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Author Topic:   a graph for borger to explain
Quetzal
Member (Idle past 3982 days)
Posts: 3228
Joined: 01-09-2002


Message 31 of 43 (21327)
11-02-2002 4:27 AM
Reply to: Message 29 by Fred Williams
11-01-2002 7:18 PM


quote:
Oh, and your implication that the imability to predict where a mutation will occur somehow disproves non-random mutation is, well, ... Hmm, I'm trying to be kind. Cockamamie. Is that kind enough?

Okay, let's rephrase the question - which has as yet not been answered. IF non-random mutations exist, how would they be identified (i.e., how do you tell the difference between non-random as to position and statistically more likely)? If the non-random mutation hypothesis is true, what evidence would we be able to find in support (or to falsify) the idea? (Please don't simply repeat "IG5, IL-1b, and ZFX/ZFY" ad nauseum - please specifically show how these sequences are non-random).


This message is a reply to:
 Message 29 by Fred Williams, posted 11-01-2002 7:18 PM Fred Williams has responded

Replies to this message:
 Message 33 by mark24, posted 11-04-2002 6:32 AM Quetzal has responded
 Message 37 by Fred Williams, posted 11-04-2002 12:50 PM Quetzal has responded

  
Mammuthus
Member (Idle past 4585 days)
Posts: 3085
From: Munich, Germany
Joined: 08-09-2002


Message 32 of 43 (21489)
11-04-2002 3:33 AM
Reply to: Message 29 by Fred Williams
11-01-2002 7:18 PM


quote:
Originally posted by Fred Williams:
quote:
Originally posted by Mammuthus:
Scrolling through this thread I see you also ducked Monkenstick's question as well as mine.....perhaps if you are smelling a read herring you should check your upper lip for the remains of your odd lunch. It is clear you rather make unsupportable statments rather than addressing the questions....so where again are the mutations going to occur in the HV1 region Mr. Nonrandom? If it is so obvious surely this should be an easy question to answer....

Uh, what question is that, ye puffed up evolutionist who refuses to ever admit a mistake, one so obvious that even fellow evolutionist and layman monkenstick recognized?

Oh, and your implication that the imability to predict where a mutation will occur somehow disproves non-random mutation is, well, ... Hmm, I'm trying to be kind. Cockamamie. Is that kind enough?


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

Well, if it is so obvious then please demonstrate non-random mutation. And if you are claiming that non-random mutation is a non falsifiable hypothesis then you have successfully proved your permanent residency in fantasyland


This message is a reply to:
 Message 29 by Fred Williams, posted 11-01-2002 7:18 PM Fred Williams has not yet responded

  
mark24
Member (Idle past 3305 days)
Posts: 3857
From: UK
Joined: 12-01-2001


Message 33 of 43 (21502)
11-04-2002 6:32 AM
Reply to: Message 31 by Quetzal
11-02-2002 4:27 AM


quote:
Originally posted by Quetzal:

Okay, let's rephrase the question - which has as yet not been answered. IF non-random mutations exist, how would they be identified (i.e., how do you tell the difference between non-random as to position and statistically more likely)? If the non-random mutation hypothesis is true, what evidence would we be able to find in support (or to falsify) the idea? (Please don't simply repeat "IG5, IL-1b, and ZFX/ZFY" ad nauseum - please specifically show how these sequences are non-random).

Quetzal,

I wish you luck, I've been asking a similar question of P.Borger for some time, until he saw fit to no longer answer my posts, that is.

www.evcforum.net/cgi-bin/dm.cgi?action=msg&f=5&t=51&m=118#118 -->www.evcforum.net/cgi-bin/dm.cgi?action=msg&f=5&t=51&m=118#118">http://www.evcforum.net/cgi-bin/dm.cgi?action=msg&f=5&t=51&m=118#118 Part C/

I can see a potential answer, but it requires a LOT of extant sequences & phylogenetic analyses, which both Peter B & Fred eschew, so they lucked out on that one. Beyond that, I don't see ANY possibility of determining hot-spots in ancient sequences from extant ones.

