SIMPLE common anscestors had fewer but MORE COMPLEX systems: genomics

[QUOTE]Originally posted by Fred Williams:
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Fred, Do you accept Ohno's claim that it takes about 10,000 million years to get a 1% change in a genome?

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No, I actually believe it’s worse than he states! (he’s assuming none of the mutations are removed via selection)

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If so how much change can one expect in 5,000 Years?

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Plenty! [/quote]Quantify please.

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Maybe this is before your time, but do you remember that annoying commercial of a German scientist who said it’s better to push a car than to pull it ? Well, imagine him today commenting on this discussion, saying it’s easier to shuffle a deck than to create it!.

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Bottlenecks, subsequent drift, radiation events, all could account for considerable diversity among genomes within 5K years. Even non-random mutations could play a role!

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So why do all of those things (minus the as yet mythical 'non-random mutations - I take it that you are proselytizing something else now?) not help evolution over the course of millions of years?How can you not see the obvious absurdity of your position?Drift, exon shuffling, etc. can make millions og extant 'kinds' from a few 'original' kinds off the ark in 5000 years, but those same processes cannot evolve anything in millions!Makes sense....Of course, I do hope that you rethink your contradictory positions on neutral mutations....

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Our starting point is 30K or so kinds, each with an information-rich genome.

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Please produce the documentation for the existence of these information-rich genome having Kinds. I should like to see the lab reports.If you cannot produce such evidence, then your entire position will have to be considered baseless speculation.

[QUOTE]Originally posted by Fred Williams:
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Of course, I do hope that you rethink your contradictory positions on neutral mutations....

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You mean that
1) neutrals incur a higher reproductive cost to fix than beneficials?
2) Neutral mutations may play a role in hyperspeciation?Do you really want to go down this road again, Scott? You apparently still refuse to realize that the above statements are not mutually exclusive. Both can be true. I’ll give you a clue: etar. [/quote]You can give me all of the asinine clues you want to, and you are still making contradictory, unrealistic claims.If they incur a higher reproductive cost, where are all of the excesses coming from? If the original kind disembarks 5000 years ago, what must the neutral rate be to account for the extant diversity? What is the evidence for this rate? And if we start with only two individuals, please explain how the costs can be paid in so short a time. Where did all the expendable individuals come from? And what is the evidence for this?
And please explain - with supporting docuemntation - how neutral mutations can result in speciation.Also, please explain - with documentation - how if these things can rescue creationary genetics in the YEC timeframe, why the same processes - which you have of course co-opted from evolutionary biology anyway - can't "help" evolution with much longer timeframes?I'm sure you will be able to provide documentation for your claims. Documentation that, unlike Borger's, actually supports what you state. Because if you can't, all will realize that you are just talking creationism.heres a hint for you:
ytilaerLook into it.[This message has been edited by SLPx, 11-15-2002]

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Originally posted by Randy:

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Bottlenecks, subsequent drift, radiation events, all could account for considerable diversity among genomes within 5K years.

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Bottlenecks, now there’s an interesting point. Don’t bottlenecks show up in the genome of species that went through a bottleneck? Why don’t all species show evidence of a bottleneck about 5,000 years ago? You are claiming that the bottleneck was down to 2 of each kind (whatever that is). Why is there no genetic evidence of all these bottlenecks? Why don’t humans have more genetic diversity than most animals? Weren’t there supposed to be 8 humans and only two of each unclean kind on the ark? Humans should have more diversity in our species than the entire genus (or maybe family or at least Kind) of unclean Kinds. Does genetic analysis show this? I don’t think so. Why not?
Randy

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I predict that this post will get no reply.Certainly no substantive one...

Fred,I was wondering if you plan on addressing my questions in this post substantively or just with the usual hand-waves and repeated assertions.Thanks.Oh - a reminder.Simply reasserting something is not evidence.Linking to your personal website is not evidence.Please provide the actual primary source documentation indicative of the veracity of your claims.

Or this one.

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Originally posted by peter borger:
In the paradigm of the MPG such bottlenecks are less relevant, since all information is already present in the genome.

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What is the evidence that all of this information is already present? Please provide some evidence, perhaps from the Human Genome.

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Besides, mutations can be introduced rapidly through non-random (directed) mechanisms.

