SIMPLE common anscestors had fewer but MORE COMPLEX systems: genomics

FW:
Bottlenecks, subsequent drift, radiation events, all could account for considerable diversity among genomes within 5K years.M: Bottlenecks and drift generate the genetic diversity we see today ??? LOL! Bottlenecks REDUCE diversity....you might actually want to learn the subject before you debate it. LOL!

[QUOTE]Originally posted by Fred Williams:
[B]

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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...

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Originally posted by Mammuthus:
FW:
Bottlenecks, subsequent drift, radiation events, all could account for considerable diversity among genomes within 5K years.

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M: Bottlenecks and drift generate the genetic diversity we see today ??? LOL! Bottlenecks REDUCE diversity....you might actually want to learn the subject before you debate it. LOL!

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Uh, Doc, please either return your hasbro PhD, or check carefully what I wrote. Do you realize the vast number of dog breeds are essentially artificial bottlenecks? You find a trait you like, then you bottleneck a pair, and before long you have another dog breed.But I see what you have done, and what your argument amounts to is a strawman. Your mind is locked into intra-species, I am thinking inter-species. I agree that bottlenecks reduce the genetic diversity of the new, bottlenecked species (INTRA). For example, I suspect poodles have much less genetic diversity than wolves. Bye bye strawman.But after various bottlenecks, the diversity of the original parent population, at least from a global perspective, has been realized (INTER). In other words, if I saw a picture of the original two domestic dogs, then a picture showing many different dog breeds, I would conclude that the 2nd picture is a reflection of the genetic diversity of the dog. This diversity was the result of various bottlenecks and subsequent mutations.Son’s birthday, gotta run(I'll be back Monday and try to catch up...)

[QUOTE]Originally posted by Fred Williams:
FW:
Uh, Doc, please either return your hasbro PhD, or check carefully what I wrote. M: Stick to changing lightbulbs...you clearly have no talent for anything else...but it is cute how jeleaous you are of Ph.D.s FW:
Do you realize the vast number of dog breeds are essentially artificial bottlenecks? You find a trait you like, then you bottleneck a pair, and before long you have another dog breed.M: And the resultant breed has less genetic variation than the original population..duhFW:
But I see what you have done, and what your argument amounts to is a strawman. Your mind is locked into intra-species, I am thinking inter-species.M: You set youself up Fred...you claimed that genetic bottlenecks result in genetic diversity...your own words...that your own words were wrong is your problem.FW:
I agree that bottlenecks reduce the genetic diversity of the new, bottlenecked species (INTRA). For example, I suspect poodles have much less genetic diversity than wolves. Bye bye strawman.M: So then why would there be more genetic diversity now than after your mythical flood 6000 years ago after all these bottlenecks occurred? Where is all that genetic diversity you claim would be resulting from all of the genetic bottlenecks?FW:
But after various bottlenecks, the diversity of the original parent population, at least from a global perspective, has been realized (INTER).M: Wrong, each bottlenecked group loses some portion of the greater original diversity...it is not sitting there static in wolves who are under selective pressures of their own. If everyone in Africa died tomorrow except for two people, the African population would have suffered a tremendous bottleneck and at the same time, the human gene pool would have lost a tremendous amount of genetic diversity...humanity would not have realized some genetic potential of the original (pre disaster) population as you are claiming.FW:
In other words, if I saw a picture of the original two domestic dogs, then a picture showing many different dog breeds, I would conclude that the 2nd picture is a reflection of the genetic diversity of the dog. This diversity was the result of various bottlenecks and subsequent mutations.M: You might actually want to read about the genetics of dog domestication before writing such a bozo paragraph as above...FW:
Son’s birthday, gotta run(I'll be back Monday and try to catch up...)M: Take your time...you have tons of catching up to do.

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Originally posted by SLPx:

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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.

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Certainly no substantive one...