Mark

------------------
Occam's razor is not for shaving with.


This message is a reply to:
 Message 31 by Quetzal, posted 11-02-2002 4:27 AM Quetzal has responded

Replies to this message:
 Message 34 by Quetzal, posted 11-04-2002 6:57 AM mark24 has not yet responded

    
Quetzal
Member (Idle past 3982 days)
Posts: 3228
Joined: 01-09-2002


Message 34 of 43 (21504)
11-04-2002 6:57 AM
Reply to: Message 33 by mark24
11-04-2002 6:32 AM


Shhhh, Mark, you'll give it away.

I know all about PB's continual referral to "non-random mutations". I'm merely trying to figure out a way of phrasing the question where he has no choice but to give an example. As far as hotspots go, all they are is a statistical "figure of speech" as it were - as I've argued with him before. I'm basically trying to get him to focus on a modern example that can definitively be attributed to non-randomness and how that can be distinguished from random. After all, if PB (and now Williams, apparently) are so all-fired sure that non-random mutations exist, they ought to be able to use that to predict something that would be different from random chance, beyond a mere statistical fluke.

I agree on the ancestral bits, although I think it's possible to show rapidly evolving, non-conserved sequences between closely related organisms. Of course, that requires an a priori acceptance that the two organisms ARE related by common descent... Which, I guess, is the point.

I know PB probably won't respond beyond re-asserting what he's already stated. However, maybe Williams is different ("hope oft springs eternal", or words to that effect).


This message is a reply to:
 Message 33 by mark24, posted 11-04-2002 6:32 AM mark24 has not yet responded

  
derwood
Member
Posts: 1457
Joined: 12-27-2001


Message 35 of 43 (21510)
11-04-2002 9:25 AM
Reply to: Message 29 by Fred Williams
11-01-2002 7:18 PM


Is this an example of projecting, or is it just superiorly ironic:

quote:
Originally posted by Fred Williams:

Uh, what question is that, ye puffed up evolutionist who refuses to ever admit a mistake, one so obvious that even fellow evolutionist and layman monkenstick recognized?


I vote a little of each.

Williams is, after all, the 'puffed up' creationist engineer that has claimed to be an 'expert' in information theory, and to have become an expert in a period of three years or so while acknowledging to have done no pertinent research, had no advanced taining, or made any contributions to the field...

Amazing...


This message is a reply to:
 Message 29 by Fred Williams, posted 11-01-2002 7:18 PM Fred Williams has not yet responded

    
derwood
Member
Posts: 1457
Joined: 12-27-2001


Message 36 of 43 (21511)
11-04-2002 9:32 AM


Well, I referred Fred to this:

http://www2.norwich.edu/spage/alignmentgam.htm

or one of my other alignments on several occasions, in order that he could direct his years of scienitfic experience, his information theory expertise, and his acute knowledge of genetics on real data and provide answers to such questions.

He claimed that it was a 'joke' and that one can't tell which mutations are random and which are not.

Apparently, one just has to have Faith...


    
Fred Williams
Member (Idle past 2965 days)
Posts: 310
From: Broomfield
Joined: 12-17-2001


Message 37 of 43 (21539)
11-04-2002 12:50 PM
Reply to: Message 31 by Quetzal
11-02-2002 4:27 AM


quote:
Q: “Okay, let's rephrase the question - which has as yet not been answered. IF non-random mutations exist, how would they be identified”

Easy. See Cairns, Hall, etc. In short, the discovery of mutation(s) that are the result of an adaptive response to some environmental stimuli. Or, mutations that cannot mathematically be attributable to a chance copying mistake in the DNA.

quote:
Q: “If the non-random mutation hypothesis is true, what evidence would we be able to find in support (or to falsify) the idea?”

