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Author Topic:   Darwin in the Genome
PaulK
Member
Posts: 17909
Joined: 01-10-2003
Member Rating: 7.2


Message 91 of 185 (32090)
02-13-2003 3:52 AM
Reply to: Message 84 by peter borger
02-12-2003 6:37 AM


PB: Thanks for your non-answers. Since you seem to hold scientific truth let's try again to start up a scientific debate on the topic. These are the points I have made and are still unsolved.
PK3 Note that this drops the ongoing discussion.
PK says:
If you want a scientific discussion we can start with your explanation of how non-random mutations actually refute NDT - after all refusing to explain your criticisms is non-scientific as you said. But itI also notice that providing the link to prove my claim - as you demanded seems to be considered a "non-answer".
PB2: Your link is a non-answer for I already rebutted mail #47 in mail #48.
PK3: No, you have not explained why the evidence of taxonomy, biogeography and the fossil record should be held to be irrelevant.
PB (cont): And, since you keep repeating that I have to demonstrate NRM to refute NDT (what I did months ago, but apparently youdon't read my mails)
PK3: Then provide a link to the post. If you can. Since we both know that you don;t understand this point we both know that all you'll ocme up wiht is assertions.
PB cont :let's find out what Dr Caporale has to say about this in her excellent book that is a big thorn in the eye of the orthodox evolutionists. From Darwin in the Genome:
"Once we learned about DNA, we saw that mistakes in copying generate mutations and so we've assumed that random mutation followed by selection underlies evolution. However, I have come to the conclusion that using our current knowledge to expand on Darwin's insights does not require that all mutations be random with respect to their potential effects on biological function". (page 42).
PK3 : So Dr. Caporale clearly says that the randomness of mutations was only "assumed" and that the assumed randomness was "with respect to biological function" (as I have said - obviously you read neither my posts nor the book) and that such a view is "not required" for evolution. Thanks for providing a quote which so neatly illustrates your errors.
Quotes cont:
"So, E coli cannot randomly try every possible change and then wait for selection to capture the very best one". (page72).
"Randomly trying out mutations in each copy of each of many thousands of gene families could mean eons spent wandering lost through the broad mutation landscape, in spite of the fact that information could be could be available to help guide the journey. Still, most people assume that mutaions happen randomly throughout the duplicated genes, and that natural selection picks those that lead to a useful new function". (page 129).
Which goes on to state that particular parts of the gene - the binding sites are more prone to mutation - and that is the limit of the "non-random" nature proposed. This is also consistent of Dr Caporales view that evolutionary theory must be expanded to include genomic strategies.
Quotes continue:
"New levels of interaction and regulation rarely arise through letter by letter random mutations of random DNA sequences". (page 144).
PK3: Which is only a problem for people - like Lee Spetner - who for some strange reason insist that evolution is limited to point mutations
"The genomic landscape is huge. Random wandering through the landscape of possible mutations is no the most efficient strategy for long term survival. In our own case, random mutation would mean that any one of the more than 3 billion spots in our genome had the same probablity of each kind of change." (page 185).
PK3 : And goes on to say "It does not mean all mutations are precisely targetted" And of course this does not refer to evolutionary theory which never seems to have cared much about the issue.
"Current evolutionary theory states that variation results from genetic changes that remain forever random, and that selection operates upon the results of this random genetic variation. It is time toincorporate the observations described in this book into evolutionary biology". (page 192).
I completely agree and I already mentioned this in a mail in May 2002: NDT RIP. Then, it was firmly denied and now here we have Dr Caporale with exactly the same claim. You can of course deny her, too.
PK3L I suggest you provide a link to this, too or I will assume that you are lying. But note that I do not deny it at all and have expressed ageement with it. It is you that has disagreed by insisting that instead of following the rourt proposed by Dr Caporale, evolution should be thrown out and replaced by your idle musings.
PK (cont): As is my list of examples which show that _Darwin in the Genome_ refutes your claim that information is never added to the genome (proving my point that the book is a greater problem for your views than for NDT).
PB: Apparently you didn't read the book properly. The mechanisms described are included in GUToB.
PK3: Then the GUToB claims that information can be added to the genome. It seems that the GUToB is inconsistent.
PK (cont): In short your idea of a "scientific" discussion means dropping the discussion because your errors are being revealed.
PB: What a humbug. I've never dropped a discussion. As a matter of fact, I have won all my discussions with evo's. (Till now, Dr Douglas Theobald from the Talk-origin was the best defender of evolutionism, but not good enough. He couldn't defend the IL-1 beta incongruence).
PK3: Since you did start this part of the discussion to stop a previous discussion, and given your habit of proclaiming victory even when you have lost (and noting your abject defeat on another thread currntly in progress) your statment is so obivously false I can only conclude that you are either a compulsive liar or deeply delusional
PB(cont) In response to:
PB: 1) Non-Random Mutations type 1 (NRM1). This type of NRM introduces mutations on the same positions and the position where they are introduced depends on the flanking DNA regions. NRM1 are also known as ‘positional NRM’. NRM1 have been also observed in the ZFY region and in mtDNA. NRM1 has been observed in T4 by Lynn Ripley and was described in Caporale’s book (page 37, 38). Implications: NRM1 will line up and give the illusion of common descent in phylogenetic analysis.
Since phylo-geneticists cannot exclude NRM1, this type of mutations invalidates the evolutionary conclusions that the alignment of genes and shared mutations is proof for common descent.
PK says:
Anyway to deal with your assertions.
1) p37-38 deal with the "hairpin" model. Since such models require that the existing sequence is similar they can only upset phylogenetic analysis at fine resolutions- which you apparently accept,