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===================You won that bet

the coalescent approach should show bottlenecks in the tree topologies of polymorhpic alleles at the time of the flood - why don't they fred?

dear All,you write:quote:
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Originally posted by SLPx:quote:
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Originally posted by Randy:quote:
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Bottlenecks, subsequent drift, radiation events, all could account for considerable diversity among genomes within 5K years.
--------------------------------------------------------------------------------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--------------------------------------------------------------------------------I predict that this post will get no reply.Certainly no substantive one...--------------------------------------------------------------------------------===================You won that betI write:There are a couple of problems here:The first one -- and I mentioned this in a previous letter to Mammuthus-- is the observation that distinct paradigms will lead to distinct interpretations of data.1) According to the evolutionists paradigm it is expected to do certain observations. The evolutionists paradigm assumes common descent and according to their paradigm this must lead to bottlenecks in the case of the flood. It is extremely important to note that one paradigm cannot be applied to the other. So, Randy's questions are invalid since he expects something from the one paradigm to be applicable for the other paradigm. They are, however, mutually exclusive and cannot be simultaneously applied.
In the paradigm of the MPG such bottlenecks are less relevant, since all information is already present in the genome. Besides, mutations can be introduced rapidly through non-random (directed) mechanisms.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. 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. That is the reason why evolutionists add 1 chimp sequence to 13 human sequences (ref: Nature 2000, vol408, p708-713.) Otherwise the data do NOT fit the evolutionary paradigm!I bet, I've seen it through. Best wishes,
Peter[This message has been edited by peter borger, 11-17-2002]

PB:
1) According to the evolutionists paradigm it is expected to do certain observations. The evolutionists paradigm assumes common descent and according to their paradigm this must lead to bottlenecks in the case of the flood.M: Actually, plain jane genetics demonstrates the effects of bottlenecks on genetic diversity. This is an observable fact experimentally and in nature...not some wishy washy religious paradigm like the truth of the bible or whatnot.PB:
It is extremely important to note that one paradigm cannot be applied to the other. So, Randy's questions are invalid since he expects something from the one paradigm to be applicable for the other paradigm. They are, however, mutually exclusive and cannot be simultaneously applied.M: Unfortunatley for your religious paradigm, there is no support from genetics. Thus, your paradigm does not merit consideration...unless you chose to come up with something that is ACTUALLY consistent with what is observed experimentally and in nature.PB:
In the paradigm of the MPG such bottlenecks are less relevant, since all information is already present in the genome. Besides, mutations can be introduced rapidly through non-random (directed) mechanisms.M: Unfortunatley, the evidence argues against all genetic information within a single genome...you still have never answered any of my posts regarding the consequences your idea would have for sexual reproduction There is also no evidence for non-random directed mutations...if there are please show the specific non-random mutations in the dataset supplied by SLPx.PB:
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].M: You should read the neandertal paper again...the 27 differences are based on comparisons to a distribution of variation in humans. Since the first publication, there are two more neandertal sequences. 10 mutations in which chimps? Bart the chimp in my freezer? Actually your above statement really does not say anything...it says there is a problem with dating and then you supply no problem.PB: 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.M: It is irrelevant to the flood coalescence NECESITY. If ALL animals were reduced to a single breeding pair on Noah's Ark (LOL!) (not counting asexual and hermaphroditic organisms) ALL organisms should show a bottleneck of roughly equal magnitude. That is not observed...worldwide biblical flood falsified...you need to convert to a new religion ...I hear the Scientologists are always looking for new members...PB:
The problem is: the evolutionary paradigm allows for interspecies comparison, while the MPG doesn't (for obvious reasons).M: Because interspecies comparisons destroy your arguements or because you don't believe there are different species on Earth?PB:
If for instance only WITHIN species comparisons are carried out we find completely distinct dates for human origin. That is the reason why evolutionists add 1 chimp sequence to 13 human sequences (ref: Nature 2000, vol408, p708-713.) Otherwise the data do NOT fit the evolutionary paradigm!M: That is your own personal religious fundie paradigm...all it says is that the molecular clock is not accurate which hardly damages the fact of evolution.

