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Author Topic:   Wright et al. on the Process of Mutation
zi ko
Member (Idle past 2555 days)
Posts: 578
Joined: 01-18-2011


Message 76 of 296 (633825)
09-16-2011 4:23 PM
Reply to: Message 70 by Wounded King
09-13-2011 11:57 AM


Re: beneficial mutations
If there were evidence for such population level interactions I'm not sure why we would not have been able to detect it.

"Molecular genetics has amply confirmed McClintock�s discovery that living organisms actively reorganize their genomes (5). It has also supported her view that the genome can "sense danger" and respond accordingly (56). " from 'A 21st century view of evolution' by J. SHAPIRO.


This message is a reply to:
 Message 70 by Wounded King, posted 09-13-2011 11:57 AM Wounded King has responded

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Wounded King
Member (Idle past 3030 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


(1)
Message 77 of 296 (633831)
09-16-2011 5:15 PM
Reply to: Message 76 by zi ko
09-16-2011 4:23 PM


Re: beneficial mutations
Those are 2 distinct things and neither of them leads to coordinated directed mutation between members of a population. Certainly there is evidence that some organisms, at least bacterial ones, have mechanisms which can increase their mutation rates in response to stress, no problem. I don't think you would find anyone here who quibbles with that. But that doesn't show directionality to the mutations that are produced.

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.

TTFN,

WK

Edited by Wounded King, : No reason given.


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shadow71
Member (Idle past 1870 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?


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 Message 73 by Taq, posted 09-13-2011 4:51 PM Taq has responded

Replies to this message:
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Wounded King
Member (Idle past 3030 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 79 of 296 (634102)
09-19-2011 8:51 AM
Reply to: Message 78 by shadow71
09-18-2011 7:08 PM


Re: beneficial mutations
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?

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?

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.

To return to your question; on the whole I'd probably say the answer is maybe, it certainly doesn't contradict anything particularly. It barely even constitutes a contradiction of Weismann's neo-Darwinism, since that was principally concerned with the distinction between germ line and somatic lineages, a distinction that doesn't exist in the model in Wright's study.

TTFN,

WK

Edited by Wounded King, : No reason given.

Edited by Wounded King, : No reason given.


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Taq
Member
Posts: 8482
Joined: 03-06-2009


Message 80 of 296 (634339)
09-20-2011 7:21 PM
Reply to: Message 78 by shadow71
09-18-2011 7:08 PM


Re: beneficial mutations
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?

Yes, it does. Randomness, as it was defined, was compared to fitness. This study shows the same thing. The mutation rate in the leuB gene is the same whether or not the bacteria need a mutation in that gene.

What would not comport with the definition from the 60's is a mechanism that sensed a specific environmental condition and specifically mutated a specific gene for a desired outcome. That is clearly not what we are seeing here.


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Taq
Member
Posts: 8482
Joined: 03-06-2009


Message 81 of 296 (634341)
09-20-2011 7:27 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.

Of course. What does this have to do with mutation?

But where this interaction stops?

It stops short of guiding mutations.

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?

Because the mechanisms that turn genes on and off do not change the DNA sequence. They change the binding of RNA polymerase to the upstream portion of the gene. There is nothing in this process that copies DNA into new DNA or changes the base sequence of DNA.

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.

You are talking about things you have no evidence for.

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.

Or we can get rid of beliefs altogether and follow the evidence. So what evidence can I follow that will show me how mutations are not random with respect to fitness. Would you agree that this evidence is not found in this Wright et al. paper?


This message is a reply to:
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Replies to this message:
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Bolder-dash
Member (Idle past 2566 days)
Posts: 983
From: China
Joined: 11-14-2009


Message 82 of 296 (634356)
09-20-2011 10:45 PM
Reply to: Message 79 by Wounded King
09-19-2011 8:51 AM


Re: beneficial mutations
Off-topic content hidden. --Admin

I know that you often refer to this "new" theory of evolution known as the modern synthesis, and you try to use this term as meaning some kind of new theory different from the past. As far as I am concerned this is a bit of a ruse to call it a new theory. I believe when you are referring to the modern synthesis all you are really saying is that there are many new mechanisms which we know of that effect how organisms develop. But I have never seen from you or anyone else a description of how this applies to a new theory of how things came to be. To me its akin to suggesting that every time you discover a new fossil or a new species that we didn't know existed before, that we now have a new theory of life-and thus we no longer accept the old one. We could have a new theory weekly by these definitions, and we could have a new modern synthesis weekly every time we discover some new molecular pathway. So which new modern synthesis are you referring to, the one from last week or the one from this week?

In other words, in what way is saying that there are many kinds of genetic transcriptions forming a new theoretical framework? I don't believe Darwin's theory, as it has been used for over 100 years ever really relied on one specific means for genetic change. He didn't even know how it happened. The theory has always been random mutations (after Darwin introduced shared ancestry) , combined with natural selection to form new forms after long periods of change.