unless you wish to claim each species is a seperate creation (which would then pose the question of why the sequences are similar enough to see such mutations). It poses no threat to the larger scale phylogenies which you seem to object to.
PB2:
At present, the hairpin model is able to explain specific NRM in T4. There is no reason to assumethat additional mechanism are not operative in the genome. As mentioned several times before, since you cannot exclude NRM, evidence of common descent based upon shared mutations is a nonscientific conclusion. You have to exclude NRM in the assessed sequence. I have demonstrated NRM for the ZFY region and mtDNA on this board and that should have far reaching consequences for evolutionism (if it is science).
PK3: Since your argument requires assuming mechanisms that have not been observed and for which there is no reason to even think that they plausibly might then I can only say that you have a strange view of science. I add that since the mechanism you did quote did not support your claims it seems that your best evidennce is wholly inadequate. And if you havve REALLY demonstrated NRM of the sort you assume for the regiosn you claim, provide a link to the relevant posts.
PB(cont)
In response to: PB: 2) Non-Random Mutations type 2 (NRM2). This type of NRM is mediated by protein and/or RNA driven mechanism that translocate preexisting DNA elements, or vary nucleotides in genes in a
similar fashion as observed for immunoglobulins. NRM2 also plays a pivotal role in parasite-host interactions, and are likely to be abundant in other interactions between organisms where ‘evolutionary armsrace’ is ongoing. They have been demonstrated beyond any doubt for the 1G5gene in Drosophila. Implications: Alignment of mutations (‘shared mutations’) in related MPGs. Variation is preexisting.
PK says:
2) Translocations - since these require that the material to be translocated is already present in the genome it would seem that your "related MPGs" are related by common descent. I thought your
assertion was that MPGs were NOT related in that way.
PB2: Correct, there is only common descent within MPGs. Related MPGs have been created. Why would the Creator reinvent the wheel? It is illogic. A gene encoding cytochrome in chimp works as good as it works in human. So, if it mutates nonrandomly in human, also in chimp. What you observe is the illusion of common descent. I have provided evidence for this view in the ZFY region in primates.
PK3: So far as is known all versions of cytochrome C work in anything which requires it. So why is yeast cytochrome-C so different from that in chimps ? Given that there are many alternative choices why did your hypothetical designer choose to produce a pattern consistent with common descent ?
PK (cont): It seems to me that again translocations can only interfere with phylogenies at the fine resolution of individual branch points and can only do so because large scale evolution is correct.
PB: Tranlocation of genetic elements may affect gene expression and thus induce variation within the MPG. That was my claim, not that they affect the illusion of common descent. It probably depends on the DNA sequences (docking sites, recognition sites) where the elements translocate to. If the MPG is similar probably such nonrandom translocation of DNA elements also line up. "Expect the unexpected"
PK3 : Gene expression would affect the phenotype so it is not relevant to my argument which only deals with the genotype. Given that both the transposed element and the area it is transposed too must already be similar, if not identical, for there to be any problem the evidence for large scale evolution remains untouched because such mutations can never explain the initial similarity required for them to even be a possible problem.
PB (cont)In response to:
3) NRM1 and NRM2 explain observed biological variation. It tells us that the mechanisms for biological variation are already preexistent in the genomes of organisms (=multipurpose genome) and can be activated upon the right triggers. Darwin was the first to discover the MPG, but his extrapolation of microbe-to-man evolution is completely, entirely unwarranted because the phenomena are unequal. (Unless you assume an uncommitted MPG of the original microbe we all evolved from). That Darwin’s extrapolation on variation in Galapagos finches to support
‘microbe-to-man-evolution’ is unwarranted is also demonstrated by observations that ‘his’ finches are still able to interbreed (Science, 26 April 2001). Thus, they are still the same MPG.
PK says:
3) Your list is hardly exhaustive and so to suggest that these two factors alone account for all variation would be an obvious error. However unless you make that error your assertion is clearly unproven.
PB: Of course there are many more preexisting/preprogrammed mechanism to induce variation in the MPG, but where does help that help you? Why would it unprove my assertion?
PK3 : It helps me to point out the additional mechanisms exist because they contradict your claims. For instance lateral transfer is one of the biggest problems in working out phylogenies in bacteria - but it contradicts the GUToB claim that information cannot be added to the genome. It would also make your presentation of your assertion more honest which I would regard as an improvement, even if it undermines the assertion itself.
PK (cont): I also note that you insist on repeating your false claim about Darwin, despite the fact that you know it to be untrue. The former is unscientific, the unscientific and dishonest.
PB: None of these remarks relates to my claim that Darwin made an unwarranted extrapolation.Maybe you could point it out. I mean how is your answer related to my claim? I almost have to believe that you agree with me on Darwin's unwarranted extrapolation.
PK3; They directly relate to precisely that claim which I regard as an outright lie.
PB (cont) Since you were unable to rebut my claims, evolutionism still stands refuted. But at least you gave it a try.
PK3: A good example of your tendancy to claim victory when in fact your have been defeated.
PB(cont) Finally, I owe you the Dr Caporales vision on Junk DNA:
"Now that our genome is available, we will be able to connect these slippery DNA regions to their-finetuning-knob role, if they have one. But we will be able to do this only if we look into our genome with
some respect, seeking to learn. We will not find them if we dismiss boring repetitive sequences asjunk DNA". (page 69).
"Transposons are found among the many repetitive sequences in the genome that have been called 'junk DNA'. They are by no stretch of imagination useless junk, however." (page 149).
PK3: I note that these deal with only a small fracton of "junk" DNA. Most "junk" DNA stilll seems to be no more than "junk"
PB: Dawkins is out.
PK3: And the reason for indulging your petty personal hatreds is ?

