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Author Topic:   Wright et al. on the Process of Mutation
zi ko
Member (Idle past 2607 days)
Posts: 578
Joined: 01-18-2011


Message 61 of 296 (632769)
09-10-2011 1:32 AM
Reply to: Message 58 by Taq
09-09-2011 6:22 PM


Re: beneficial mutations
i think you miss my point. 999,9999,998 of bacteria had got the mutation they needed according to organism's knowledge of the environment's virieties and instability. After all the organism had been living in the old environment for millions of years. Also there is the possibility that organism in succeeded generations will produce more of the "apropriate" mutations if it sees it usefull. the research as i know had not focused on this last possibility.

Edited by zi ko, : No reason given.


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Replies to this message:
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Wounded King
Member (Idle past 3082 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 62 of 296 (632779)
09-10-2011 4:32 AM
Reply to: Message 61 by zi ko
09-10-2011 1:32 AM


Re: beneficial mutations
Also there is the possibility that organism in succeeded generations will produce more of the "apropriate" mutations if it sees it usefull.

How on Earth would this latest ad hoc nonsense work? The organisms where the mutation is beneficial already have it. In what way would the other wild-type organisms 'see' that a particular mutation was beneficial in successive generations. You are going far beyond directed mutation mechanisms in a cell here to some sort of population wide communication phenomenon directing the de novo replication of specific mutations. In other words from a tenuous hypothesis to one that is a complete fabrication without a scintilla of evidence.

Of course there already exists a well known mechanism by which beneficial mutations will tend to proliferate in subsequent generations, it is called natural selection.

TTFN,

WK

Edited by Wounded King, : No reason given.


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zi ko
Member (Idle past 2607 days)
Posts: 578
Joined: 01-18-2011


Message 63 of 296 (632954)
09-11-2011 1:14 PM
Reply to: Message 62 by Wounded King
09-10-2011 4:32 AM


Re: beneficial mutations
How on Earth would this latest ad hoc nonsense work? The organisms where the mutation is beneficial already have it. In what way would the other wild-type organisms 'see' that a particular mutation was beneficial in successive generations. You are going far beyond directed mutation mechanisms in a cell here to some sort of population wide communication phenomenon directing the de novo replication of specific mutations. In other words from a tenuous hypothesis to one that is a complete fabrication without a scintilla of evidence.

Of course there already exists a well known mechanism by which beneficial mutations will tend to proliferate in subsequent generations, it is called natural selection.

Of couers natural selection is an established mechanism, but does not exclude an increaseof beneficial mutations, as we already know, by other mechanisms. Nature has many times proved its inherit ability to invent very complicated ways of organizing life in away we just simply don't know yet. Random mutations and selection are some of them. Not all.

Edited by zi ko, : No reason given.


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Taq
Member
Posts: 8488
Joined: 03-06-2009
Member Rating: 7.4


Message 64 of 296 (633086)
09-12-2011 11:02 AM
Reply to: Message 61 by zi ko
09-10-2011 1:32 AM


Re: beneficial mutations
i think you miss my point. 999,9999,998 of bacteria had got the mutation they needed according to organism's knowledge of the environment's virieties and instability.

No, they hadn't. When grown in the absence of leucine only 2 out of every billion bacteria survived. They didn't have the mutation they needed.

Also there is the possibility that organism in succeeded generations will produce more of the "apropriate" mutations if it sees it usefull.

For the bacteria without the needed mutation there were no successive generations. They stopped growing and were incapable of reproducing.


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shadow71
Member (Idle past 1921 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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Taq
Member
Posts: 8488
Joined: 03-06-2009
Member Rating: 7.4


(1)
Message 66 of 296 (633119)
09-12-2011 3:28 PM
Reply to: Message 65 by shadow71
09-12-2011 2:59 PM


Re: I'm not so sure
taken in conjunction with her paper discussed on this tread where she finds metabolic activities specifically targeting the leu operon . . .

This is false. The increased mutation rate is specific to single stranded DNA (ssDNA), not the leuB gene. The authors went on to show that they could change the mutation rate of leuB by using a lac promoter and IPTG, both of which are unrelated to leucine.

