Bonus question: what is their explanation for why and how periodic colonization events occur?  Finally, you claim that sea turtles have never been observed to change nesting sites.  Yet the paper clearly identifies several instances of this occuring - in the same paragraph they largely rejected the interbreeding argument. I highly recommend that in the future you read your sources before citing them, if at all possible.  It will help prevent you from making such egregious errors.  Unfortunately, some people never do learn this lesson, and I enjoy rubbing their face in it after the first few times they make that error.  Of course, not all articles are free, and you might find yourself taking a calculated risk to make a point.  Just be prepared for the fall-out if your interpretation of the abstract is incorrect. For now, I will assume poor scholarship on your part, rather than deliberate dishonesty.  Keep it up, though, and you will soon find yourself being called a pubjacker.

W. Kevin Vicklund Posts: 68 Joined: Oct. 2005 (Permalink) Posted: Oct. 24 2007,10:10    Quote Another example is a study done by Scott Baker (from the abstracts on Google Scholar, I was unsure which one corresponds to this study) between Atlantic and Pacific humpback whales - which have been geographically isolated for 3 million years (since the isthmus of Panama separated the two oceans).  Again - based on a sequence divergence rate of 2% per million years - the estimated difference between these two isolated species was 6%.  The actual difference however, was found to be 0.27%.  Again, this forced the scientists to speculate about gene flows occurring between the oceans from time to time, or much slower sequence divergence rates. I'm going to call shenanigans on this one.  In a 1993 paper, Baker et al. took samples from three major population groups of humpbacked whales.  Geographically, these are located in the North Atlantic, the North Pacific, and the southern oceans.  The results: there was a 3.808% difference in mitochondrial DNA between the North Atlantic and North Pacific populations, which would be the populations affected by the forming of the isthmus.  That's more than 1% per million years, well within the tolerance limit of the very rough 2%/my rule of thumb.  The paper, "Abundant mitochondrial DNA variation and world-wide population structure in humpback whales," can be found at PubMedCentral.  Please note: there's a lot of information there which I didn't bother to communicate, but needless to say, it doesn't uphold Daniel's numbers. My guess is that Daniel found a paper that dealt solely with the southern oceans population, which is sub-divided into 6 groups.  These 6 groups are not geographically isolated, as others have noted.

JAM Posts: 517 Joined: July 2007 (Permalink) Posted: Oct. 24 2007,11:15    Quote (W. Kevin Vicklund @ Oct. 24 2007,10:10)   Quote Another example is a study done by Scott Baker (from the abstracts on Google Scholar, I was unsure which one corresponds to this study) between Atlantic and Pacific humpback whales - which have been geographically isolated for 3 million years (since the isthmus of Panama separated the two oceans).  Again - based on a sequence divergence rate of 2% per million years - the estimated difference between these two isolated species was 6%.  The actual difference however, was found to be 0.27%.  Again, this forced the scientists to speculate about gene flows occurring between the oceans from time to time, or much slower sequence divergence rates. I'm going to call shenanigans on this one.  In a 1993 paper, Baker et al. took samples from three major population groups of humpbacked whales.  Geographically, these are located in the North Atlantic, the North Pacific, and the southern oceans.  The results: there was a 3.808% difference in mitochondrial DNA between the North Atlantic and North Pacific populations, which would be the populations affected by the forming of the isthmus.  That's more than 1% per million years, well within the tolerance limit of the very rough 2%/my rule of thumb.  The paper, "Abundant mitochondrial DNA variation and world-wide population structure in humpback whales," can be found at PubMedCentral.  Please note: there's a lot of information there which I didn't bother to communicate, but needless to say, it doesn't uphold Daniel's numbers. My guess is that Daniel found a paper that dealt solely with the southern oceans population, which is sub-divided into 6 groups.  These 6 groups are not geographically isolated, as others have noted. We don't even have to read the paper. All we need to do is look at a globe to see the idiocy of Daniel's claim that the isthmus of Panama separated the two oceans. The fact that humpback whales are prevalent at the junction between them (somewhat south of Panama) is a bonus.

Daniel Smith Posts: 970 Joined: Sep. 2007 (Permalink) Posted: Oct. 24 2007,20:59    Quote (swbarnes2 @ Oct. 22 2007,20:55)   Quote anytime a colony of Acromobacter guttatus Sp. K172 is subjected to an environment where it must consume nylon to survive, the same frame shift will occur within some members of that colony, resulting in Flavobacterium Sp. KI72". So I take a sample of Acromobacter, I spread it on a plate.  I grow colonies from that. I replica plate those colonies onto nylon plates, and you claim that there will be a survivor in every colony? Of every plate, prepped by every lab worker in 50 labs? Now, claiming that all of the survivors (because, you suppose, there is only a single possible evolutionary solution to the problem, which is ridiculous) would have the exact same mutation, that's at least imaginable.  But what you suggest now is certifiably crazy.   So yes, you made it clear.  Clear that your understanding of biology is insane. Well, I guess you weren't interested in hearing the evidence that nylon-eating can be acquired through mutations in other genes after all.  Which makes it a lie when you said you were.  A pretty pathically transparent one at that. I never said there was only one possible solution to the nylon problem.  I merely said that I would expect the same frame shift to occur more often and more rapidly than random mutations could account for. -------------- "If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright "The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