This message is a reply to:
 Message 84 by peter borger, posted 02-12-2003 6:37 AM peter borger has replied

Replies to this message:
 Message 94 by peter borger, posted 02-13-2003 8:16 PM PaulK has replied
 Message 104 by peter borger, posted 02-14-2003 7:50 PM PaulK has replied

derwood
Member (Idle past 2126 days)
Posts: 1457
Joined: 12-27-2001


Message 92 of 185 (32137)
02-13-2003 2:59 PM
Reply to: Message 87 by peter borger
02-12-2003 7:10 PM


Yes, Borger - the reason is I DIDN'T SEE IT.
I know your condition makes you think that you are both a target and the center of attention, but no Petey, not everyone hurries hgome to see the latest Borger bilge-spewing spectacular...
You, on the other hand, are still ignoring the answer I gave to your naive question.

This message is a reply to:
 Message 87 by peter borger, posted 02-12-2003 7:10 PM peter borger has replied

Replies to this message:
 Message 93 by peter borger, posted 02-13-2003 5:46 PM derwood has not replied

peter borger
Member (Idle past 7915 days)
Posts: 965
From: australia
Joined: 07-05-2002


Message 93 of 185 (32155)
02-13-2003 5:46 PM
Reply to: Message 92 by derwood
02-13-2003 2:59 PM


hi Page,
PB: Thanks for you response.
Page: Yes, Borger - the reason is I DIDN'T SEE IT.
I know your condition makes you think that you are both a target and the center of attention, but no Petey, not everyone hurries hgome to see the latest Borger bilge-spewing spectacular...
PB: If this is true, than you make me the target isn't it? Because I can rebut all your rebuttals, I guess? Remember our little chat about ancient mtDNA and the primate ZFY region? Both clear victories for 'creationist' Borger.
Page: You, on the other hand, are still ignoring the answer I gave to your naive question.
PB: Ignoring? I think you provided me with one of several interesting options. It doesn't have to be the right one. The issue is that you simply mail stuff and I have to guess what the abbreviations stand for. If you, for once showed a bit of coopration, it would improve our discussion. But it seems that you like to keep it blur. If not, provide all full names for the abbreviations and a phylogenetic tree, than we are able to discuss your ultimate evidence for common descent in detail. The good thing about your example is that we can pin it down to point mutations.
Best wishes,
Peter

This message is a reply to:
 Message 92 by derwood, posted 02-13-2003 2:59 PM derwood has not replied

peter borger
Member (Idle past 7915 days)
Posts: 965
From: australia
Joined: 07-05-2002


Message 94 of 185 (32170)
02-13-2003 8:16 PM
Reply to: Message 91 by PaulK
02-13-2003 3:52 AM


dear Paul,
First this one:
PK3: It helps me to point out the additional mechanisms exist because they contradict your claims. For instance lateral transfer is one of the biggest problems in working out phylogenies in bacteria - but it contradicts the GUToB claim that information cannot be added to the genome. It would also make your presentation of your assertion more honest which I would regard as an improvement, even if it undermines the assertion itself.
PB: According to GUToB eubacteria are one (or probably a few) MPGs. It remains to be assed how many. They exchange and recombine DNA all the time. Like stone corals (MPG).
(A complete reply will follow soon)
best wishes,
Peter

This message is a reply to:
 Message 91 by PaulK, posted 02-13-2003 3:52 AM PaulK has replied

Replies to this message:
 Message 95 by PaulK, posted 02-14-2003 2:38 AM peter borger has replied

PaulK
Member
Posts: 17909
Joined: 01-10-2003
Member Rating: 7.2


Message 95 of 185 (32204)
02-14-2003 2:38 AM
Reply to: Message 94 by peter borger
02-13-2003 8:16 PM


Lateral transfers - if they are to have any effect at all - must add information to the genome (in the sense that the genome has information).
Quoting Dr Caporale "In one bacterial genome, the gene encoding an enzyme that digests a carbohydrate was pieced together out of DNA from two different species" p79
Don't forget the links - you wouldn't want us to think you were lying about those posts, would you ?

