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Author Topic:   for Conspirator
derwood
Member (Idle past 1985 days)
Posts: 1457
Joined: 12-27-2001


Message 1 of 19 (25569)
12-05-2002 10:07 AM


From the site you plagiarised that amazing list from, Tim Harwood's "theory":
"This theory can be described as one of directed mutation."
Shame that Timmy does not keep up with (or apparently read at all) the primary literature - at least he seems to ignore anything to the contrary of his "theory".
If he had, he would know that "directed mutations" aren't.References
Andersson, D. I., E. S. Slechta, et al. (1998). Evidence that gene amplification underlies adaptive mutability of the bacterial lac operon. Science 282(5391): 1133-1135.
Bull, H. J., M. J. Lombardo, et al. (2001). Stationary-phase mutation in the bacterial chromosome: Recombination protein and DNA polymerase IV dependence. Proceedings of the National Academy of Sciences of the United States of America 98(15): 8334-8341.
Bull, H. J., G. J. McKenzie, et al. (2000). Evidence that stationary-phase hypermutation in the Escherichia coli chromosome is promoted by recombination. Genetics 154(4): 1427-1437.
Bull, H. J., G. J. McKenzie, et al. (2000). Response to John Cairns: The contribution of transiently hypermutable cells to mutation in stationary phase. Genetics 156(2): 925-926.
Harris, R. S., H. J. Bull, et al. (1997). A direct role for DNA polymerase III in adaptive reversion of a frameshift mutation in Escherichia coli. Mutation Research-Fundamental and Molecular Mechanisms of Mutagenesis 375(1): 19-24.
Harris, R. S., G. Feng, et al. (1999). Mismatch repair is diminished during stationary-phase mutation. Mutation Research-Reviews in Mutation Research 437(1): 51-60.
Harris, R. S., G. Feng, et al. (1997). Mismatch repair protein MutL becomes limiting during stationary-phase mutation. Genes & Development 11(18): 2426-2437.
Hastings, P. J., H. J. Bull, et al. (2000). Adaptive amplification: An inducible chromosomal instability mechanism. Cell 103(5): 723-731.
Hendrickson, H., E. S. Slechta, et al. (2002). Amplification-mutagenesis: Evidence that "directed" adaptive mutation and general hypermutability result from growth with a selected gene amplification. Proceedings of the National Academy of Sciences of the United States of America 99(4): 2164-2169.
Lombardo, M. J. and S. M. Rosenberg (1999). Hypermutation in stationary-phase E-coli: tales from the lac operon. Journal of Genetics 78(1): 13-20.
Lombardo, M. J., J. Torkelson, et al. (1999). Mechanisms of genome-wide hypermutation in stationary phase. Annals of the New York Academy of Sciences 870: 275-289.
McKenzie, G. J., R. S. Harris, et al. (2000). The SOS response regulates adaptive mutation. Proceedings of the National Academy of Sciences of the United States of America 97(12): 6646-6651.
McKenzie, G. J., P. L. Lee, et al. (2001). SOS mutator DNA polymerase IV functions in adaptive mutation and not adaptive amplification. Molecular Cell 7(3): 571-579.
McKenzie, G. J., M. J. Lombardo, et al. (1998). Recombination-dependent mutation in Escherichia coli occurs in stationary phase. Genetics 149(2): 1163-1165.
McKenzie, G. J. and S. M. Rosenberg (2001). Adaptive mutations ; mutator DNA polymerases and genetic change strategies of pathogens. Current Opinion in Microbiology 4(5): 586-594.
Motamedi, M. R., S. K. Szigety, et al. (1999). Double-strand-break repair recombination in Escherichia coli: physical evidence for a DNA replication mechanism in vivo. Genes & Development 13(21): 2889-2903.
Petrosino, J. F., A. R. Pendleton, et al. (2002). Chromosomal system for studying AmpC-mediated beta-lactam resistance mutation in Escherichia coli. Antimicrobial Agents and Chemotherapy 46(5): 1535-1539.
Rosenberg, S. M. (1997). Mutation for survival. Current Opinion in Genetics & Development 7(6): 829-834.
Rosenberg, S. M. (2001). Evolving responsively: Adaptive mutation. Nature Reviews Genetics 2(7): 504-515.
Rosenberg, S. M., C. Thulin, et al. (1998). Transient and heritable mutators in adaptive evolution in the lab and in nature. Genetics 148(4): 1559-1566.
