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Author Topic:   Wright et al. on the Process of Mutation
Taq
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Message 152 of 296 (636005)
10-03-2011 5:17 PM
Reply to: Message 151 by shadow71
10-03-2011 3:40 PM


Re: Nitpicks and an interesting reference
I do not understand the data from a scientific standpoint.
Then it doesn't matter what Wright et al. actually conclude. You can't tell if that conclusion is supported or not. The same goes for Shapiro.
Also, the entire purpose of this thread was to help you understand the data from a scientific standpoint. So what specific questions do you have? How can we help you understand the data? I like talking science, so no question is a bad question as long as it is asked by a curious mind.
I can only rely on the author who provides the data, and I still think Wright, based upon all her writings is of the opinion there is some type of directed mutations.
If that opinion is contradicted by the data then it is not a worthwhile opinion.
The last paper I read by Wright, the Review, was dated I believe 2000. Since then Shapiro has given the opinon there is evidence of mutations that are beneficial and non random. He talks about ..."adaptive inventions with a spontaneous probability of occurrence that is vanishingly small."
Then please find the primary lit paper where we can look at this data and discuss it in another thread.
So I am still not convinced that all mutations are random for beneficial adapation.
What data convinced you that mutations are not random with respect to fitness? What data WOULD convince you that mutations are random with respect to fitness? Why is the data in this paper unconvincing?
I guess I will go back to my old thread in re Darwinism and is there a need for changes in the Darwin's theory, neo-Darwinism and the modern synthesis, with a discussion of the developments since the 1960's.
Why? You were not looking for discussion in that thread. You kept repeating the same thing over and over as if that constituted an argument. It doesn't. Yeah, we get it. You think Shapiro and Wright are arguing for non-random mutations with repsect to fitness. So what? If Wright thought that fire was made of fire pixies it still wouldn't be true. You are making nothing but an argument from authority while ignoring the actual evidence. That is a worthless discussion to have.

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 Message 151 by shadow71, posted 10-03-2011 3:40 PM shadow71 has replied

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 Message 156 by shadow71, posted 10-09-2011 1:24 PM Taq has replied

  
Taq
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Posts: 9944
Joined: 03-06-2009
Member Rating: 4.8


Message 161 of 296 (636943)
10-12-2011 12:18 PM
Reply to: Message 156 by shadow71
10-09-2011 1:24 PM


Re: Nitpicks and an interesting reference
You interpret the data as not showing a non-random beneficial adapation.
Where is my interpretation incorrect? It is not enough to claim that someone is interpretting the data. That is what everyone does with the data. You need to show that my interpretation is incorrect or admit that it is correct.
Wright and Shapiro, as confirmed by Merlin's paper posted by Wounded King, do argue for non-random adapation for fitness.
This misses the mark since we are discussing non-random MUTATION, not adaptation. Of course adaptation is non-random since natural selection is involved. The question is how variation is produced which is then acted on by natural selection.
If you step outside of your data and look at the wholistic marvel of evolution, it is pretty hard to rule out non-randomness for beneficia adapations.
Actually, no it isn't. Lineage specific adaptations are exactly what we should see if mutation is random with respect to fitness, and that is exactly what we see.
Why do we need a bigger ratio for non random adapation for fitness, when one is all that is needed?
For a colony of 100,000 bacteria (about the standard size for a colony on an agar plate) a mutation rate of 1 in 500 million is not enough. Gene regulation is a non-random process with respect to fitness, and 99.9999% of bacterial clones show the same gene regulation patterns with respect to environment every time. That is what we expect from a non-random process. This is NOT what we see with the process of mutation. Bacterial clones do NOT produce the same mutations. Only 2 out of 1 billion produce the same mutation. This is the EXACT OPPOSITE of what we see with non-random processes such as gene regulation.
Edited by Taq, : No reason given.

