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Author Topic:   Wright et al. on the Process of Mutation
shadow71
Member (Idle past 1162 days)
Posts: 706
From: Joliet, il, USA
Joined: 08-31-2010


Message 13 of 296 (627655)
08-03-2011 8:49 AM
Reply to: Message 10 by Taq
08-02-2011 9:44 PM


I assume in message 3, 1st sentence, you meant to type "transcripton" correct? Not being picky, just want to make sure I am not missing something.

So far so good in following your explanations.


This message is a reply to:
 Message 10 by Taq, posted 08-02-2011 9:44 PM Taq has responded

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shadow71
Member (Idle past 1162 days)
Posts: 706
From: Joliet, il, USA
Joined: 08-31-2010


Message 19 of 296 (627956)
08-05-2011 4:27 PM
Reply to: Message 16 by Taq
08-04-2011 10:03 PM


As I told Aristotle when I visited Athens, this is pretty much all Greek to me.
I will keep reading and learning.
This message is a reply to:
 Message 16 by Taq, posted 08-04-2011 10:03 PM Taq has responded

Replies to this message:
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shadow71
Member (Idle past 1162 days)
Posts: 706
From: Joliet, il, USA
Joined: 08-31-2010


Message 50 of 296 (631560)
09-01-2011 6:59 PM
Reply to: Message 49 by Taq
08-10-2011 12:05 PM


Taq writes:


It would seem that you are arguing over semantics. No matter what word you use there is still the observation that specific alleles increase the chances of an organism producing more offspring than others in a given environment.

If specific alles increase the chances of an organism producing more offspring than others in a given enviroment, and these alles production are more than those w/o the mutation, this sound alot like mutations for fitness, that are not "random" as per Darwin.
Am I wrong in this observation?


This message is a reply to:
 Message 49 by Taq, posted 08-10-2011 12:05 PM Taq has responded

Replies to this message:
 Message 51 by Taq, posted 09-01-2011 7:18 PM shadow71 has responded

    
shadow71
Member (Idle past 1162 days)
Posts: 706
From: Joliet, il, USA
Joined: 08-31-2010


Message 52 of 296 (631576)
09-01-2011 7:55 PM
Reply to: Message 51 by Taq
09-01-2011 7:18 PM


Taq writes:


The facts of the matter is that your supposed "genetic engineering systems" can only produce 2 bacteria per BILLION that carry a mutation that is beneficial in the given environment. How do you explain such a low mutation rate? Shouldn't an engineered system produce 500 million per billion beneficial mutations (i.e. 50%)? Why only 2?

Maybe because those are the beneficial mutations necessary for the system. Engineering systems are designed to be specific and not wasteful.

If 2 mutations are all that are needed to bring about the desired outcome, why would there be a need for more?


This message is a reply to:
 Message 51 by Taq, posted 09-01-2011 7:18 PM Taq has responded

Replies to this message:
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shadow71
Member (Idle past 1162 days)
Posts: 706
From: Joliet, il, USA
Joined: 08-31-2010


Message 65 of 296 (633114)
09-12-2011 2:59 PM
Reply to: Message 54 by Wounded King
09-02-2011 4:43 AM


Re: I'm not so sure
Barbara Wright, "A Biochemical Mechankism for Nonrandom Mutations and Evoltion." 2000. writes:

The extent to which normal background mutations in nature are due to derepression mechanisms is difficult to estimate, but the location of most C-to-T transitions on the nontranscribed strand suggest that it may be significant. Regardless, a mechanism that limits an increase in mutation rates to genes that must mutate in order to overcome prevailing conditions of stress would surely be beneficial and therefore selected during evolution.The environment gave rise to life and continues to direct evolution. Environmental conditions are constantly controlling and fine-tuning the transcriptional machinery of the cell. Feedback mechanisms represent the natural interactive link between an organism and its environment. An obvious selective advantage exists for a relationship in which particular environmental changes are metabolically linked through transcription to genetic changes that help an organism cope with new demands of the environment. In nature, nutritional stress and associated genetic derepression must be rampant. If mutation rates can be altered by the many variables controlling specific, stress-induced transcription, one might reasonably argue that many mutations are to some extent directed as a result of the unique metabolism of every organism responding to the challenges of its environment. Thus, mutations are brought within the realm of metabolic events to become the final, irreversible act of metabolism in the constant struggle to adapt or die.

taken in conjunction with her paper discussed on this tread where she finds metabolic activities specifically targeting the leu operon suggesting that the higher rates of mutation are specifically assosciated with the depressed leu operon.

this I take to mean that there are in fact targeted directed responses to specific condidtions that trigger benefical mutations.