Slechta, E. S., J. Harold, et al. (2002). The effect of genomic position on reversion of a lac frameshift mutation (lacIZ33) during non-lethal selection (adaptive mutation). Molecular Microbiology 44(4): 1017-1032.
Torkelson, J., R. S. Harris, et al. (1997). Genome-wide hypermutation in a subpopulation of stationary-phase cells underlies recombination-dependent adaptive mutation. Embo Journal 16(11): 3303-3311.
*********************************
Quotes from a few:
: EMBO J 1997 Jun 2;16(11):3303-11
: Genome-wide hypermutation in a subpopulation of stationary-phase cells underlies recombination-dependent adaptive mutation.
: Torkelson J, Harris RS, Lombardo MJ, Nagendran J, Thulin C, Rosenberg SM
: Stationary-phase mutation in microbes can produce selected ('adaptive') mutants preferentially. In one system, this occurs via a distinct, recombination-dependent mechanism. Two points of controversy have surrounded these adaptive reversions of an Escherichia coli lac mutation. First, are the mutations directed preferentially to the selected gene in a Lamarckian manner?
: Second, is the adaptive mutation mechanism specific to the F plasmid replicon carrying lac? We report that lac adaptive mutations are associated with hypermutation in unselected genes, in all replicons in the cell. The associated mutations have a similar sequence spectrum to the adaptive reversions. Thus, the adaptive mutagenesis mechanism is not directed to the lac genes, in a Lamarckian manner,nor to the F' replicon carrying lac. Hypermutation was not found in non-revertants exposed to selection. Therefore, the genome-wide hypermutation underlying adaptive mutation occurs in a differentiated subpopulation. The existence of mutable subpopulations in non-growing cells is important in bacterial evolution and could be relevant to the somatic mutations that give rise to cancers in multicellular organisms.
: ******************************
: "Researchers first noticed this happening in 1988 when John Cairns, then at Harvard University, showed that mutation rates in the bacterium Escherichia coli increased when the microbes needed to evolve new capabilities in order to survive changes in their environment.
: At the time, it seemed that only those genes directly involved with the adaptation changed,and this idea of adapative or directed evolution caused quite a stir.
: But then last year, molecular geneticist Susan Rosenberg at Baylor College of Medicine in Houston and her colleagues showed that mutation rates increase throughout the genome, although only in a subset of the population. Another group also found that more than just the relevant genes changed." (How the Genome Readies Itself for Evolution, Elizabeth Pennisi, Science, vol 281,
: Number 5380, Issue of 21 Aug 1998, p1131-1134)
: *******************************
: Mutat Res 1999 Jul;437(1):51-60
: Mismatch repair is diminished during stationary-phase mutation.
: Harris RS, Feng G, Ross KJ, Sidhu R, Thulin C, Longerich S, Szigety SK, Hastings PJ, Winkler ME,Rosenberg SM.
: Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
: This paper is an invited Response to a recent Commentary [P.L. Foster, Rev. Mut. Res. 436 (1999) 179-184] entitled "Are adaptive mutations due to a decline in mismatch repair? The evidence is lacking". The Commentary argues that no evidence exists supporting the idea that mismatch repair is limiting specifically during stationary-phase mutation. A primary concern of the author is to question the method that we used previously to measure growth-dependent mutation. In this method, mutation rates are calculated using counts of mutant colonies taken at times when those colonies arise, rather than at a predetermined, fixed time. Here we show further data that illustrate why this must be done to ensure accurate mutation measurements. Such accuracy was necessary for our published determination that mismatch repair proteins are not limiting during growth-dependent mutation, but become so during stationary-phase mutation. We review the evidence supporting the idea that stationary-phase reversion of a lac frameshift mutation occurs in an environment of decreased mismatch repair capacity. Those data are substantial. The data presented in the Commentary, in apparent contradiction to this idea, do not justify the conclusion presented there. Copyright 1999 Elsevier Science B.V.