This message is a reply to:
 Message 94 by peter borger, posted 02-13-2003 8:16 PM peter borger has replied

Replies to this message:
 Message 98 by peter borger, posted 02-14-2003 12:03 PM PaulK has replied

derwood
Member (Idle past 2126 days)
Posts: 1457
Joined: 12-27-2001


Message 96 of 185 (32233)
02-14-2003 10:52 AM


quote:
Page: Yes, Borger - the reason is I DIDN'T SEE IT.
I know your condition makes you think that you are both a target and the center of attention, but no Petey, not everyone hurries hgome to see the latest Borger bilge-spewing spectacular...
PB: If this is true, than you make me the target isn't it?
Please read what was actually written. I said that in fact I do NOT read each of your supidity parades.
quote:
Because I can rebut all your rebuttals, I guess?
Yes, that must be it.... Just like tou disproved evolution by observing the 'change' between Tob and Cap...
quote:
Remember our little chat about ancient mtDNA and the primate ZFY region? Both clear victories for 'creationist' Borger.
Now THAT is funny. I did not realize that ignoring reality and employing double standards would be coinsidered aq 'victory', but I forget that you are a creationist. I will gladly revisit those issues if you think you actually had something legitimate to discuss. But this time, I will not be so pleasant when you start misrepresenting my position to erect strawmen.
quote:
Page: You, on the other hand, are still ignoring the answer I gave to your naive question.
PB: Ignoring? I think you provided me with one of several interesting options. It doesn't have to be the right one.
LOL!
Yes, i guess the fact that you didn't know what the species were is just 'one option.' The creationist mind is a sight to behold...
quote:
The issue is that you simply mail stuff and I have to guess what the abbreviations stand for.
I mailed nothing. I provided a link. If you didn't know what the abbreviationswere, why on earth did you make the stupid choice of pontification?
quote:
If you, for once showed a bit of coopration, it would improve our discussion. But it seems that you like to keep it blur. If not, provide all full names for the abbreviations and a phylogenetic tree, than we are able to discuss your ultimate evidence for common descent in detail. The good thing about your example is that we can pin it down to point mutations.
I thought you said that you had read my stuff?
Was that a lie, too?

Replies to this message:
 Message 97 by peter borger, posted 02-14-2003 10:57 AM derwood has replied

peter borger
Member (Idle past 7915 days)
Posts: 965
From: australia
Joined: 07-05-2002


Message 97 of 185 (32234)
02-14-2003 10:57 AM
Reply to: Message 96 by derwood
02-14-2003 10:52 AM


Dear Page,
Apparently you do not want to discuss anymore.
You make it to easy for me.
Best wishes,
Peter

This message is a reply to:
 Message 96 by derwood, posted 02-14-2003 10:52 AM derwood has replied

Replies to this message:
 Message 99 by derwood, posted 02-14-2003 1:01 PM peter borger has replied

peter borger
Member (Idle past 7915 days)
Posts: 965
From: australia
Joined: 07-05-2002


Message 98 of 185 (32242)
02-14-2003 12:03 PM
Reply to: Message 95 by PaulK
02-14-2003 2:38 AM


Dear Paul,
PK: Lateral transfers - if they are to have any effect at all - must add information to the genome (in the sense that the genome has information).
PB: Elaborate on this one please.
PK: Quoting Dr Caporale "In one bacterial genome, the gene encoding an enzyme that digests a carbohydrate was pieced together out of DNA from two different species" p79
PB: ever heard of recombination?
PK: Don't forget the links - you wouldn't want us to think you were lying about those posts, would you ?
PB: You already have all necessary links in message #48. Probably you didn't read them yet.
[Us?]
Best wishes,
Peter

This message is a reply to:
 Message 95 by PaulK, posted 02-14-2003 2:38 AM PaulK has replied

Replies to this message:
 Message 100 by PaulK, posted 02-14-2003 2:38 PM peter borger has replied

derwood
Member (Idle past 2126 days)
Posts: 1457
Joined: 12-27-2001


Message 99 of 185 (32258)
02-14-2003 1:01 PM
Reply to: Message 97 by peter borger
02-14-2003 10:57 AM


quote:
Apparently you do not want to discuss anymore.
You make it to easy for me.
Discuss what?
Your naievete?
You display that daily.
I really have no idea what you are blsabbering about now.
Then, you probably don't either.
I understand that lithium can help your condition.