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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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As Peter stated this truly is an irrelevant question. I believe even from the evolutionary POV, there is nowhere near enough data to even make speculations, let alone draw any conclusions as to when various species bottlenecks occurred. There is much in the genetic code that is still a big mystery. For example, there are these jumping genes (retrotransposons) that can cause dramatic rearrangement of the genome, and we seem to be light-years away from reverse-engineering these (which BTW give all the appearance of non-random, pre-programmed "mutations").

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FW:But after various bottlenecks, the diversity of the original parent population, at least from a global perspective, has been realized (INTER).
M: Wrong, each bottlenecked group loses some portion of the greater original diversity...it is not sitting there static in wolves who are under selective pressures of their own. If everyone in Africa died tomorrow except for two people, the African population would have suffered a tremendous bottleneck and at the same time, the human gene pool would have lost a tremendous amount of genetic diversity...humanity would not have realized some genetic potential of the original (pre disaster) population as you are claiming.

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I suspect most understand the point I am making, and I suspect you are one of them but are obfuscating with the aid of strawman arguments. It was asked how the diversity of life can be explained given a starting point of 5K years ago with some number of kinds of animals. I illustrated how bottlenecks and subsequent drift would easily account for some if not much of the diversity we see, and I provided dogs as an illustration. I did not say the genome or the gene pool became more diverse. Its diversity was realized . A deck of cards contains some diverse number of different cards (13 in the case of a poker deck). By itself its diversity is not apparent or interesting. When you fan the cards out its diversity is realized, becoming both apparent and interesting. Bottlenecks in a sense help fan the cards because various traits can be amplified. Radiating a population would also fan the cards (or melt them ). Directed mutations (pre-programmed variation) would also fan the cards. Is this really that hard to understand?

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PB:
The problem is: the evolutionary paradigm allows for interspecies comparison, while the MPG doesn't (for obvious reasons).
M: Because interspecies comparisons destroy your arguements

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No, they actually contradict evolutionist arguments: 404 Not Found

Dear mammuthus,PB:
If for instance only WITHIN species comparisons are carried out we find completely distinct dates for human origin. That is the reason why evolutionists add 1 chimp sequence to 13 human sequences (ref: Nature 2000, vol408, p708-713.) Otherwise the data do NOT fit the evolutionary paradigm!M: That is your own personal religious fundie paradigm...all it says is that the molecular clock is not accurate which hardly damages the fact of evolution.PB: It has nothing to do with my own personal religious paradigm. And by the way you know nothing about my religious paradigms. Maybe I do not even have a religious paradigm. All I did is expose your religion as scientifically false.
I studied almost all recent papers in Science and Nature on evolutionism and I know I've seen it through. I know how they keep up the appearance of evolutionism. It has, however, nothing in common with science (add one chimp to a couple of human sequences and voila, everything looks fine!!!). Now, you try to backpedal by questioning the validity if the genetic clock. I do not only question the validity of the clock, I question the paradigm of common descent in general.
As I see it, evolutionism has fallen through molecular biology. Better believe it!
By now, you should have convinced me that evolutionism is true. All you do is defend the old paradigm and rebut my new hypothesis. It looks a lot like the up-side-down world.Best wishes,
Peter

Dear mammuthus,PB:
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].M: You should read the neandertal paper again...the 27 differences are based on comparisons to a distribution of variation in humans. Since the first publication, there are two more neandertal sequences.PB: the other two sequences demonstratede 23 and 28 differences. (Nature 2000, 404: 490-94)M: 10 mutations in which chimps?PB: Not chimp, but an ancient (62ky) human demonstrated 10 diferences compared to the modern human reference sequence.M: Bart the chimp in my freezer? Actually your above statement really does not say anything...it says there is a problem with dating and then you supply no problem.PB: That demonstrates it. Evolutionism is NO science.best wishes,
Peter