So with this new modern synthesis how has this theory changed? Not how have the mechanisms changed, how has the theory changed. Can you present this theory in any way that makes it universally true and falsifiable? Is it no longer random mutations? Is it no longer slow change, but is rapid change? Because I am quite sure that no one, including the scientists who use this term 'new synthesis" really knows what the heck it means. All they are saying is that we have discovered all kinds of different genetic ways of change. they are not saying anything about how these different methods of change came to be, or why. They are not saying anything about where all of these grand epigenetic developments got their start, or why so many genes have combined to effect so many different regions of an organism.

This new modern synthesis hasn't clarified anything about the development of life on earth, it has in fact done the opposite.it has completely muddied the water about trying to see how we got here, and how life changed the way it did. If you disagree with this, then I think you have to state what exactly this theory is saying about how we got here and why. Does the modern synthesis have rules about what can't be included in the new ways that things can change? Does it make predictions? Does it attempt to answer where it got its start? I don't think you will do that because you never have, all you ever say is that the "modern synthesis' allows you to include any new thing you discover and throw it into a bowl and call it the result of random mutations. Does the modern synthesis have rules about what can't be included in the new ways that things can change? Does it make predictions? Does it attempt to answer where it got its start?

That's not a theory, that's just a way out of having to explain anything in a step by step fashion.

Let's be honest, this term "modern synthesis" doesn't mean anything specifically. It just means we found out a whole heck of a lot of things we never guessed were going on in development (and that appear to be just the tip of the iceberg), and we actually have no idea how or why these came to be. How is that a theory?

Edited by Bolder-dash, : No reason given.

Edited by Admin, : Hide off-topic content.


This message is a reply to:
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Replies to this message:
 Message 83 by Dr Adequate, posted 09-21-2011 12:43 AM Bolder-dash has responded

  
Dr Adequate
Member
Posts: 16112
Joined: 07-20-2006


Message 83 of 296 (634362)
09-21-2011 12:43 AM
Reply to: Message 82 by Bolder-dash
09-20-2011 10:45 PM


Re: beneficial mutations
I'm not sure that this is the right place to express general incomprehension of the theory of evolution. The thread has an actual topic, you know, and it is not "Things Bolder-dash still doesn't understand".

This message is a reply to:
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Replies to this message:
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Bolder-dash
Member (Idle past 2566 days)
Posts: 983
From: China
Joined: 11-14-2009


Message 84 of 296 (634364)
09-21-2011 1:23 AM
Reply to: Message 83 by Dr Adequate
09-21-2011 12:43 AM


Re: beneficial mutations
Off-topic content hidden. --Admin

It is an entirely appropriate question to ask that it be explained what the theory of the 'modern synthesis" is, since it is this which is being used to the claim that "that living organisms actively reorganize their genomes..and can sense danger and respond accordingly." is simply another aspect of the modern synthesis.

If one is saying this is an aspect of the modern synthesis, they need to show what is and what isn't the modern synthesis, if it is anything at all, other than a plea to admit that we don't understand what is going on and why.

Of course, I can certainly understand why you would object to such a question-as it puts those on your side in an uncomfortable position for having to explain something-but claiming it is off topic is not a very good defense-although it is a popular one for you to try to use here, I fully realize.

Its is sort of like Dr.A's get out of jail free card..."Hey hey, wait, that is OFF TOPIC, we don't have to answer that!" Can't you even come up with some new tricks A?

Edited by Admin, : Off-topic content hidden.


This message is a reply to:
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Dr Adequate
Member
Posts: 16112
Joined: 07-20-2006


Message 85 of 296 (634369)
09-21-2011 2:09 AM
Reply to: Message 84 by Bolder-dash
09-21-2011 1:23 AM


Re: beneficial mutations
It is an entirely appropriate question to ask that it be explained what the theory of the 'modern synthesis" is, since it is this which is being used to the claim that "that living organisms actively reorganize their genomes..and can sense danger and respond accordingly." is simply another aspect of the modern synthesis.
If one is saying this is an aspect of the modern synthesis, they need to show what is and what isn't the modern synthesis, if it is anything at all, other than a plea to admit that we don't understand what is going on and why.

Of course, I can certainly understand why you would object to such a question-as it puts those on your side in an uncomfortable position for having to explain something-but claiming it is off topic is not a very good defense-although it is a popular one for you to try to use here, I fully realize.

Its is sort of like Dr.A's get out of jail free card..."Hey hey, wait, that is OFF TOPIC, we don't have to answer that!" Can't you even come up with some new tricks A?

Obviously my ability to identify faults in your posts is restricted to the extremely limited number of faults that you have so far learned to commit. If you ever come up with a new way to make a fool of yourself, I shall point that out too.