This message is a reply to:
 Message 97 by peter borger, posted 02-14-2003 10:57 AM peter borger has replied

Replies to this message:
 Message 102 by peter borger, posted 02-14-2003 6:17 PM derwood has replied

PaulK
Member
Posts: 17909
Joined: 01-10-2003
Member Rating: 7.2


Message 100 of 185 (32268)
02-14-2003 2:38 PM
Reply to: Message 98 by peter borger
02-14-2003 12:03 PM


Lateral transfer is where DNA froum OUTSIDE the genome is incorporated INTO the genome. Therefore lateral transfer adds information not previously in the genome. Isn't that obvious ?
PK: Quoting Dr Caporale "In one bacterial genome, the gene encoding an enzyme that digests a carbohydrate was pieced together out of DNA from two different species" p79
PB: ever heard of recombination?
PK2: Yes. It does not take genes out of OTHER SPECIES. Did you actually READ the quote ?
PK: Don't forget the links - you wouldn't want us to think you were lying about those posts, would you ?
PB: You already have all necessary links in message #48. Probably you didn't read them yet.
PK2: If the links to the messages I asked for are there then it should be easy for you to identify which link links to which message. If on the other hand then it is not the case that you have provided the links. All I am doing is asking you to back up your statements in the same way you demanded of me.
And since at least four people other than you are reading this thread, and will have noticed that you demanded a link - not a list of LONG threads one of which might contain one of the messages somewhere - my use of "us" is entirely reasonable.
[This message has been edited by PaulK, 02-14-2003]

This message is a reply to:
 Message 98 by peter borger, posted 02-14-2003 12:03 PM peter borger has replied

Replies to this message:
 Message 101 by derwood, posted 02-14-2003 3:28 PM PaulK has not replied
 Message 103 by peter borger, posted 02-14-2003 6:48 PM PaulK has not replied

derwood
Member (Idle past 2126 days)
Posts: 1457
Joined: 12-27-2001


Message 101 of 185 (32279)
02-14-2003 3:28 PM
Reply to: Message 100 by PaulK
02-14-2003 2:38 PM


quote:
my use of "us" is entirely reasonable.
Yeah, Borger got on me for using the word "us" as well.
He just doesn't get it...

This message is a reply to:
 Message 100 by PaulK, posted 02-14-2003 2:38 PM PaulK has not replied

peter borger
Member (Idle past 7915 days)
Posts: 965
From: australia
Joined: 07-05-2002


Message 102 of 185 (32292)
02-14-2003 6:17 PM
Reply to: Message 99 by derwood
02-14-2003 1:01 PM


Dear Page,
quote:
--------------------------------------------------------------------------------
Apparently you do not want to discuss anymore.
You make it to easy for me.
--------------------------------------------------------------------------------
Page: Discuss what? Your naievete? You display that daily. I really have no idea what you are blsabbering about now. Then, you probably don't either. I understand that lithium can help your condition.
PB: This message once more marks your defeat.
Why, I wonder, didn't you follow Dawkins advice not to discuss with creationists? You would have been better of. Now you keep making a fool of yourself.
O, I see, you are a PhD-ed evobiologist.
Even a better reason not to become involved in such debates.
Best wishes,
Peter

This message is a reply to:
 Message 99 by derwood, posted 02-14-2003 1:01 PM derwood has replied

Replies to this message:
 Message 118 by derwood, posted 02-18-2003 1:28 PM peter borger has replied

peter borger
Member (Idle past 7915 days)
Posts: 965
From: australia
Joined: 07-05-2002


Message 103 of 185 (32295)
02-14-2003 6:48 PM
Reply to: Message 100 by PaulK
02-14-2003 2:38 PM


Dear Paul,
PK: Lateral transfer is where DNA froum OUTSIDE the genome is incorporated INTO the genome. Therefore lateral transfer adds information not previously in the genome. Isn't that obvious ?
PB2: And therefore it is GUToB. I already mentioned that bacteria are probably a few MPG that can exchange and recombine DNA all the time. It is guided by hihly specific preexisting/preprogrammed DNA uptake mechanisms of which the details are nor even understoof yet. I guess, these mechanism arose from scratch?
PK: Quoting Dr Caporale "In one bacterial genome, the gene encoding an enzyme that digests a carbohydrate was pieced together out of DNA from two different species" p79
PB: a never heard of recombination?
PK2: Yes. It does not take genes out of OTHER SPECIES. Did you actually READ the quote ?
PB2: Yes, I did. It holds that a 'novel' gene recombined from two preexisting genes. Sounds a lot like GUToB rule #3. So it is recombination of preexisting DNA elements, not evolution.
PK: Don't forget the links - you wouldn't want us to think you were lying about those posts, would you ?
PB: You already have all necessary links in message #48. Probably you didn't read them yet.
PK2: If the links to the messages I asked for are there then it should be easy for you to identify which link links to which message. If on the other hand then it is not the case that you have provided the links. All I am doing is asking you to back up your statements in the same way you demanded of me.
PB2: About NRM in the 1G5 gene in drosophila:
http://EvC Forum: molecular genetic proof against random mutation (1) -->EvC Forum: molecular genetic proof against random mutation (1)
About NRM in the ZFY region in primates:
http://EvC Forum: Dr Page's best example of common descent easily --and better-- explained by the GUToB -->EvC Forum: Dr Page's best example of common descent easily --and better-- explained by the GUToB
About the ancient human mtDNAs in:
http://EvC Forum: Nucleotide sequence variation in ancient human mtDNA -->EvC Forum: Nucleotide sequence variation in ancient human mtDNA
PK: And since at least four people other than you are reading this thread, and will have noticed that you demanded a link - not a list of LONG threads one of which might contain one of the messages somewhere - my use of "us" is entirely reasonable.
PB: That explains. Some people use us as pluralis majestatis.
Best wishes,
Peter