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Please provide the evidence that such mechanisms exist. Please also demonstrate why the following article does not demonstrate that 'directed mutations' are not what they are claimed to be:******************************************Amplification-mutagenesis: evidence that "directed" adaptive mutation and general hypermutability result from growth with a selected gene amplification.Proc Natl Acad Sci U S A 2002 Feb 19;99(4):2164-9Hendrickson H, Slechta ES, Bergthorsson U, Andersson DI, Roth JR.Department of Biology, University of Utah, Salt Lake City, UT 84112, USA.When a particular lac mutant of Escherichia coli starves in the presence of lactose, nongrowing cells appear to direct mutations preferentially to sites that allow growth (adaptive mutation). This observation suggested that growth limitation stimulates mutability. Evidence is provided here that this behavior is actually caused by a standard Darwinian process in which natural selection acts in three sequential steps. First, growth limitation favors growth of a subpopulation with an amplification of the mutant lac gene; next, it favors cells with a lac(+) revertant allele within the amplified array. Finally, it favors loss of mutant copies until a stable haploid lac(+) revertant arises and overgrows the colony. By increasing the lac copy number, selection enhances the likelihood of reversion within each developing clone. This sequence of events appears to direct mutations to useful sites. General mutagenesis is a side-effect of growth with an amplification (SOS induction). The F' plasmid, which carries lac, contributes by stimulating gene duplication and amplification. ,b>Selective stress has no direct effect on mutation rate or target specificity, but acts to favor a succession of cell types with progressively improved growth on lactose. The sequence of events--amplification, mutation, segregation--may help to explain both the origins of some cancers and the evolution of new genes under selection.

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2) The second problem is the DNA dating analysis [see my comments on mtDNA --> 10 mutations/62000 years in human, 24 in chimps (5-10.000.000 years) and 27 in neanderthaler (500.000 years), and see the ZFY region in human/primates]. In conclusion, DNA dating analysis are not accurate, and are probably not even valid. They are always calibrated subject paleontological data, and/or with respect to interspecies comparison.

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Please explain then how molecular dating techniques (not global clock)are congruent with fossil data. Coincidence?

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The problem is: the evolutionary paradigm allows for interspecies comparison, while the MPG doesn't (for obvious reasons). If for instance only WITHIN species comparisons are carried out we find completely distinct dates for human origin.

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Citation please?

PB: The ancient human data on mtDNA in comparison with chimp demonstrate a common ancestor of human and chimp around 150.000 BP (or non-random mechanisms) [b]Wow, Borger the creationist really is on the incompetent side. I do hope the research he does in his area of expertise is of higher quality.Pete - can I call you Pete? - The LCA being referred to here is between modern Homo and Neanderthal, noit human and chimp.I mean, really....

PB:
"PB: Apparently you didn't have a look at Dr Page's data set. There are both random and non-random sites. The non-random mutations are the mutations you take as evidence for common descent. The random mutations are scattered. As obvious as that." [b]What hokum.I guess YOU did not look at the data.If you did, please tell us in which genomic areas the bulk of your 'directed mutations' occurred in, and please explain how that would be.

PB:
"PB: Atheists religion = evolutionism. That's why you are the most fanatic defender. Dear Mammuthus, maybe you didn't get it, but I attack you religion." [b]So you are a religious bigot?

Just a few comments:

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Originally posted by peter borger:
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Originally posted by peter borger:
In the paradigm of the MPG such bottlenecks are less relevant, since all information is already present in the genome.
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Page: What is the evidence that all of this information is already present? Please provide some evidence, perhaps from the Human Genome.

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PB:1) genetic redundancies having no association with gene duplication and no correlation with mutation rate, 2) jumping DNA elements affecting gene expression, 3) the human genome demonstrates approx 40000 genes, 90% with unknown function (a lot of redundancies included, I expect from MPG).

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Speculation all.

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Besides, mutations can be introduced rapidly through non-random (directed) mechanisms.
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Page: Please provide the evidence that such mechanisms exist.

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PB: Already discussed the 1G5 gene, and the mtDNA in ancient humans. They demonstrate both random and non-random mutations. Randomness with respect to nucleotide and position. Not yet proven is non-randomness as a response to the environment (when?).

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So that is a zero.

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Page: Please also demonstrate why the following article does not demonstrate that 'directed mutations' are not what they are claimed to be:

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******************************************

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Amplification-mutagenesis: evidence that "directed" adaptive mutation and general hypermutability result from growth with a selected gene amplification.