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

You got the target wrong. The target in this case is ssDNA. This process will increase the mutation rate in all actively transcribed genes, including those that do not need any mutations whatsoever. In fact, this process will also create deleterious mutations in genes that are not leuB.

Even then, you still can not explain why a targetted system only hits its target once very 500 million tries. That doesn't sound like a targetted system to me. You might as well claim that the Powerball lottery is targetted towards a specific person after that person wins.


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zi ko
Member (Idle past 2607 days)
Posts: 578
Joined: 01-18-2011


Message 67 of 296 (633244)
09-13-2011 10:09 AM
Reply to: Message 62 by Wounded King
09-10-2011 4:32 AM


Re: beneficial mutations
How on Earth would this latest ad hoc nonsense work? The organisms where the mutation is beneficial already have it. In what way would the other wild-type organisms 'see' that a particular mutation was beneficial in successive generations. You are going far beyond directed mutation mechanisms in a cell here to some sort of population wide communication phenomenon directing the de novo replication of specific mutations. In other words from a tenuous hypothesis to one that is a complete fabrication without a scintilla of evidence.

You seem at first look right , but only in the perspectives of narrow lab conditions. Nature works on broad scale,with great varieties and areas of more or less affinity of an event,where organisms "see" and understand the changes happening around.There are according to Shapiro decision making loci even in one cell organisms. We know it happens in plants.
2 beneficial mutations in a billion of cells maybe is the right number,as it is proved by life. The 999,999,999,998 was again the right number for an an experience of same kind of environmet over millions of years. But you don't mention at all how many were the none beneficial mmutations in that particular event. that i think would be very helpful to to estimate any probability rate.


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Replies to this message:
 Message 70 by Wounded King, posted 09-13-2011 11:57 AM zi ko has responded
 Message 71 by Taq, posted 09-13-2011 12:33 PM zi ko has responded

  
zi ko
Member (Idle past 2607 days)
Posts: 578
Joined: 01-18-2011


Message 68 of 296 (633249)
09-13-2011 10:25 AM
Reply to: Message 64 by Taq
09-12-2011 11:02 AM


Re: beneficial mutations
For the bacteria without the needed mutation there were no successive generations. They stopped growing and were incapable of reproducing.

In real nature there are organisms in the fringes of an event that are affected some how. They survived and continued to reproduce.
I think you should provide the number of deleterious and indifferent mutations, so to be able to estimate any probability rate of beneficial mutations. Don't you think so?

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 Message 64 by Taq, posted 09-12-2011 11:02 AM Taq has responded

Replies to this message:
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Taq
Member
Posts: 8488
Joined: 03-06-2009
Member Rating: 7.4


Message 69 of 296 (633263)
09-13-2011 10:58 AM
Reply to: Message 68 by zi ko
09-13-2011 10:25 AM


Re: beneficial mutations
In real nature there are organisms in the fringes of an event that are affected some how.

Yes, they are affected by random mutations (with respect to fitness) and selective pressures.

I think you should provide the number of deleterious and indifferent mutations, so to be able to estimate any probability rate of beneficial mutations. Don't you think so?

It is the same rate as the leuB gene for genes that are actively transcribed. Gyrase is a good example. It is a "housekeeping" gene that is transcribed throughout the bacterium's lifetime. If there is a point mutation that would result in dysfuncitonal gyrase then that mutation has the same chance of occuring as the mutation that produces the leuB- reversion. That is what this study demonstrated. The author's did a great job of showing that the increased leuB- reversion rate was due to leuB- upregulation, so any gene that is upregulated will see the same effects.

Edited by Taq, : No reason given.


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Wounded King
Member (Idle past 3082 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 70 of 296 (633269)
09-13-2011 11:57 AM
Reply to: Message 67 by zi ko
09-13-2011 10:09 AM


Re: beneficial mutations
Again you seem loathe to put forward anything that might constitute evidence of any sort. If there were evidence for such population level interactions I'm not sure why we would not have been able to detect it. The mechanisms by which discrete unicellular Dictyostelium amoebae can interact to form motile colonial aggregates in response to stress is well understood, why is a similar mechanism for directed mutation in the heavily studied field of bacterial population genetics so febrile and cryptic?