This message is a reply to:
 Message 100 by PaulK, posted 02-14-2003 2:38 PM PaulK has not replied

peter borger
Member (Idle past 7915 days)
Posts: 965
From: australia
Joined: 07-05-2002


Message 104 of 185 (32300)
02-14-2003 7:50 PM
Reply to: Message 91 by PaulK
02-13-2003 3:52 AM


Dear Paul,
PB: Thanks for your non-answers. Since you seem to hold scientific truth let's try again to start up a scientific debate on the topic. These are the points I have made and are still unsolved.
PK3 Note that this drops the ongoing discussion.
PK says:
If you want a scientific discussion we can start with your explanation of how non-random mutations actually refute NDT - after all refusing to explain your criticisms is non-scientific as you said. But itI also notice that providing the link to prove my claim - as you demanded seems to be considered a "non-answer".
PB2: Your link is a non-answer for I already rebutted mail #47 in mail #48.
PK3: No, you have not explained why the evidence of taxonomy, biogeography and the fossil record should be held to be irrelevant.
PB3: There is nothing in taxonomy, biogegraphy and fossil record that cannot be explained alternatively. It certainly doesn't unequivaocal evidence for evolution from microbe to man. It even better supports GUToB.
PB (cont): And, since you keep repeating that I have to demonstrate NRM to refute NDT (what I did months ago, but apparently youdon't read my mails)
PK3: Then provide a link to the post. If you can. Since we both know that you don;t understand this point we both know that all you'll ocme up wiht is assertions.
PB3: I already did that in message #103.
PB cont :let's find out what Dr Caporale has to say about this in her excellent book that is a big thorn in the eye of the orthodox evolutionists. From Darwin in the Genome:
"Once we learned about DNA, we saw that mistakes in copying generate mutations and so we've assumed that random mutation followed by selection underlies evolution. However, I have come to the conclusion that using our current knowledge to expand on Darwin's insights does not require that all mutations be random with respect to their potential effects on biological function". (page 42).
PK3 : So Dr. Caporale clearly says that the randomness of mutations was only "assumed" and that the assumed randomness was "with respect to biological function" (as I have said - obviously you read neither my posts nor the book) and that such a view is "not required" for evolution. Thanks for providing a quote which so neatly illustrates your errors.
PB3: evolution unequals NDT. I claimed to overthrow NDT and that is what I did. Caporale's quotes back me up. That you think Caporale's book is entirely consistent with evolutionism is your believe. Problem is now you have to explain Caporale's observation from NDT. That there is selection for such mechanism is not the question. But the origin of such mechanism from scratch is the question. And that unique proteins are involved NRM has been demonstraed in mammals. They have a unique protein to carry out recombinations in the germline of immunoglobulins.
Quotes cont:
"So, E coli cannot randomly try every possible change and then wait for selection to capture the very best one". (page72).
"Randomly trying out mutations in each copy of each of many thousands of gene families could mean eons spent wandering lost through the broad mutation landscape, in spite of the fact that information could be could be available to help guide the journey. Still, most people assume that mutaions happen randomly throughout the duplicated genes, and that natural selection picks those that lead to a useful new function". (page 129).
PK3: Which goes on to state that particular parts of the gene - the binding sites are more prone to mutation - and that is the limit of the "non-random" nature proposed. This is also consistent of Dr Caporales view that evolutionary theory must be expanded to include genomic strategies.
PB3: Yep, and is the end of NDT.
Quotes continue:
"New levels of interaction and regulation rarely arise through letter by letter random mutations of random DNA sequences". (page 144).
PK3: Which is only a problem for people - like Lee Spetner - who for some strange reason insist that evolution is limited to point mutations.
PB3: Spetner -at least- thought thoroughly on the issue evo's try to address, that's for sure. Building a living cell from scratch, which requires at least 1000-2000 regulated and expressed genes, through an utter random mechanism is not-to-discuss nonsense. People who think it is possible are like medieval alchemists trying to make gold from lead. They didn't understand the laws of nature. It has proven to be a waste of time.
quotes (cont):
"The genomic landscape is huge. Random wandering through the landscape of possible mutations is no the most efficient strategy for long term survival. In our own case, random mutation would mean that any one of the more than 3 billion spots in our genome had the same probablity of each kind of change." (page 185).
PK3 : And goes on to say "It does not mean all mutations are precisely targetted" And of course this does not refer to evolutionary theory which never seems to have cared much about the issue.
PB3: Still, not all mutations are random.
(cont)
"Current evolutionary theory states that variation results from genetic changes that remain forever random, and that selection operates upon the results of this random genetic variation. It is time toincorporate the observations described in this book into evolutionary biology". (page 192).
PB: I completely agree and I already mentioned this in a mail in May 2002: NDT RIP. Then, it was firmly denied and now here we have Dr Caporale with exactly the same claim. You can of course deny her, too.