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Wounded King
Member (Idle past 3030 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


(1)
Message 86 of 296 (634374)
09-21-2011 4:37 AM


Balderdash
Anyone interested in Boulder-dash's persistent failure to comprehend the different ways the term 'Modern synthesis' is used can read the last time he and I discussed this issue starting at Message 284 in the Criticizing neo-Darwinism thread.

I'm not going to have the same discussion again here and drag this thread even further off topic, if BD wants to continue this line of argument I suggest he return to the thread where he was already making it.

Remember when this thread was going to be a focused discussion of a specific scientific paper and what it showed? Great days.

TTFN,

WK

Edited by Wounded King, : No reason given.


  
Admin
Director
Posts: 12719
From: EvC Forum
Joined: 06-14-2002


Message 87 of 296 (634385)
09-21-2011 7:55 AM
Reply to: Message 84 by Bolder-dash
09-21-2011 1:23 AM


Moderator on Duty
As I've barely participated in this thread, and not recently, I'll take over moderator responsibility.

Hi Bolder-dash,

This thread is for discussing Wright's ideas within the framework in which they were constructed. If you're more interested in challenging the framework than the ideas then please do it in a thread where it would be on topic. Proposing a new thread to discuss the definition of the modern synthesis over at Proposed New Topics would be a good idea because it doesn't look like it has had its own thread in quite a while.

Because of your long history of determination and persistence at being off-topic, there will be no further warnings. Administrative action will be the next step. Please, no replies to this message in this thread.

Edited by Admin, : Grammar.


--Percy
EvC Forum Director

This message is a reply to:
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Taq
Member
Posts: 8482
Joined: 03-06-2009


Message 88 of 296 (634416)
09-21-2011 11:29 AM


Reiteration
It is probably worth my time to reiterate my stance on the definition of random mutations and how it relates to the study in question. From my opening post:

quote:
Just to get it out of the way, 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. With respect to the paper, I will attempt to demonstrate that the same mechanisms that produce reversions in leuB- organisms will also cause deleterious mutations in very important and vital genes as well as mutations which do not change the fitness of offspring.

IOW, the processes that create mutations are blind to the impact these mutations will have on fitness. Specifically for this study, the mechanism under question increases the mutation rate in all genes that are upregulated. This was confirmed by Wright et al. by replacing the wild type promoter of leuB with an IPTG inducible promoter (derived from the lac promoter if memory serves) that is independent of leucine concentrations in the environment. These mutations will run the gambit from lethal to strongly beneficial. For example, lethal mutations in vital housekeeping genes like DNA gyrase will be increased due to this mechanism.

Edited by Taq, : No reason given.


  
zi ko
Member (Idle past 2555 days)
Posts: 578
Joined: 01-18-2011


Message 89 of 296 (634463)
09-21-2011 9:51 PM
Reply to: Message 81 by Taq
09-20-2011 7:27 PM


Re: beneficial mutations
It stops short of guiding mutations.
.
There is no reason to go go any further. Guiding had been completed by all preceded paving work. Nonandom mutations are not any more needed. Nature is clever to use all ways of action, as "random" mutations.

You are talking about things you have no evidence for.

The only difference between me and you is that I accept nature's intelligence, which i see all over around, while you accept randomness as the cause of mystery of life and evolution as well without any evidence. We are both just believers.

Or we can get rid of beliefs altogether and follow the evidence. So what evidence can I follow that will show me how mutations are not random with respect to fitness. Would you agree that this evidence is not found in this Wright et al. paper?

You are right . Mutations are random, but only to fitness, not to life perseverance.

Edited by zi ko, : No reason given.

Edited by zi ko, : No reason given.


This message is a reply to:
 Message 81 by Taq, posted 09-20-2011 7:27 PM Taq has responded

Replies to this message:
 Message 90 by Wounded King, posted 09-22-2011 4:18 AM zi ko has not yet responded
 Message 91 by Taq, posted 09-22-2011 11:28 AM zi ko has responded

  
Wounded King
Member (Idle past 3030 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 90 of 296 (634486)
09-22-2011 4:18 AM
Reply to: Message 89 by zi ko
09-21-2011 9:51 PM


Life's persistence
Mutations are random, but only to fitness, not to life perseverance.

This is essentially a tautology, although life is hard to define precisely many proposed definitions involve the capacity for change and adaptation including mutation and reproduction (Koshland, 2002; Clelland and Chyba, 2002; McKay, 2004).

All you seem to be saying here is that for life to persevere there need to be things continuing to exist which still show the characteristic properties of life. Which is kind of obvious.

TTFN,

WK

Edited by Wounded King, : No reason given.

Edited by Wounded King, : No reason given.

Edited by Wounded King, : No reason given.


This message is a reply to:
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