Is this so and if so if this beyond Darwin and Neo-Darwinanism up to apporx 1960?

Edited by shadow71, : spelling


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shadow71
Member (Idle past 1162 days)
Posts: 706
From: Joliet, il, USA
Joined: 08-31-2010


Message 72 of 296 (633337)
09-13-2011 4:41 PM
Reply to: Message 71 by Taq
09-13-2011 12:33 PM


Re: beneficial mutations
Wright writes:

in her paper cited on this tread:

Our data indicate that transcription (starvation-induced derepression) is unique in augmenting variant availability in a specific manner, i.e., by stimulating rates of transcription (and associated phenomena such as RNA polymerase pausing) in targeted operons, thereby increasing the concentration of single-stranded DNA (ssDNA), which is more vulnerable to mutations than double-stranded DNA. Although the mutations per se are random, as described above for background mutations, the mechanisms that target operons for increased rates of transcription are highly specific. This specificity is not compatible with current neo-Darwinian dogma. And yet, evidence in the literature supports the two major.

Do you agree that this specificity is not compatable with Neo-Darwinism as it was expressed up until the 1960s?


This message is a reply to:
 Message 71 by Taq, posted 09-13-2011 12:33 PM Taq has responded

Replies to this message:
 Message 73 by Taq, posted 09-13-2011 4:51 PM shadow71 has responded

    
shadow71
Member (Idle past 1162 days)
Posts: 706
From: Joliet, il, USA
Joined: 08-31-2010


Message 78 of 296 (634061)
09-18-2011 7:08 PM
Reply to: Message 73 by Taq
09-13-2011 4:51 PM


Re: beneficial mutations
wounded king message 77 writes:


Wright argues reasonably that there is something that could be considered directionality favouring more actively transcribed genomic regions, and that relevant genes may be more likely to be transcribed as part of a stress response. So far that is as far as the evidence goes, and it goes nowhere near the enormous leaps beyond the evidence you are taking. Indeed, neither of the things referred to in the Shapiro quote are about population level effects.

taq writes:


No, I do not. These findings fit quite well with the random mutations described by the Lederberg's, Luria, and Delbruck. These mutations are random with respect to fitness. As I discussed, this mechanism also produces neutral and detrimental mutations through the same mechanism. In fact, this elevated mutation rate is occuring in housekeeping genes even in the presence of leucine when the bacteria does not need any mutations whatsoever.

My question is does directionality favoring more actively transcribed genomic regions where more revelant genes may be more likely transcribed concur with the Neo-Darwinism of the late 1960s?


This message is a reply to:
 Message 73 by Taq, posted 09-13-2011 4:51 PM Taq has responded

Replies to this message:
 Message 79 by Wounded King, posted 09-19-2011 8:51 AM shadow71 has responded
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shadow71
Member (Idle past 1162 days)
Posts: 706
From: Joliet, il, USA
Joined: 08-31-2010


Message 92 of 296 (634546)
09-22-2011 1:52 PM
Reply to: Message 79 by Wounded King
09-19-2011 8:51 AM


Re: beneficial mutations
Wounded King writes:

I'm not sure why you want to specifically argue against evolutionary theory as it stood more than 50 years ago, but then Wright seems to want to argue against evolutionary theory from the end of the 19th century (She identifies the neo-Darwinism that her results call into question as that of Weismann, citing a reference from 1893), so at least your target is a bit more relevant. Ernst Mayr would disagree with you and Wright that what you are discussing is neo-Darwinism as he drew a clear distinction between Weismann's theory and the modern synthesis as formulated in the 30s and 40s.