PK3: I suggest you provide a link to this, too or I will assume that you are lying. But note that I do not deny it at all and have expressed ageement with it. It is you that has disagreed by insisting that instead of following the rourt proposed by Dr Caporale, evolution should be thrown out and replaced by your idle musings.
PB: Lying about what. That Caporale's examples are the end of NDT?
PK (cont): As is my list of examples which show that _Darwin in the Genome_ refutes your claim that information is never added to the genome (proving my point that the book is a greater problem for your views than for NDT).
PB: Apparently you didn't read the book properly. The mechanisms described are included in GUToB.
PK3: Then the GUToB claims that information can be added to the genome. It seems that the GUToB is inconsistent.
PB3: The GUToB claims that 'novel' genes are always related to preexisting DNA elements.
PK (cont): In short your idea of a "scientific" discussion means dropping the discussion because your errors are being revealed.
PB: What a humbug. I've never dropped a discussion. As a matter of fact, I have won all my discussions with evo's. (Till now, Dr Douglas Theobald from the Talk-origin was the best defender of evolutionism, but not good enough. He couldn't defend the IL-1 beta incongruence).
PK3: Since you did start this part of the discussion to stop a previous discussion, and given your habit of proclaiming victory even when you have lost (and noting your abject defeat on another thread currntly in progress) your statment is so obivously false I can only conclude that you are either a compulsive liar or deeply delusional
PB3: I dragged it back in focus. This thread is about NRM as described in Dr Caporale's book. I summarised the 2 types of NRM and what they mean for evolutionism.
PB(cont) In response to:
PB: 1) Non-Random Mutations type 1 (NRM1). This type of NRM introduces mutations on the same positions and the position where they are introduced depends on the flanking DNA regions. NRM1 are also known as ‘positional NRM’. NRM1 have been also observed in the ZFY region and in mtDNA. NRM1 has been observed in T4 by Lynn Ripley and was described in Caporale’s book (page 37, 38). Implications: NRM1 will line up and give the illusion of common descent in phylogenetic analysis.
Since phylo-geneticists cannot exclude NRM1, this type of mutations invalidates the evolutionary conclusions that the alignment of genes and shared mutations is proof for common descent.
PK says:
Anyway to deal with your assertions.
1) p37-38 deal with the "hairpin" model. Since such models require that the existing sequence is similar they can only upset phylogenetic analysis at fine resolutions- which you apparently accept,
unless you wish to claim each species is a seperate creation (which would then pose the question of why the sequences are similar enough to see such mutations). It poses no threat to the larger scale phylogenies which you seem to object to.
PB2:
At present, the hairpin model is able to explain specific NRM in T4. There is no reason to assumethat additional mechanism are not operative in the genome. As mentioned several times before, since you cannot exclude NRM, evidence of common descent based upon shared mutations is a nonscientific conclusion. You have to exclude NRM in the assessed sequence. I have demonstrated NRM for the ZFY region and mtDNA on this board and that should have far reaching consequences for evolutionism (if it is science).
PK3: Since your argument requires assuming mechanisms that have not been observed and for which there is no reason to even think that they plausibly might then I can only say that you have a strange view of science.
PB3: What's the big deal? Evolutionism relies also on mechanism that have never been observed. Ever observed the evolution from microbe to man? I didn't, neither did you. It is all inference.
Also, ever observed a graviton?
PK3 (cont): I add that since the mechanism you did quote did not support your claims it seems that your best evidennce is wholly inadequate. And if you havve REALLY demonstrated NRM of the sort you assume for the regiosn you claim, provide a link to the relevant posts.
PB3: links to be found in message #103.
PB(cont):
In response to: PB: 2) Non-Random Mutations type 2 (NRM2). This type of NRM is mediated by protein and/or RNA driven mechanism that translocate preexisting DNA elements, or vary nucleotides in genes in a similar fashion as observed for immunoglobulins. NRM2 also plays a pivotal role in parasite-host interactions, and are likely to be abundant in other interactions between organisms where ‘evolutionary armsrace’ is ongoing. They have been demonstrated beyond any doubt for the 1G5gene in Drosophila. Implications: Alignment of mutations (‘shared mutations’) in related MPGs. Variation is preexisting.
PK says:
2) Translocations - since these require that the material to be translocated is already present in the genome it would seem that your "related MPGs" are related by common descent. I thought your
assertion was that MPGs were NOT related in that way.
PB2: Correct, there is only common descent within MPGs. Related MPGs have been created. Why would the Creator reinvent the wheel? It is illogic. A gene encoding cytochrome in chimp works as good as it works in human. So, if it mutates nonrandomly in human, also in chimp. What you observe is the illusion of common descent. I have provided evidence for this view in the ZFY region in primates.
PK3: So far as is known all versions of cytochrome C work in anything which requires it. So why is yeast cytochrome-C so different from that in chimps ? Given that there are many alternative choices why did your hypothetical designer choose to produce a pattern consistent with common descent?