Actually Fred, you didn't answer the question as to how X number of "kinds" becomes the diversity of living organisms we see today. You have utterly failed to explain how the homogenizing action of inbreeding depression ("bottleneck") actually creates diversity - merely asserted it does. Your dog example is spurious - they remain the same kind, after all, and their diversity is nowhere near fully "realized" (if I understand whatever the hell that means) since new breeds, cross breeds and backcrosses are being "created" on a regular basis. Genetic drift doesn't create much in the way of diversity (in the sense of being a major mechanism of speciation) either - it merely CAN change the relative frequency of certain alleles and their linkages through a random walk. It can just as easily eliminate alleles as it can change the dominance or preponderance of alleles already present or appearing through random mutation. The only time this leads to speciation is as an adjunct to allopatry (i.e., drift changing the frequency of alleles enough in two separated populations that one or the other can be designated as a separate species).Here's a poser for you: given the historical bottlenecks in cheetahs and elephant seals (I'm feeling generous so I'll let you slide for the moment on the plants we've talked about) where we know from actual records that the populations have been drastically reduced to a few individuals - why haven't new species of cheetahs and elephant seals been produced before our very eyes? After all, you're the one who's claiming that bottlenecks produced lots of new species from the Flood. This IS your mechanism, right?While you're at it - why don't you take a shot at the questions posed to TB on post-Flood biodiversity? I'd be fascinated to hear your answers.

M: It is funny that in the post above you claim that all examples that require a substantive answer from you to support your claims you dismiss as irrelevant..and you wonder that people don't take you seriously....as to inablility to engineer retrotransposons...we do it all the time ...read up, learn, then debate.FW:
I suspect most understand the point I am making, and I suspect you are one of them but are obfuscating with the aid of strawman arguments.M: Definition of FW strawman: Any question Fred has to answer that he cannot.FW:
It was asked how the diversity of life can be explained given a starting point of 5K years ago with some number of kinds of animals. I illustrated how bottlenecks and subsequent drift would easily account for some if not much of the diversity we see, and I provided dogs as an illustration.M: Except that your proposal of dog domestication rests on an incorrect premise. Here is a molecular study on the subject and a releated one for domestication of horses. I don't know if you have access to the second or not.Vila C, Leonard JA, Gotherstrom A, Marklund S, Sandberg K, Liden K, Wayne RK, Ellegren H.
Widespread origins of domestic horse lineages.
Science. 2001 Jan 19;291(5503):474-7.Wayne RK, Ostrander EA. Related Articles, Links
Origin, genetic diversity, and genome structure of the domestic dog.
Bioessays. 1999 Mar;21(3):247-57. ReviewFW:
I did not say the genome or the gene pool became more diverse. Its diversity was realized . A deck of cards contains some diverse number of different cards (13 in the case of a poker deck). By itself its diversity is not apparent or interesting. When you fan the cards out its diversity is realized, becoming both apparent and interesting.M: You are making subjective and qualitative statements on what is interesting with regards to diversity...inbreeding does not release "captive" variation. A severe bottleneck would leave you with a four of hearts and no deck of cards...hardly "realized" diversity.FW:
Bottlenecks in a sense help fan the cards because various traits can be amplified. Radiating a population would also fan the cards (or melt them ).M: This is X files pseudo science babble and has no bearing on the reality of genetic bottlenecks. Bottlenecks leave you with one or two cards from the deck and at their most extreme..no cards i.e. extinction....By the way, none of this helps explain why there is no evidence of bottlenecks in ALL species that would have to have occurred if the ark myth were true...yet another bible killer that you ignored.FW:
Directed mutations (pre-programmed variation) would also fan the cards. Is this really that hard to understand?M: Not hard to understand but it is a myth with no scientific support.