I really don't see why you picked the late 60s, that is well after the formulation of the modern synthesis. Is there any reason why you don't want to discuss actual modern evolutionary theory?

Lets discuss Darwin's theory, and the modern synthesis up to the late 60's, when molecular genetics became more prevelant. Are you of the opinion that "directionality favoring more actively transcribed genomic regions where more revelant genes may be more likely transcribed " concur with the theory of evolution as expressed to this period?

Wounded King writes:


If you could specify a particular theorist or group it might help, it isn't as if evolutionary theory in the late 60's was a monolithic block with everyone marching in lock step any more than it is today. There were a number of heterodox theories at the time many of which have since fallen out of view as they were not supported by the evidence but some of which, as with Kimura's neutral theory, have become widely accepted.

I am thinking of the cytogenetic observations, molecular genetic findings and Shaprio's "natrural genetic engineering" system, and the rapid changes such as symbiosis, interspecific hybridization and whole genome doubling, that I think the theories up to and including the modern synthesis do not account for. I don't think evolution by slow gradual, random changes is an acceptable theory. It may be for micro changes after rapid changes, but does not account for the rapid changes.


This message is a reply to:
 Message 79 by Wounded King, posted 09-19-2011 8:51 AM Wounded King has not yet responded

Replies to this message:
 Message 93 by Percy, posted 09-22-2011 2:08 PM shadow71 has responded

    
shadow71
Member (Idle past 1162 days)
Posts: 706
From: Joliet, il, USA
Joined: 08-31-2010


Message 94 of 296 (634556)
09-22-2011 4:19 PM
Reply to: Message 93 by Percy
09-22-2011 2:08 PM


Do you agree that this specificity is not compatable with NeoRe: beneficial mutations
Do you agree that this specificity is not compatable with Neo-Darwinism as it was expressed up until the 1960s?

This was part of my message 72

This is part of my message 78

taq writes:

No, I do not. These findings fit quite well with the random mutations described by the Lederberg's, Luria, and Delbruck. These mutations are random with respect to fitness. As I discussed, this mechanism also produces neutral and detrimental mutations through the same mechanism. In fact, this elevated mutation rate is occuring in housekeeping genes even in the presence of leucine when the bacteria does not need any mutations whatsoever.

Shadow answers

My question is does directionality favoring more actively transcribed genomic regions where more revelant genes may be more likely transcribed concur with the Neo-Darwinism of the late 1960s?

Percy writes:


Do your recent posts relate to the topic? If so, can you make clear how they relate to the topic for the benefit of those of us trying to follow along?

Just trying to establish if Wright's paper does in fact comply with the Darwinian theory up to the modern synthesis, or if in fact Wright is of the opinion that her findings in the paper are not compatable with Darwinian theory up to the modern synthesis.


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 Message 93 by Percy, posted 09-22-2011 2:08 PM Percy has responded

Replies to this message:
 Message 95 by Percy, posted 09-22-2011 5:17 PM shadow71 has not yet responded
 Message 96 by Taq, posted 09-23-2011 12:05 PM shadow71 has not yet responded
 Message 97 by Dr Adequate, posted 09-23-2011 12:57 PM shadow71 has responded

    
shadow71
Member (Idle past 1162 days)
Posts: 706
From: Joliet, il, USA
Joined: 08-31-2010


Message 99 of 296 (634742)
09-23-2011 4:26 PM
Reply to: Message 97 by Dr Adequate
09-23-2011 12:57 PM


Re: Do you agree that this specificity is not compatable with NeoRe: beneficial mutations
shadow71 writes:

Do you agree that this specificity is not compatable with Neo-Darwinism as it was expressed up until the 1960s?

Dr Adequate writes:

If you mean to say that we didn't know in the 1960s about something that we only discovered after the 1960s, then this is perfectly correct.

No, what I am asking is, is this specificity compatable with the Modern synthesis?

Is this specificity random mutation and natual selection?
Doesn't this specificity lead to the conclusion that it cannot be completely random and does lead to beneficial changes in the bacteria?