PB3: I am not so sure whether or not Cyt C can be interchanged between organisms without any effect. Does is imply that you can also interchange all other proteins without effect? Than, it would suggest that proteins are not relevant in specifiying the species. Probably there are not so many alternatives. And the pattern is probably not consistent with common descent (Zhang and Chinappa, Mol Biol Evol 1994, 11:365).
PK (cont): It seems to me that again translocations can only interfere with phylogenies at the fine resolution of individual branch points and can only do so because large scale evolution is correct.
PB3: Translocations usually take place at exacly the same spot. As observed for several types of leukemia that are due to translocation. Translocation that are neutral are usually not observed, but might be present in the same spot too.
PB: Translocation of genetic elements may affect gene expression and thus induce variation within the MPG. That was my claim, not that they affect the illusion of common descent. It probably depends on the DNA sequences (docking sites, recognition sites) where the elements translocate to. If the MPG is similar probably such nonrandom translocation of DNA elements also line up. "Expect the unexpected"
PK3 : Gene expression would affect the phenotype so it is not relevant to my argument which only deals with the genotype.
PB3: Since when is the phenotype irrelevant to evolution?
PK3 (cont): Given that both the transposed element and the area it is transposed too must already be similar, if not identical, for there to be any problem the evidence for large scale evolution remains untouched because such mutations can never explain the initial similarity required for them to even be a possible problem.
PB3: depends on the DNA region/chromosome you study.
PB (cont): In response to:
3) NRM1 and NRM2 explain observed biological variation. It tells us that the mechanisms for biological variation are already preexistent in the genomes of organisms (=multipurpose genome) and can be activated upon the right triggers. Darwin was the first to discover the MPG, but his extrapolation of microbe-to-man evolution is completely, entirely unwarranted because the phenomena are unequal. (Unless you assume an uncommitted MPG of the original microbe we all evolved from). That Darwin’s extrapolation on variation in Galapagos finches to support
‘microbe-to-man-evolution’ is unwarranted is also demonstrated by observations that ‘his’ finches are still able to interbreed (Science, 26 April 2001). Thus, they are still the same MPG.
PK says:
3) Your list is hardly exhaustive and so to suggest that these two factors alone account for all variation would be an obvious error. However unless you make that error your assertion is clearly unproven.
PB: Of course there are many more preexisting/preprogrammed mechanism to induce variation in the MPG, but where does help that help you? Why would it unprove my assertion?
PK3 : It helps me to point out the additional mechanisms exist because they contradict your claims. For instance lateral transfer is one of the biggest problems in working out phylogenies in bacteria - but it contradicts the GUToB claim that information cannot be added to the genome. It would also make your presentation of your assertion more honest which I would regard as an improvement, even if it undermines the assertion itself.
PB3: Where does this help you rebutting point 3? It doesn't.
PK (cont): I also note that you insist on repeating your false claim about Darwin, despite the fact that you know it to be untrue. The former is unscientific, the unscientific and dishonest.
PB: None of these remarks relates to my claim that Darwin made an unwarranted extrapolation.Maybe you could point it out. I mean how is your answer related to my claim? I almost have to believe that you agree with me on Darwin's unwarranted extrapolation.
PK3; They directly relate to precisely that claim which I regard as an outright lie.
PB3: Even if Darwin had more such examples (e.g. mockingbirds, pigeons, cats, dogs, etc) they don't go beyond his finches. It is all MPG (=GUToB).
PB (cont) Since you were unable to rebut my claims, evolutionism still stands refuted. But at least you gave it a try.
PK3: A good example of your tendancy to claim victory when in fact your have been defeated.
PB3: You didn't rebut claim 3. Or maybe I missed it. Point it out, please.
PB(cont): Finally, I owe you the Dr Caporales vision on Junk DNA:
"Now that our genome is available, we will be able to connect these slippery DNA regions to their-finetuning-knob role, if they have one. But we will be able to do this only if we look into our genome with
some respect, seeking to learn. We will not find them if we dismiss boring repetitive sequences asjunk DNA". (page 69).
"Transposons are found among the many repetitive sequences in the genome that have been called 'junk DNA'. They are by no stretch of imagination useless junk, however." (page 149).
PK3: I note that these deal with only a small fracton of "junk" DNA. Most "junk" DNA stilll seems to be no more than "junk"
PB: Dawkins is out.
PK3: And the reason for indulging your petty personal hatreds is ?
PB: Good riddance to atheistic nihilism. (nothing personal, though)
Best wishes,
Peter
[This message has been edited by peter borger, 02-14-2003]

This message is a reply to:
 Message 91 by PaulK, posted 02-13-2003 3:52 AM PaulK has replied

Replies to this message:
 Message 106 by PaulK, posted 02-15-2003 12:51 PM peter borger has replied

Quetzal
Member (Idle past 6122 days)
Posts: 3228
Joined: 01-09-2002


Message 105 of 185 (32317)
02-15-2003 4:19 AM


PaulK and Peter Borger: Could you folks please learn to use the UBB "quote /quote" and "qs /qs" functions? The last exchange was practically incomprehensible. I couldn't figure out who said what to whom when and what replies were current. Thanks.
Quetzal: the other thread reader...

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