Daniel Smith Posts: 970 Joined: Sep. 2007 (Permalink) Posted: Oct. 24 2007,21:41    Quote (W. Kevin Vicklund @ Oct. 23 2007,15:01) Your claims as to what Bowen and Avise wrote are rather... odd.  Let me guess: you read the abstract, but did not actually read the paper, which is freely avaible from the link you provided.  This is extremely dishonest for anyone who claims to be interested in the evidence. First, the hypothesized isolation was 40 million years or longer, rather than 60-80 million years.  While this is certainly nitpicking on my part (since 60-80 million years is longer than 40), it suggests that you didn't read the paper - very poor scholarship indeed.  But this is merely a semantic error.  Your other errors are much worse.  For example, the study included a Pacific colony as an outgroup.  The Pacific isolation only occured 3 million years ago (as you yourself noted), yet the Pacific colony showed more changes than the putative 40 million year separation!  Another major error is that you claim they postulated these populations interbred.  This is not quite true - they considered and mostly rejected it, and gave reasons for that rejection.  Rather, they postulated that it was the result of a recent colonization event, and that these events occur periodically.  Bonus question: what is their explanation for why and how periodic colonization events occur?  Finally, you claim that sea turtles have never been observed to change nesting sites.  Yet the paper clearly identifies several instances of this occuring - in the same paragraph they largely rejected the interbreeding argument. I highly recommend that in the future you read your sources before citing them, if at all possible.  It will help prevent you from making such egregious errors.  Unfortunately, some people never do learn this lesson, and I enjoy rubbing their face in it after the first few times they make that error.  Of course, not all articles are free, and you might find yourself taking a calculated risk to make a point.  Just be prepared for the fall-out if your interpretation of the abstract is incorrect. For now, I will assume poor scholarship on your part, rather than deliberate dishonesty.  Keep it up, though, and you will soon find yourself being called a pubjacker. You are right.  I did not read the paper.  My source was a book I've been reading called "Patterns in Evolution" by Roger Lewin.  I decided that it would be better to try to find a link when I posted it; so I found the abstract and just linked to it. Now that I've read the paper, I see that it's not exactly what I characterized it to be.  I was however, struck by their hypothesis that sea turtles do not accumulate mutations in their mitochondrial DNA as fast as they had expected - and even the 3 million year Atlantic/Pacific separation produced far less variation than the 2% per million years that has generally been accepted. I must say also here that I've been a bit presumptuous in declaring my "hypothesis" - since (as I said when I first arrived here) my ideas are still in development.  My main goal is to find out what really happened.  I will go wherever the data leads.  So I don't really have a hypothesis that's set in stone.  I have more in the way of expectations due to my variant interpretation of the data. One thing I've learned recently (from the same book) is that; even among interbreeding populations, sequence divergence can vary widely (one study found a species of skink with an 8% divergence and a subwren species with 0.1% sequence divergence in the same Australian environment). This has led me to re-evaluate my views. I'm thinking that perhaps these divergence percentages correlate to Schindewolf's proposed three-stage evolutionary theory; with the "typolosis" (or degenerative, over-specialized) phase corresponding to the species with the lowest sequence diversity. I'll have to do more study. -------------- "If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright "The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

Richard Simons Posts: 425 Joined: Oct. 2006 (Permalink) Posted: Oct. 25 2007,00:00    Back to Schindewolf! I am not sure why a hypothesis that has been essentially dead for 50 years holds so much fascination for you. However, given that it does perhaps you could explain how the information to constrain an organism's evolutionary pathway is held. What conceivable mechanism could stop evolution from taking place, or enable parts to evolve before they became useful? I am also curious about the saltational events. Do you see these as creating a new genus, order, phylum or what? What actually occurs during a saltational event? How does the DNA get changed and how does it know what to become, as I gather it is preparing for the next few million years of evolution and changing conditions? When did the last saltational event take place? I don't even know if the proposal is that one day a dinosaur chick hatched that had feathers and wings or if the process was spread over many generations, which might make it little different from the rapid evolution phase of punctuated equilibrium. I'm looking forward to your answers. -------------- All sweeping statements are wrong.

Albatrossity2 Posts: 2780 Joined: Mar. 2007 (Permalink) Posted: Oct. 25 2007,06:01    Quote (Richard Simons @ Oct. 25 2007,00:00) I'm looking forward to your answers. I'm not. It's already clear that the conclusion is more important than the data. Merely looking for an alternative path to the conclusion is a sure sign that the conclusion is hardwired in Daniel's psyche. Unless he shows signs of looking at the evidence and then forming a conclusion, his next post will be just as unsatisfactory as the rest of them have been. -------------- Flesh of the sky, child of the sky, the mind Has been obligated from the beginning To create an ordered universe As the only possible proof of its own inheritance.                         - Pattiann Rogers

Richard Simons Posts: 425 Joined: Oct. 2006 (Permalink) Posted: Oct. 25 2007,08:39    Quote (Albatrossity2 @ Oct. 25 2007,06:01)   Quote (Richard Simons @ Oct. 25 2007,00:00) I'm looking forward to your answers. I'm not. It's already clear that the conclusion is more important than the data. Merely looking for an alternative path to the conclusion is a sure sign that the conclusion is hardwired in Daniel's psyche. Unless he shows signs of looking at the evidence and then forming a conclusion, his next post will be just as unsatisfactory as the rest of them have been. Perhaps I should have phrased it more carefully. I would like to see answers but I think the questions are mostly unanswerable. I expect that either they will be ignored or there will be a lot of beating of bushes that fails to provide answers. I have noticed (but I have not followed everything in detail) that he seems to be following the usual Creationist/ID tactic of scouring the literature for something that could superficially be seen to support his views and pouncing on it, rather than looking at the evidence as a whole and seeing where it leads. -------------- All sweeping statements are wrong.

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