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Proc Natl Acad Sci U S A 2002 Feb 19;99(4):2164-9

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Hendrickson H, Slechta ES, Bergthorsson U, Andersson DI, Roth JR.

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Department of Biology, University of Utah, Salt Lake City, UT 84112, USA.

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When a particular lac mutant of Escherichia coli starves in the presence of lactose, nongrowing cells appear to direct mutations preferentially to sites that allow growth (adaptive mutation). This observation suggested that growth limitation stimulates mutability. Evidence is provided here that this behavior is actually caused by a standard Darwinian process in which natural selection acts in three sequential steps. First, growth limitation favors growth of a subpopulation with an amplification of the mutant lac gene; next, it favors cells with a lac(+) revertant allele within the amplified array. Finally, it favors loss of mutant copies until a stable haploid lac(+) revertant arises and overgrows the colony. By increasing the lac copy number, selection enhances the likelihood of reversion within each developing clone. This sequence of events appears to direct mutations to useful sites. General mutagenesis is a side-effect of growth with an amplification (SOS induction). The F' plasmid, which carries lac, contributes by stimulating gene duplication and amplification. ,b>Selective stress has no direct effect on mutation rate or target specificity, but acts to favor a succession of cell types with progressively improved growth on lactose. The sequence of events--amplification, mutation, segregation--may help to explain both the origins of some cancers and the evolution of new genes under selection.

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PB: Most importantly, it involves a DNA region that is PREEXISTING in these bacteria.

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That has no bearing whatsoever on whether or not the mutations involved were non-random. Red herring noted.

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2) The second problem is the DNA dating analysis [see my comments on mtDNA --> 10 mutations/62000 years in human, 24 in chimps (5-10.000.000 years) and 27 in neanderthaler (500.000 years), and see the ZFY region in human/primates]. In conclusion, DNA dating analysis are not accurate, and are probably not even valid. They are always calibrated subject paleontological data, and/or with respect to interspecies comparison.
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Page: Please explain then how molecular dating techniques (not global clock) are congruent with fossil data. Coincidence?

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PB: They are not. Have a look at the species comparison of the ancient mtDNA. Chimp 24 differences with a human reference sequence, Neanderthaler 27 differences (or 23 or 28 depending on the specimen studied). Furthermore, it depends on the sequence one studies.

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Indeed.
[hoping this reproduces properly]
This is from my dissertation:*****************************************************************
Estimates of Branching-Times Within the families Cercopithecidae and Hominidae
Branch-Point Local Clock DNA-DNA Hybridization Fossil Based
Clock Estimates
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Colobinae - 15-14 Ma 14 Ma ~12-14 Ma CercopithecinaeAsian — 10- 9 Ma 10 Ma ~12-13 Ma African ColobinesNasalis - 6-5 Ma n/a ~3-4 Ma
TrachypithecusCercopithecini - 10-9 Ma 10 Ma ~9 Ma PapioniniMacaca - 8 Ma 7 Ma ~7-8 Ma rest of Papionini
n/aHylobatini — 17-18 Ma 16 Ma 14 Ma
HomininiHomo — Gorilla 6-10 Ma 8 Ma 8 MaHomo(Homo) — 5- 6 Ma 6 Ma 6 Ma Homo(Pan)
*****************************************************************The local clock calculations were done using the dataset I have linked to.Yeah, just coincidence, I suppose...

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The problem is: the evolutionary paradigm allows for interspecies comparison, while the MPG doesn't (for obvious reasons). If for instance only WITHIN species comparisons are carried out we find completely distinct dates for human origin.
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Page: Citation please?

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PB: From the mtDNA in ancient humans and primates (PNAS 2001, vol98, p537-542). It demonstrates a common ancestor 150.000 BP (or non-random mechanisms).

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You know, its funny. I just downloaded that paper and there is nothing even remotely indicated that your 'interpretation' is based in reality. Indeed, the date of 150,000 years does not even appear in the paper, but it is clear that the ancestor being mentioned is not the LCA of chimps and humans.I do suggest that your zeal to be 'right' has clouded your ability to think straight. This is a clear misrepresentation of that paper.Unless you are citing the wrong one - this is the Adcock et al. paper, right?