See Rosenberg, et al. A good paper is “EVOLVING RESPONSIVELY: ADAPTIVE MUTATION”, VOLUME 2, JULY 2001. It’s been over a year so I suspect this paper might be available for free now on the internet. To summarize, Rosenberg claims there is nothing anti-NDT at all about the apparent Lac+ adaptive mutation. She cited data that indicates a sub-population hypermutation occurred which included many unselected mutations within the Lac+ mutants genome, which would be expected if the mutations were behaving in a random, NDT fashion.

As Page pointed out, Cairns recanted some aspect of his original study, but from recent literature Cairns obviously still holds to adaptive mutation, disputing an important claim of the anti-adaptive mutation crowed that virtually all the mutations are occurring in a hyper-mutating sub-population. See

http://www.genetics.org/cgi/content/full/156/2/923?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&author1=Cairns&searchid=1027378300880_2030&stored_search=&FI RSTINDEX=0&journalcode=genet%20ics

As for my stand on non-random mutations, see Messages 44, 59 from July in “molecular genetic proof against random mutation”. To summarize, the primary purpose of my entry into that thread was to defend Peter’s claim that discovery of such mutations falsify the current NDT paradigm, and I provided a quote from leading NDT advocate Dr Futuyma proving it. I stated that I believe there is evidence for non-random mutations, but nothing to hang one’s hat on (Transposons for one have all the appearance of being a non-random, pre-programmed type of mutation). I also once believed non-random mutations would explain Haldane’s Dilemma as it applies to rapid diversification since a flood 5K years ago, but backed off this observation as later personal studies of the dilemma demonstrated that rapid diversification could easily occur without the aid of non-random mutations. Page nevertheless continues to quote statements of mine that I have backed off of (messages 44 & 59 are proof of this, in case Page denies I never told him). This is like those dishonest atheists who will use quotes of Abraham Lincoln before he was a Christian in their attempt to show he was not Christian!

For now, I’m on the sidelines watching the drama play out. I pop into this drama now and then mostly to expose erroneous statements or bad logic like Mamuthus's "good one" in this thread.


This message is a reply to:
 Message 31 by Quetzal, posted 11-02-2002 4:27 AM Quetzal has responded

Replies to this message:
 Message 38 by derwood, posted 11-04-2002 2:17 PM Fred Williams has responded
 Message 40 by Mammuthus, posted 11-04-2002 5:46 PM Fred Williams has not yet responded
 Message 42 by Quetzal, posted 11-05-2002 2:37 AM Fred Williams has not yet responded

    
derwood
Member
Posts: 1457
Joined: 12-27-2001


Message 38 of 43 (21540)
11-04-2002 2:17 PM
Reply to: Message 37 by Fred Williams
11-04-2002 12:50 PM


The creationist is nothing if not predictable and overconfident...

quote:
Originally posted by Fred Williams:
quote:
Q: “Okay, let's rephrase the question - which has as yet not been answered. IF non-random mutations exist, how would they be identified”

Easy. See Cairns, Hall, etc. In short, the discovery of mutation(s) that are the result of an adaptive response to some environmental stimuli. Or, mutations that cannot mathematically be attributable to a chance copying mistake in the DNA.


Well, it isn't that easy in reality. The knowledgible creationist knows that Hall's and Cairn's original conclusions were based on 'partial knowledge' (like Haldane's) - further studies indicated that the effewcts seen by Cairns et al. were the result of genome-wide hypermutation in response to oxidative stress.

But why does math come into play here? And why doesn't the creationist EXPLAIN this 'math'?

quote:

quote:
Q: “If the non-random mutation hypothesis is true, what evidence would we be able to find in support (or to falsify) the idea?”