: **********************
: Ann N Y Acad Sci 1999 May 18;870:275-89
: Mechanisms of genome-wide hypermutation in stationary phase.
: Lombardo MJ, Torkelson J, Bull HJ, McKenzie GJ, Rosenberg SM.
: Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030-3498, USA.
: Stationary-phase mutation (a subset of which was previously called adaptive mutation) occurs in apparently nondividing, stationary-phase cells exposed to a nonlethal genetic selection. In one experimental system, stationary-phase reversion of an Escherichia coli F'-borne lac frameshift mutation occurs by a novel molecular mechanism that requires homologous recombination functions of the RecBCD system. Chromosomal mutations at multiple loci are detected more frequently in Lac+ stationary-phase revertants than in cells that were also exposed to selection but did not become Lac+. Thus, mutating cells represent a subpopulation that experiences hypermutation throughout the genome. This paper summarizes current knowledge regarding stationary-phase mutation in the lac system. Hypotheses for the mechanism of chromosomal hypermutation are discussed, and data are presented that exclude one hypothetical mechanism in which chromosomal mutations result from Hfr formation.
: ***************************
: Science 1998 Nov 6;282(5391):1133-5
: Evidence that gene amplification underlies adaptive mutability of the bacterial lac operon.
: Andersson DI, Slechta ES, Roth JR.
: Department of Biology, University of Utah, Salt Lake City, UT 84112, USA.
: Adaptive mutability is the apparent alteration in specificity or rate of mutability seen in bacteria during stress. A model is proposed by which gene amplification during selective growth can give the appearance of adaptive mutability without requiring any change in mutability. The model is based on two assumptions, that a mutant lac locus with residual function allows growth if its copy number is increased, and that true reversion events are made more likely by replication of chromosomes with many copies of the locus. Apparent directed mutability, its recombination requirement, and its apparent independence of cell growth are all accounted for by the model. Evidence is provided for the required residual function and gene amplification.
: ***********************************
: Mutat Res 2001 Jan 25;473(1):109-19
: Effect of endogenous carotenoids on "adaptive" mutation in Escherichia coli FC40.
: Bridges BA, Foster PL, Timms AR.
: MRC Cell Mutation Unit, University of Sussex, Falmer, BN1 9RR, Brighton, UK. b.a.bridges@sussex.ac.uk
: The appearance over many days of Lac(+) frameshift mutations in Escherichia coli strain FC40 incubated on lactose selection plates is a classic example of apparent "adaptive" mutation in an episomal gene. We show that endogenously overproduced carotenoids reduce adaptive mutation under selective conditions by a factor of around two. Carotenoids are known to scavenge singlet oxygen suggesting that the accumulation of oxidative base damage may be an integral part of the adaptive mutation phenomenon. If so, the lesion cannot be 7,8-dihydro-8-oxoguanine since adaptive mutation in FC40 is unaffected by mutM and mutY mutations. If active oxygen species such as singlet oxygen are involved in adaptive mutation then they should also induce frameshift mutations in FC40 under non-selective conditions. We show that such mutations can be induced under non-selective conditions by protoporphyrin photosensitisation and that this photodynamic induction is reduced by a factor of just over two when endogenous carotenoids are present. We argue that the involvement of oxidative damage would in no way be inconsistent with current understanding of the mechanism of adaptive mutation and the role of DNA polymerases.
: *******************************
:
Still have confidence in Harwood's assessments?