--------------------------------------------------------------------------------


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 Message 97 by Dr Adequate, posted 09-23-2011 12:57 PM Dr Adequate has responded

Replies to this message:
 Message 101 by Taq, posted 09-23-2011 4:39 PM shadow71 has not yet responded
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shadow71
Member (Idle past 1162 days)
Posts: 706
From: Joliet, il, USA
Joined: 08-31-2010


Message 104 of 296 (634921)
09-24-2011 8:34 PM
Reply to: Message 102 by Dr Adequate
09-23-2011 5:31 PM


Re: Do you agree that this specificity is not compatable with NeoRe: beneficial mutations
DrAdequate writes:


But what the fuck do you mean by that?

Thank you for you patience and understanding. I know it must be hard to know it all and deal with these other idiots, especially when they challenge your absoutely unassailable beliefs.

There is life beyond "biology." Like what the hell does it all mean, and how did it come about.

You should read Shapiro, Koonin, Caporale, and others and find out how outmoded your belieft in "random" is today.

If you don't see a reason to inquire as to whether "random mutations and natural selection" is questionalble, then live in your safe little world.


This message is a reply to:
 Message 102 by Dr Adequate, posted 09-23-2011 5:31 PM Dr Adequate has not yet responded

Replies to this message:
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shadow71
Member (Idle past 1162 days)
Posts: 706
From: Joliet, il, USA
Joined: 08-31-2010


Message 106 of 296 (635005)
09-25-2011 3:04 PM
Reply to: Message 105 by Percy
09-24-2011 8:43 PM


Re: Do you agree that this specificity is not compatable with NeoRe: beneficial mutations
Wright et al writes: Taken from an earlier Percy message.

The current paradigm of neo-Darwinism as formulated by Weisman (59) rejects any influence of the environment on the direction of variation. However, prolonged nutritional stress results in a general increase in mutation rates; the introduction of environmental effects on specific mutation rates is a reasonable extension of what is known, especially because mechanisms by which starvation can immediately and specifically affect rates of transcription and mutation are consistent with accepted principles of molecular biology. The proposed mechanism of derepression-induced hypermutation provides the critical link between mutations and the metabolic activities evoked by specific conditions of environmental stress, increasing the availability of variants most likely to evolve in that environment.

Percy writes:


Back to the topic. This thread is about the Wright paper's demonstration that environmental factors do not direct evolution in specific directions.

I cannot agree that Wright's paper demonstrates that enviormental facors do not direct evolution in specific directions.
If you read the Wright quote above she seems to be saying that in fact the enviomental factors are directing evolution in specific directions.

I emphasize the later part of her quote:

Wright writes:

However, prolonged nutritional stress results in a general increase in mutation rates; the introduction of environmental effects on specific mutation rates is a reasonable extension of what is known, especially because mechanisms by which starvation can immediately and specifically affect rates of transcription and mutation are consistent with accepted principles of molecular biology. The proposed mechanism of derepression-induced hypermutation provides the critical link between mutations and the metabolic activities evoked by specific conditions of environmental stress, increasing the availability of variants most likely to evolve in that environment.

Am I interpreting this incorrectly?


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 Message 105 by Percy, posted 09-24-2011 8:43 PM Percy has responded

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shadow71
Member (Idle past 1162 days)
Posts: 706
From: Joliet, il, USA
Joined: 08-31-2010


Message 110 of 296 (635101)
09-26-2011 5:03 PM
Reply to: Message 109 by Taq
09-26-2011 12:03 PM


Re: Do you agree that this specificity is not compatable with NeoRe: beneficial mutations
Wright writes:

The proposed mechanism of derepression-induced hypermutation provides the critical link between mutations and the metabolic activities evoked by specific conditions of environmental stress, increasing the availability of variants most likely to evolve in that environment.

Taq, my question is do you believe Wright is opining by this sentence that these are non-random mutations that are most likely to be beneficial?