See Rosenberg, et al. A good paper is “EVOLVING RESPONSIVELY: ADAPTIVE MUTATION”, VOLUME 2, JULY 2001. It’s been over a year so I suspect this paper might be available for free now on the internet. To summarize, Rosenberg claims there is nothing anti-NDT at all about the apparent Lac+ adaptive mutation. She cited data that indicates a sub-population hypermutation occurred which included many unselected mutations within the Lac+ mutants genome, which would be expected if the mutations were behaving in a random, NDT fashion.


So why again is this supportive of non-random mutations?[/quote]

As Page pointed out, Cairns recanted some aspect of his original study, but from recent literature Cairns obviously still holds to adaptive mutation, disputing an important claim of the anti-adaptive mutation crowed that virtually all the mutations are occurring in a hyper-mutating sub-population. See

http://www.genetics.org/cgi/content/full/156/2/923?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&author1=Cairns&searchid=1027378300880_2030&stored_search=&FI RSTINDEX=0&journalcode=genet%20ics[/quote]

Has Cairns - or anyone else - observed this phenomenon in multicellular eukaryotes? Or is the continued creationist insistence upon this as a panacea for their mythology a reflection of their naivete?

But I have to wonder how well the creationist read his link:

"These results imply that most single (Lac+) mutants are arising in cells that have a lower mutation rate than the cells that produce double mutants. As Rosche and Foster pointed out, the most reasonable hypothesis is that all cells are undergoing mutation, but a small minority have a much higher mutation rate. In other words, when there is selection for just a single novel trait, most of the survivors will not be burdened with multiple changes in the rest of their genome."

Not only does that not sound like a ringing endorsement for the creationist extrapolation on 'non-random mutations', but in fact sounds very Darwinian.

quote:

As for my stand on non-random mutations, see Messages 44, 59 from July in “molecular genetic proof against random mutation”. To summarize, the primary purpose of my entry into that thread was to defend Peter’s claim that discovery of such mutations falsify the current NDT paradigm, and I provided a quote from leading NDT advocate Dr Futuyma proving it. I stated that I believe there is evidence for non-random mutations, but nothing to hang one’s hat on (Transposons for one have all the appearance of being a non-random, pre-programmed type of mutation).

You have been stating such a 'belief' for some time, and claimed to be writing an 'article' on it as reason not to supply citations supportive of this 'belief' in the past, and this inability to supply supportive documentation has not changed. The mechanisms of insertion are hardly the silver bullet you want. To see if you can figure out why, perhaps you can explain how transposons 'find' an insertion site.

Here is a hint - there is a simple explanation for it.

quote:

I also once believed non-random mutations would explain Haldane’s Dilemma as it applies to rapid diversification since a flood 5K years ago, but backed off this observation as later personal studies of the dilemma demonstrated that rapid diversification could easily occur without the aid of non-random mutations.

"Personal study"? Let me guess - you are writing an 'article' about this for your personal web site and so deign not to grace us with your sound scientific observations - supported with documentation, of course - on this issue.

But that brings up an interesting conundrum - if you think that 'rapid diversification' is possible regardless of Haldane's model, I see no rationale for insisting that human evolution from an ape-like ancestor is untenable.

Care to explain this paradox?

quote:

Page nevertheless continues to quote statements of mine that I have backed off of (messages 44 & 59 are proof of this, in case Page denies I never told him). This is like those dishonest atheists who will use quotes of Abraham Lincoln before he was a Christian in their attempt to show he was not Christian!

What about those dishonest Christians that claim that thsi country was built on Judeo-Christian 'values'?

Anyway, Williams, I like to quote your 'backed off' of statements not to 'misrepresent' you, but to point out your arrogance and hypocrisy.

Did you not at one time insult myself, sumac, and others for daring to disagree with you on SNPs and phylogenetic analysis? Did you not repeatedly claim that "informed evos" (whoever they are - you never did supply a single name!) know that were right, and that we were "morons", "knuckleheads", etc. for not acknowledging yo8ur supreme knowlegde? Only to later (much later) see you claim to have known all along that we were right, and the seeming 'disagreement' was due to the 'shortcomings of the medium' - the medium being written English?