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Taq
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Posts: 9944
Joined: 03-06-2009
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Message 162 of 296 (636945)
10-12-2011 12:29 PM
Reply to: Message 159 by zi ko
10-11-2011 1:12 PM


Re: beneficial mutations
So mutations can be: entirely random as regards fitness, semi-directed (by this term I mean mutations enhanced in rate or facilitated to happen in special loci, or otherwise), or entirely directed; but all of them are really directed in regard to life’s preservation (or death). "
So what are they with regards to the paper under discussion: entirely random, semi-directed, or entirely directed? Please support your argument with reference to the data found in the paper.
Also, how do detrimental mutations fit into your argument?
Intelligence: I don’t give it the original meaning of the word (namely, to choose between contingent alternatives). What I really mean is: in response to environmental and other factors, a naturally inside organism pre-existing mechanism, and by force of chemistry and physics, causes changes in the genome.
Do you consider it "intelligent" when it produces detrimental mutations? If so, why? Why is it a good idea to produce detrimental mutations?
So I think of it as a mechanism, but not intelligence in any traditional sense.
Then why don't you just call it a mechanism?

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 Message 159 by zi ko, posted 10-11-2011 1:12 PM zi ko has replied

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Taq
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Posts: 9944
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Member Rating: 4.8


Message 170 of 296 (637119)
10-13-2011 2:39 PM
Reply to: Message 168 by zi ko
10-13-2011 10:49 AM


Re: beneficial mutations
If you mean by this that evolution it is based on complete randomness, . . .
Look up the term "conflation". This is what you are doing here. Again and again we have said that MUTATIONS are random with respect to fitness. Nowhere do we say that EVOLUTION is random. Mutation and evolution are two different things. Mutation is just one mechanism within the larger process of evolution. This larger process also consists of natural SELECTION. Selection, by the very definition, is NOT RANDOM.

This message is a reply to:
 Message 168 by zi ko, posted 10-13-2011 10:49 AM zi ko has replied

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Taq
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Posts: 9944
Joined: 03-06-2009
Member Rating: 4.8


Message 171 of 296 (637120)
10-13-2011 2:42 PM
Reply to: Message 164 by zi ko
10-12-2011 5:53 PM


Re: beneficial mutations
Random as regards fitness, but directed as regards life preservation.
How so? Please cite data from the paper which demonstrates that mutations are directed with respect to life preservation.
Yes. because it makes the job for nature.
Makes what job? I would call a detrimental mutation the exact opposite of an intelligent choice. What type of mutation would be inconsistent with an intelligent mechanism?
It is a mechanism that stems from nature's innate intelligence,
Please cite data from this paper which supports this assertion.
because this mechanism i don't believe could be created by chance,
Evidence please. Beliefs are not evidence.
Edited by Taq, : No reason given.

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Taq
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Posts: 9944
Joined: 03-06-2009
Member Rating: 4.8


Message 179 of 296 (637252)
10-14-2011 11:46 AM
Reply to: Message 172 by zi ko
10-14-2011 6:26 AM


Re: beneficial mutations
A detrimental mutation is the exact opposite only to a part of the intelligence,which can include detriment products, as far as the life preservation primary target is succeeded.
So the intelligence is only in effect if the mutation is beneficial?
Then I can prove to you that I have ESP. It is quite simple, really. Just give me a billion dollars and I will buy a billion lottery tickets, using my ESP to choose each number on each ticket. You can just ignore all of the tickets that don't win. The proof that my ESP is accurate is the handful of tickets that do win.
Would you be convinced by this display of my ESP powers?

This message is a reply to:
 Message 172 by zi ko, posted 10-14-2011 6:26 AM zi ko has replied

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Taq
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Posts: 9944
Joined: 03-06-2009
Member Rating: 4.8


Message 182 of 296 (637298)
10-14-2011 4:04 PM
Reply to: Message 181 by zi ko
10-14-2011 2:55 PM


Re: beneficial mutations
while you believe man has been created by pure chance,
Where did Percy ever say that?