Replies to this message:
 Message 2 by Percy, posted 12-05-2002 1:38 PM derwood has not replied
 Message 3 by Coragyps, posted 12-05-2002 2:21 PM derwood has not replied

  
Percy
Member
Posts: 22682
From: New Hampshire
Joined: 12-23-2000
Member Rating: 3.8


Message 2 of 19 (25597)
12-05-2002 1:38 PM
Reply to: Message 1 by derwood
12-05-2002 10:07 AM


Excepting the opening and closing, this post's strong objective focus is very helpful and informative, especially the excerpts.
It might make sense for you to delete this thread and repost this in response to Conspirator's original thread.
--Percy

This message is a reply to:
 Message 1 by derwood, posted 12-05-2002 10:07 AM derwood has not replied

  
Coragyps
Member (Idle past 843 days)
Posts: 5553
From: Snyder, Texas, USA
Joined: 11-12-2002


Message 3 of 19 (25602)
12-05-2002 2:21 PM
Reply to: Message 1 by derwood
12-05-2002 10:07 AM


I could be wrong, SLPx, but I think you aimed that post too high. Way too high.

This message is a reply to:
 Message 1 by derwood, posted 12-05-2002 10:07 AM derwood has not replied

Replies to this message:
 Message 4 by Percy, posted 12-05-2002 3:33 PM Coragyps has not replied

  
Percy
Member
Posts: 22682
From: New Hampshire
Joined: 12-23-2000
Member Rating: 3.8


Message 4 of 19 (25616)
12-05-2002 3:33 PM
Reply to: Message 3 by Coragyps
12-05-2002 2:21 PM


Coragyps writes:
I could be wrong, SLPx, but I think you aimed that post too high. Way too high.
It is not an uncommon event here for someone to take a list of questions they find somewhere and post them (though usually with attribution). But one of the problems with responding to these questions is that since the person didn't compose the questions himself there is no way to know if he understands the questions, or even agrees with all of them. You often find that the questions posted represent views that the person posting them is ill-equipped to defend. The whole approach is indicative of intellectual laziness combined with unfamiliarity with the details of the topic.
--Percy

This message is a reply to:
 Message 3 by Coragyps, posted 12-05-2002 2:21 PM Coragyps has not replied

Replies to this message:
 Message 5 by wj, posted 12-05-2002 5:38 PM Percy has replied
 Message 7 by gene90, posted 12-05-2002 7:25 PM Percy has not replied

  
wj
Inactive Member


Message 5 of 19 (25628)
12-05-2002 5:38 PM
Reply to: Message 4 by Percy
12-05-2002 3:33 PM


True, Percy, but should that constrain a respondent from utilising the full range of evidence, literature and logic to support their position which contradicts the ill-informed shopping list poster? If the shopping list poster can't understand the response then they could always ask for a simplification. But at the very least other interested readers will appreciate the background of scientific evidence which supports conventional science's position.
Maybe responding in depth to one of the shopping list assertions will give that poster a hint of what they don't know or have been informed by their source and cause them to more critically analyse their source. Optimistic I know, but there are many examples of former yecs who have discovered the error of their ways due to the information they have received.

This message is a reply to:
 Message 4 by Percy, posted 12-05-2002 3:33 PM Percy has replied

Replies to this message:
 Message 6 by Percy, posted 12-05-2002 7:24 PM wj has not replied

  
Percy
Member
Posts: 22682
From: New Hampshire
Joined: 12-23-2000
Member Rating: 3.8


Message 6 of 19 (25642)
12-05-2002 7:24 PM
Reply to: Message 5 by wj
12-05-2002 5:38 PM


Sorry, you're right, I didn't mean to discourage anyone from responding. But it *does* help to keep in mind the possibility that the person for whom the effort of a detailed reply is being made doesn't care about the actually science and isn't interested in understanding the issues, but is simply upset by the threat of evolution and is lashing out. And even when that does turn out to be the case, an informed response may prove very helpful to others.
--Percy
[This message has been edited by Percipient, 12-06-2002]

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gene90
Member (Idle past 3932 days)
Posts: 1610
Joined: 12-25-2000


Message 7 of 19 (25643)
12-05-2002 7:25 PM
Reply to: Message 4 by Percy
12-05-2002 3:33 PM


Other problems are that the posts are long and demanding (in this case) and cover way to many topics. Also, it takes maybe five minutes to cut and paste that sort of thing but it could take days to answer to those demands. In that time, how many hundreds of more claims could be posted? This is the Gish Gallop at work.

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 Message 4 by Percy, posted 12-05-2002 3:33 PM Percy has not replied

Replies to this message:
 Message 8 by wj, posted 12-05-2002 8:50 PM gene90 has not replied

  
wj
Inactive Member


Message 8 of 19 (25652)
12-05-2002 8:50 PM
Reply to: Message 7 by gene90
12-05-2002 7:25 PM


I don't think Conspirator is galloping at the moment - he/she/it seems to have come to a complete standstill on this thread and the original shopping list thread Top questions I think evolutionists need to answer.
Perhaps the embarassment of being found out as a plagiariser, or having at least one of the questions seriously addressed has been too much to bear.