Come on...

quote:

For now, I’m on the sidelines watching the drama play out. I pop into this drama now and then mostly to expose erroneous statements or bad logic like Mamuthus's "good one" in this thread.

Shame that you don't pop in to support your claims, instead of this asinine post-and-run-and-ignore technique that you seem to favor.

So - what is the status of 'information' when:

A gene duplication results in a shift in phenotype?

A mutation results in increased gene expression that provides pesticide resistance?

Or are you going to ignore these scenarios?

You are the 'information theory' expert, are you not? Why not educate all us underlings?


This message is a reply to:
 Message 37 by Fred Williams, posted 11-04-2002 12:50 PM Fred Williams has responded

Replies to this message:
 Message 41 by Fred Williams, posted 11-04-2002 7:05 PM derwood has responded

    
derwood
Member
Posts: 1457
Joined: 12-27-2001


Message 39 of 43 (21541)
11-04-2002 2:20 PM


Interesting statement on the Rosenberg link - the one provided by Williams supposedly in support of the notion of 'directed mutations':

quote:
The term ‘adaptive’mutation was used by Delbrück
to indicate mutations formed in response to an
environment in which the mutations were selected. The
term does not imply that non-adaptive (unselected)
mutations would not also be induced, or that the useful
mutations would be induced preferentially (this latter
idea is called ‘directed’mutation).

I eagerly await the announcement from Borger that this really means that directed mutations disprove NDT....


    
Mammuthus
Member (Idle past 4585 days)
Posts: 3085
From: Munich, Germany
Joined: 08-09-2002


Message 40 of 43 (21548)
11-04-2002 5:46 PM
Reply to: Message 37 by Fred Williams
11-04-2002 12:50 PM


FW:
As for my stand on non-random mutations, see Messages 44, 59 from July in “molecular genetic proof against random mutation”. To summarize, the primary purpose of my entry into that thread was to defend Peter’s claim that discovery of such mutations falsify the current NDT paradigm, and I provided a quote from leading NDT advocate Dr Futuyma proving it. I stated that I believe there is evidence for non-random mutations, but nothing to hang one’s hat on (Transposons for one have all the appearance of being a non-random, pre-programmed type of mutation). I also once believed non-random mutations would explain Haldane’s Dilemma as it applies to rapid diversification since a flood 5K years ago, but backed off this observation as later personal studies of the dilemma demonstrated that rapid diversification could easily occur without the aid of non-random mutations.

M: Out of curiosity, what specifically made you back off of the non-random mutation idea? What were the "personal studies"? Peter in no way has backed off of the non-random mutation hypothesis of his so why do you disagree that it is unecessary? He claims it is a falsification of NDT but you seem to have different criteria. Care to explain?

FW:
Page nevertheless continues to quote statements of mine that I have backed off of (messages 44 & 59 are proof of this, in case Page denies I never told him). This is like those dishonest atheists who will use quotes of Abraham Lincoln before he was a Christian in their attempt to show he was not Christian!

M: Aha, agenda exposed. You are yet another christian bigot. Big surprise there. You probably have never even met an atheist yet feel you are such a wonderful superior ubermensch that you can judge us all.

FW:
For now, I’m on the sidelines watching the drama play out. I pop into this drama now and then mostly to expose erroneous statements or bad logic like Mamuthus's "good one" in this thread.

M: It was a good one. And you have not supported your position. But don't feel bad, Borger is much smarter than you and has not had any success with his various lines of reasoning either


This message is a reply to:
 Message 37 by Fred Williams, posted 11-04-2002 12:50 PM Fred Williams has not yet responded

  
Fred Williams
Member (Idle past 2965 days)
Posts: 310
From: Broomfield
Joined: 12-17-2001


Message 41 of 43 (21554)
11-04-2002 7:05 PM
Reply to: Message 38 by derwood
11-04-2002 2:17 PM


quote:
Not only does that not sound like a ringing endorsement for the creationist extrapolation on 'non-random mutations', but in fact sounds very Darwinian.