This message is a reply to:
 Message 181 by zi ko, posted 10-14-2011 2:55 PM zi ko has replied

Replies to this message:
 Message 214 by zi ko, posted 12-14-2011 11:33 AM Taq has replied

  
Taq
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Posts: 9944
Joined: 03-06-2009
Member Rating: 4.8


Message 188 of 296 (637680)
10-17-2011 12:18 PM
Reply to: Message 186 by zi ko
10-15-2011 10:15 AM


Re: beneficial mutations
I understand that current theory has a (superficially ?) powered logical form for evolution entirely mechanistic and simple: Random mutations- natural selection and we have solved the problem of life evolution. But there are some nags here.fe.c 1.The number of random mutations needed for a succesfull phenotype or genotype advance. Mathematicians think they are needed many more than the given time permits (even millions of years). 2.The instinct formation.
Two things:
1. This has nothing to do with this thread. This thread is focusing on a single paper, and how the data demonstrates the randomness of mutations (not evolution).
2. You have not acknowledged the mistakes that I have pointed out. You keep saying that evolution is random. It isn't. Trying to change the subject does not make this mistake go away.

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 Message 186 by zi ko, posted 10-15-2011 10:15 AM zi ko has replied

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Taq
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Posts: 9944
Joined: 03-06-2009
Member Rating: 4.8


Message 194 of 296 (643853)
12-12-2011 12:06 PM
Reply to: Message 189 by Kaichos Man
12-12-2011 6:43 AM


Re: Long time no contradict
So although mutation, remixing and recombination are clearly random, natural selection isn't?
Nope, it isn't. Let's use the Wright et al. paper as our example since it is the topic of this thread. In this study they consistently ended up with colonies of bacteria with a specific mutation in the leuB gene. This mutation only occurred once very 500 million cell divisions, and yet those 1 in 500 million oddballs were the only ones growing on the plate every time. The other 499,999,999 bacteria did not grow on that plate. Obviously, you can not get this consistent result with a random process.
But surely the conditions bringing about selection are random.
Random with respect to what?
If the conditions deciding selection are random, how can selection itself not be random?
Natural selection is not random with respect to fitness. The most fit individuals within a population have a higher probability of passing on their genes.
Are you seriously suggesting that a random cause can have a non-random effect?
Are you saying it can't? If you randomly add antibiotics to random bacterial cultures you still get non-random selection of antibiotic resistant mutants.
And of course, the longer we make that list of random causes, the more obvious it becomes that selective fitness can best be described as ...luck.
It is best described as being fitter and therefore having a higher probability of passing on your genes.
Which, at the risk of annoying you, brings us back to the position of our old mate Kimura.
You mean the guy who described the random nature of neutral mutations compared to the non-random nature of mutations under selection?
ABE:
[quote]The neutral theory asserts that the great majority of evolutionary changes at the molecular level, as revealed by comparative studies of protein and DNA sequences, are caused not by Darwinian selection but by random drive of selectively neutral or nearly neutral mutants. The theory does not deny the role of natural selection in determining the course of adaptive evolution, but it assumes that only a minute fraction of DNA changes in evolution are adapative in nature, while the great majority of phenotypically silent molecular substitutions exert no significant influence on survival and reproduction and drift randomly throught he species--Kimura, (not sure on the specific source for this since I am pulling it from a Google Books preview of a secondary source).
Edited by Taq, : No reason given.

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Taq
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Posts: 9944
Joined: 03-06-2009
Member Rating: 4.8


Message 200 of 296 (643974)
12-13-2011 4:54 PM
Reply to: Message 197 by Kaichos Man
12-13-2011 7:50 AM


Re: Long time no contradict
To my suggestion that luck might be the deciding factor in selection, in line with kimura's beliefs, you wrote:
Please show how the selection of leuB revertant mutants in the Wright et al. paper was due to luck. Remember, the mutation only occurred once in every 500 million divisions. So how is it that they always ended up with these same mutants after selection and not the other 499,999 bacteria without the mutation?