But you don't mention at all how many were the none beneficial mmutations in that particular event.

Because the Wright paper does not provide any way to get that information. The only mutation rate figures they provide are for the Leu reversion.

TTFN,

WK


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Taq
Member
Posts: 8488
Joined: 03-06-2009
Member Rating: 7.4


Message 71 of 296 (633276)
09-13-2011 12:33 PM
Reply to: Message 67 by zi ko
09-13-2011 10:09 AM


Re: beneficial mutations
You seem at first look right , but only in the perspectives of narrow lab conditions.

So Shapiro et al. use narrow lab conditions and you and shadow cite their work as supporting guided mutations. When a closer look at those studies does not support your view you abandon those studies. Sounds a bit hypocritical to me.

Nature works on broad scale,with great varieties and areas of more or less affinity of an event,where organisms "see" and understand the changes happening around.There are according to Shapiro decision making loci even in one cell organisms.

You are using a sleight of hand. We are talking about mutations, not the ability of organisms to change their DNA expression patterns in response to the environment. As the Wright paper demonstrated, the bacteria did not sense a mutation in leuB and a lack of leucine in the environment as part of a decision making process to mutate leuB and only leuB. Rather, all actively transcribed genes (e.g. gyrase) will experience an increased rate of mutation at any given time regardless of the effect of those mutations.

The 999,999,999,998 was again the right number for an an experience of same kind of environmet over millions of years.

That makes zero sense. That number is a direct reflection of the random mutation rate in those bacteria, including those out in the wild.

But you don't mention at all how many were the none beneficial mmutations in that particular event. that i think would be very helpful to to estimate any probability rate.

It will be the same as the rate of leuB- reversion for all genes that are transcribed at the same levels as leuB-. That is what Wright et al. demonstrated in this paper. They even replaced the wild type leuB promoter with a lac promoter. They then used IPTG to upregulate leuB. They observed the same phenomenon as with the native leuB promoter. Therefore, the effect is tied to transcription, not an ability to directly sense leucine in the environment and guide mutations specifically to the leuB gene.


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Replies to this message:
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shadow71
Member (Idle past 1921 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?


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 Message 71 by Taq, posted 09-13-2011 12:33 PM Taq has responded

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Taq
Member
Posts: 8488
Joined: 03-06-2009
Member Rating: 7.4


Message 73 of 296 (633338)
09-13-2011 4:51 PM
Reply to: Message 72 by shadow71
09-13-2011 4:41 PM


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

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.


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zi ko
Member (Idle past 2607 days)
Posts: 578
Joined: 01-18-2011


Message 74 of 296 (633818)
09-16-2011 3:44 PM
Reply to: Message 71 by Taq
09-13-2011 12:33 PM


Re: beneficial mutations
I define random mutations as changes in the DNA sequence that are blind to the needs of the organism. IOW, mutations are random with respect to fitness. I am not saying that mutation rates are constant through time, nor am I saying that each base has an equal chance of being substituted, inserted, or deleted....... We are talking about mutations, not the ability of organisms to change their DNA expression patterns in response to the environment.

So you accept organisms are able to change their DNA expression patterns in responce to the environment. But where this interaction stops? If you accept that there is a mechanism for this, why this mechanism function does not reach to the point to involve inherited changes in genome? Forget all about I.D. I am talking only about nature,s own intelligence, that paves the way to random mutations regarding fitness, but not at all random regarding to life percervence.
Note that nature intelligence, so evident around us , man's brain the outmost examble,can equally be a result of evolution, with no supernatural involvement if you wish. It is a matter of belief choice.
--------------------------------------------------------------------------------


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New Cat's Eye
Inactive Member


Message 75 of 296 (633822)
09-16-2011 4:06 PM
Reply to: Message 74 by zi ko
09-16-2011 3:44 PM


Re: beneficial mutations
So you accept organisms are able to change their DNA expression patterns in responce to the environment. But where this interaction stops?

At the chemistry level...

nature intelligence, so evident around us

What are you talking about? Intelligence requires consciousness and nature ain't conscious.


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