I agree! Too bad you have a comprehension problem. Q asked for evidence that would falsify non-random mutation, and I provided his answer for him. I agree that Rosenberg is providing evidence *against* Cairns, Hall et al. I then added that Cairns disputes this evidence. He writes: “Their argument is unsound and, furthermore, makes a prediction that is contradicted by their own results”.

BTW, don’t try to claim I did not know Rosenberg’s work sought to rebut adaptive mutations. I posted something similar in message 60 back in July in the “molecular genetic proof against random mutation”, but you never responded.

I have to run. I have a project I have to work on tomorrow and may not have time at work to post here. So, I just might violate my personal goal to stay away from boards during my personal time and will try to pop in tonight. Anybody have a doghouse they can spare for a few nights?

PS. Mams, I am not backing away from non-random mutation per se, I am backing away from their being an essential component to explain the Haldane fixation/reproductive capacity problem as it relates to rapid diversification in 5K years since the flood (you know, that world-wide deluge you guys pretend never happened).


This message is a reply to:
 Message 38 by derwood, posted 11-04-2002 2:17 PM derwood has responded

Replies to this message:
 Message 43 by derwood, posted 11-05-2002 11:11 AM Fred Williams has not yet responded

    
Quetzal
Member (Idle past 3982 days)
Posts: 3228
Joined: 01-09-2002


Message 42 of 43 (21565)
11-05-2002 2:37 AM
Reply to: Message 37 by Fred Williams
11-04-2002 12:50 PM


quote:
Easy. See Cairns, Hall, etc. In short, the discovery of mutation(s) that are the result of an adaptive response to some environmental stimuli. Or, mutations that cannot mathematically be attributable to a chance copying mistake in the DNA.

Exactly. I am aware of the Cairns paper - and the fact that it is disputed, to say the least.

That being the case, perhaps you or PB could give an example of an actual organism where this has been observed. That's really what I'm after. The Rosenberg paper, as has been pointed out already, doesn't lend support to "non-randomness". Fast evolving genes, hotspots, etc, are all well explained within standard theory. You state that "there's nothing to hang a hat on". I think from the published literature that there isn't even a hat.


This message is a reply to:
 Message 37 by Fred Williams, posted 11-04-2002 12:50 PM Fred Williams has not yet responded

  
derwood
Member
Posts: 1457
Joined: 12-27-2001


Message 43 of 43 (21590)
11-05-2002 11:11 AM
Reply to: Message 41 by Fred Williams
11-04-2002 7:05 PM


quote:
Originally posted by Fred Williams:

BTW, don’t try to claim I did not know Rosenberg’s work sought to rebut adaptive mutations. I posted something similar in message 60 back in July in the “molecular genetic proof against random mutation”, but you never responded.


As usual, the hypocrisy - and irony - is thick enough to walk on....

quote:

PS. Mams, I am not backing away from non-random mutation per se, I am backing away from their being an essential component to explain the Haldane fixation/reproductive capacity problem as it relates to rapid diversification in 5K years since the flood (you know, that world-wide deluge you guys pretend never happened).

Don't you mean the 'world-wide deluge' that there is no evidence for that you biblical litearlist cultists insists happened? The story that is "coincidentaqlly" quite similar to the tales of Gilgamesh that predate the bible?

That one?

I cannot wait to see if you will actually respond - substantively - to the 'information' scenarios I posited, and the fact that you basically refuted creationary 'genetics' ....

So - I guess you will not be "prosyletizing" NREH as a cretin panacea anymore?

Or only when you get a 'fresh' audience that does not know about the literature indicating its true nature?


This message is a reply to:
 Message 41 by Fred Williams, posted 11-04-2002 7:05 PM Fred Williams has not yet responded

    
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