This message is a reply to:
 Message 109 by Taq, posted 09-26-2011 12:03 PM Taq has responded

Replies to this message:
 Message 111 by Percy, posted 09-26-2011 5:16 PM shadow71 has not yet responded
 Message 112 by Taq, posted 09-26-2011 6:46 PM shadow71 has responded

    
shadow71
Member (Idle past 1162 days)
Posts: 706
From: Joliet, il, USA
Joined: 08-31-2010


Message 115 of 296 (635108)
09-26-2011 7:50 PM
Reply to: Message 112 by Taq
09-26-2011 6:46 PM


Re: Do you agree that this specificity is not compatable with NeoRe: beneficial mutations
Merlin in the paper cited by Wounded King writes:

The main purpose of this paper is to defend the “chance” character of genetic mutations, which I claim is a Darwinian tenet and part of the Modern Synthesis’ consensus view, against recent challenges, especially those advanced by Jablonka and Lamb (1995, 2005). During the last thirty years, experimental research in molecular genetics, in particular on microorganisms, has shown that certain molecular mechanisms – the so-called “mutator mechanisms” – can regulate mutation rates (increasing or decreasing them) in response to certain selective forces. Because of this causal connection between mutation rates and selective substrates, Jablonka and Lamb, along with other biologists, historians and philosophers of biology (Shapiro 1999, 2005;

Wright et al. 1999, 2000; Sternberg 2002; Keller 2000), have questioned the Modern Synthesis’ claim that all genetic mutations occur by “chance” or at “random.”

From Message 112 by Taq:

Shadow 71 asks;

Taq, my question is do you believe Wright is opining by this sentence that these are non-random mutations that are most likely to be beneficial?

taq writes:


No, I do not. Wright is stating that hypermutation is an increase in the random mutation rate in genes that are upregulated, exactly what I have been saying all along. This is consistent with the Modern Synthesis, but perhaps not consistent with Weissman's definition of the Modern Synthesis before there was a Modern Synthesis.

The paper cited by Wounded King clearly states that Wright et. al. including Shaprio challenge the Modern Synthesis claim that all genetic mutation occur by chance or at random.

So your interpretation of Wright's opinion is challenged by Merlin. You may or may not be correct about mutations being random, but my reading of Wright is correct. She is in fact challenging whether all mutations are random in the paper you cited. So both you and Percy should read my messages more carefully, and not jump to conclusions, such as Percy's, that I am "daft".
If you read Wright's paper carefully it is clear she is challenging this Modern Synthesis point.


This message is a reply to:
 Message 112 by Taq, posted 09-26-2011 6:46 PM Taq has responded

Replies to this message:
 Message 116 by Taq, posted 09-26-2011 7:53 PM shadow71 has responded
 Message 118 by Percy, posted 09-26-2011 9:09 PM shadow71 has responded

    
shadow71
Member (Idle past 1162 days)
Posts: 706
From: Joliet, il, USA
Joined: 08-31-2010


Message 125 of 296 (635160)
09-27-2011 12:47 PM
Reply to: Message 116 by Taq
09-26-2011 7:53 PM


Re: Do you agree that this specificity is not compatable with NeoRe: beneficial mutations
Taq writes:

Wright didn't show that in this paper, and it was never stated outright in the section you quoted.

Even more importantly, the data does not support non-random mutations. Wright's opinion does not trump the data.

You miss my point. I am not arguing that Wright is correct, she may be, but I am stating that there are in fact competent, qualified scientists arguing that mutations are not, or may not be, random for fitness or adapation.
Whenever I give this interpretation from a papers such as Shapiro's and Wright's you, Percy and others tell me I am a wackjob, creationists who only interprets papers as to what I want them to say.
I, as Shapiro as stated about me on this board, understand his findings and opinions.
Therefore I am correct in most cases where I state an author is favoring the position that mutations may not be or are not random for fitness.

It is becoming more and more clear that this school of thought is asserting itself in the scientific community.
That's why I am of the opinion that the Darwinian theory includilng neo-Darwinism, and the modern synthesis are in need or revision and change, maybe radical.

--------------------------------------------------------------------------------


This message is a reply to:
 Message 116 by Taq, posted 09-26-2011 7:53 PM Taq has responded

Replies to this message:
 Message 127 by Taq, posted 09-27-2011 3:00 PM shadow71 has responded

    
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