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 Message 7 by gene90, posted 12-05-2002 7:25 PM gene90 has not replied

  
Conspirator
Inactive Member


Message 9 of 19 (25753)
12-06-2002 12:09 PM


I understand the questions perfectly. And I'm not embarrassed that I plagiarized it, I knew I did and I don't care. I'm just real busy right now and don't have a lot of time to come here and post. And the topic isn't going to be a standstill because I'm going to post in it right about now...

Replies to this message:
 Message 10 by John, posted 12-06-2002 12:14 PM Conspirator has not replied
 Message 11 by Admin, posted 12-06-2002 12:23 PM Conspirator has not replied
 Message 13 by derwood, posted 12-07-2002 4:36 PM Conspirator has not replied

  
John
Inactive Member


Message 10 of 19 (25755)
12-06-2002 12:14 PM
Reply to: Message 9 by Conspirator
12-06-2002 12:09 PM


quote:
Originally posted by Conspirator:
And I'm not embarrassed that I plagiarized it, I knew I did and I don't care.
Glad to see that you're ethical then.
quote:
And the topic isn't going to be a standstill because I'm going to post in it right about now...
????? ok
------------------
No webpage found at provided URL: www.hells-handmaiden.com

This message is a reply to:
 Message 9 by Conspirator, posted 12-06-2002 12:09 PM Conspirator has not replied

  
Admin
Director
Posts: 13084
From: EvC Forum
Joined: 06-14-2002
Member Rating: 2.5


Message 11 of 19 (25756)
12-06-2002 12:23 PM
Reply to: Message 9 by Conspirator
12-06-2002 12:09 PM


Conspirator writes:
And I'm not embarrassed that I plagiarized it, I knew I did and I don't care.
You're not required to be embarrassed. You're not required to care.
You're only required to follow the Forum Guidelines. Please follow them if you care about retaining your posting privileges.
------------------
--EvC Forum Administrator

This message is a reply to:
 Message 9 by Conspirator, posted 12-06-2002 12:09 PM Conspirator has not replied

  
Conspirator
Inactive Member


Message 12 of 19 (25769)
12-06-2002 4:19 PM


I know. I'll try to follow them from now on.

  
derwood
Member (Idle past 1985 days)
Posts: 1457
Joined: 12-27-2001


Message 13 of 19 (25839)
12-07-2002 4:36 PM
Reply to: Message 9 by Conspirator
12-06-2002 12:09 PM


quote:
Originally posted by Conspirator:
I understand the questions perfectly.
Interesting. So, you have taken college-level evolutionary biology/genetics courses? Geology? Paleontology? Taphonomy? Etc.?
Wow. A regular polymath...
Odd how there are so many creationist polymaths...

This message is a reply to:
 Message 9 by Conspirator, posted 12-06-2002 12:09 PM Conspirator has not replied

  
Conspirator
Inactive Member


Message 14 of 19 (26035)
12-09-2002 12:33 PM


Not only have I not taken those classes, but I've studies all of them long enough so that I know what I'm talking about so I don't need to take those classes. Man...

Replies to this message:
 Message 15 by derwood, posted 12-09-2002 2:42 PM Conspirator has not replied

  
derwood
Member (Idle past 1985 days)
Posts: 1457
Joined: 12-27-2001


Message 15 of 19 (26048)
12-09-2002 2:42 PM
Reply to: Message 14 by Conspirator
12-09-2002 12:33 PM


quote:
Originally posted by Conspirator:
Not only have I not taken those classes, but I've studies all of them long enough so that I know what I'm talking about so I don't need to take those classes. Man...
I see... A self-taught polymath...
Fine.
Well, please address my responses to your post in which you proudly presented someone else's propaganda as your own.
http://EvC Forum: Top questions I think evolutionists need to answer -->EvC Forum: Top questions I think evolutionists need to answer
[This message has been edited by SLPx, 12-09-2002]

This message is a reply to:
 Message 14 by Conspirator, posted 12-09-2002 12:33 PM Conspirator has not replied

  
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