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Originally posted by Fred Williams:
Consider that there are at least 32 species of bats. Each species could easily be the result of population isolation (pseudo-bottleneck) from a parent population (bat kind).

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LOL!No, Williams, there are over 900 species of bat.No wonder creationism makes sense to layman - they have no idea what they are talkiing about from the get-go...

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My source for species is:

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Page Not Found | World Resources Institute

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4,000 Mammals
4,184 Amphibians
6,300 Reptiles
9,040 Birds

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Is there any actual evidence for this (on the ark), or is it just cretin number games?[This message has been edited by SLPx, 11-21-2002]

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Originally posted by Fred Williams:

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How much information gain might that entail? I am guessing a bunch.

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That would be a bad guess.

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After all, if loss of diversity in the cheetah population is a loss of information,

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Yes, and a new species. Catching on?

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Please provide the documentation that there are new species of cheetah due to their bottleneck.

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I am pretty confident that a kind giving rise to 30 species would involve a pretty hefty creation of new information.

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I’m extremely confident it would not, because we have even observed the arrival of new species, all without any new genetic information.

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Documentation please.

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In fact, many are likely to be the result of lost genetic information. The cheetah is a great example!

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See above. Sounds like the usual Williams ad hoc unsupported gibberish.

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BTW, I’m still waiting for any evidence that new genetic information has arisen naturalistically.

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I am still waiting for evidence that evolution requires it - at least as it is impklied by the likes of internet pseudogeniuses and experts. I am also still waiting for controlled lab experiments demonstrating Yahweh's creative abilities.
I would also settle for lab observations of information arising supernaturally

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Originally posted by peter borger:
Dear Dr Page,

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Before you reply have a look at the papers.

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I have the paper in my hand.

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The figure demonstrates a bonobo, a chimp, a Neanderthaler and (ancient) human. A lot of data go undiscussed. Like the common ancestor for chimp and human around 150 kyr BP.

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Like I said, there is no such figure anywhere in the paper (150,000 kyr ancestor). It goes undiscussed, apparently, because it s not in existence.I submit, Borger, that you simply do not know how to interpret the tree. In fact, and I suggest you actually look at it for comprehension THIS TIME, in the tree humans branch first from Neanderthals, THEN the great apes. There is no time scale given at all, so your 150,000 bit seems completely fabricated. The scale bar in that figure is for branch length changes, not time.

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I recommend evolutionists not to show the raw sequence data anymore, since it immediately falsifies their own theories. Read the papers, otherwise, don't waste my time with.

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Best wishes,
Peter

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Pardon my language, but Borger, you are so full of shit that I have a hard time forcing myself to read your incoherent creationist claptrap anymore.I understand full well that you simply do not know how to understand raw data. Your treatment of the alignment I linked to demonstrated that nicely - your naive, unsupported assertions were comically inept, to say the least.You and WIlliams are a wonferful pair.Again - Borger has totally made up this common ancestor of chimps and humans at 150,000 years nonsense. The paper that HE cited does not contain the "facts" he claims - and still is claiming, apparently - are in it.I therefore consider Borger to be a charlatan, and no longer worth wasting time on. He is incompetent, dishonest, and clearly quite ignorant of the very topics he brings up.Good day to you Borger - I sincerely hope the output in your ACTUAL area of research is not plagued with such incompetentce and dishonesty.

FW:Why do you have trouble with this? Taking in too much of Page's canned rhetoric? [b]Canned rhetoric? Is that like saying that you want observed instances of evolution, lest it must be false, then IGNORING requests for observed evidence for the YEC cult beliefs?Your projection is starting to exceed your pseudocertainty.Everyone, Fred, EVERYONE can see that you toss out ad hoc nonsense, just-so stories, and repeated assertions as your 'evidence.' And EVERYONE can see that you IGNORE requests for ACTUAL evidence.You and Borger...Put Rowan and Martin to shame...Oh - still waiting for observed occurrances of information arising supernaturally.

FW:We are not required to account for all the species of algae, fungi, insects, fish, mollusks, etc. (note that there are almost a million catalogued species of insects/spiders!). [b]Well, if some of those things were not on the ark, how did they survive? Surely you do not think that freshwater molluscs and plants could have survived for more than a yewar in salt water? Insects? How did they survive?The creationist has to go way extra-biblical to try to amke sense of the bible. Look at Woodmorappe and his pelletized food and animals trained to poop into buckets on command...