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Taq
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Posts: 9944
Joined: 03-06-2009
Member Rating: 4.8


Message 220 of 296 (644046)
12-14-2011 3:06 PM
Reply to: Message 214 by zi ko
12-14-2011 11:33 AM


Re: Are there RANDOM MUTATIONS?
If Percy and you really believe that random mutations exist, then you believe that man has been created by pure chance, becouse mutations is the critical factor in evolution.
Selection and mutation are equally important. Mutation is important for creating variability, and it is random with respect to fitness. Selection is important for filtering these variations in phenotype so that the population adapts to their environment over many generations. So which is more important, having variation or adapting to your environment?
As to the Wright paper, the end result is obviously non-random. All of the colonies growing on the plates lacking leucine had a specific mutation. Compare this to the population before plating where only 1 in 500 million had this mutation. That can't happen through chance time after time.

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 Message 214 by zi ko, posted 12-14-2011 11:33 AM zi ko has replied

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Taq
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Posts: 9944
Joined: 03-06-2009
Member Rating: 4.8


Message 221 of 296 (644047)
12-14-2011 3:10 PM
Reply to: Message 209 by Kaichos Man
12-14-2011 7:00 AM


Re: Kimura redux
Hey, you can still pretend that selection somehow -magically- evolves the phenotype while leaving the genotype untouched.
Who is claiming that? In fact, this thread is focused on mutations that lead to a change in phenotype. Perhaps you could discuss that?
What the found in the paper is that before plating in the absence of leucine that a specific mutation existed in 1 in every 500 million bacteria. After selection 1 in every 1 had this mutation. How can this occur by chance as you suggest?

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Taq
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Posts: 9944
Joined: 03-06-2009
Member Rating: 4.8


Message 223 of 296 (644749)
12-20-2011 12:26 PM
Reply to: Message 222 by zi ko
12-15-2011 12:44 AM


Re: Are there RANDOM MUTATIONS?
quote:
This is where we really disagree; the degree of other types of evolution participation and of course manly if there are other types of evolution.
Could you please point to the "other types of evolution" that appear in the Wright et al. paper?

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Taq
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Posts: 9944
Joined: 03-06-2009
Member Rating: 4.8


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Message 226 of 296 (645083)
12-23-2011 1:50 AM
Reply to: Message 225 by herebedragons
12-22-2011 8:12 PM


1. The authors do seem to be arguing for at least a form of directed mutation.
I agree. They are arguing just that. However, they fail miserably IMHO. What they are arguing is analogous to a poor person buying more lottery tickets. They argue that since the the poor person increases their odds of winning the lottery by buying more lottery tickets that the lottery is no longer random. I see no reason to agree with them. Do you?
I am unclear as to what their actual hypothesis was in this paper. It seems to be derepression-induced hypermutation being the link between mutations and environmental stress. Is that a fair summary of their position?
That is a fair summary. The result of this mechanism is an increase in random mutations, and a higher rate of random mutations within regions of the genome that are actively transcribed. This means that there is an increase in mutations within the leuB- gene which increases the rate of beneficial mutations in an environment which lacks leucine. At the same time, this also increases the rate of mutations in important housekeeping genes that were functioning just fine in the given environment. This mechanism increases the beneficial, neutral, and detrimental mutation rate based on the rate of gene regulation, not on what is or is not beneficial to the organism in a given environment. If the situation were different, there could be a case where the needed beneficial mutation would be found in a gene that was downregulated in a given environment. This would mean that this mechanism could just as well work against the "directed" evolution of the organism.
At the end of the day this is no different than a beggar on the corner getting an extra ten dollars to spend on the lottery. The non-random increase in the purchase of tickets in no way makes the actual lottery drawing non-random with respect to financial need.
I did not see where you did this. Not that I doubt that the premise would be true, but I don’t think the data in the paper supports rates of deleterious or neutral mutations.
That is a very fair criticism of my post. The evidence for what I stated is very subtle and hard to understand unless you have a background in molecular biology. My lottery analogy is applicable in this case.
The support for my argument is the experiments with the lac promoter. They removed the wild type (i.e. normal) promoter from the lueB gene and replaced it with a lac promoter that could be turned off and on with the addition of exogenous chemicals (I presume that they are using IPTG). What they found is that they could increase the mutation rate in the lueB gene by adding the chemical that turned on the lac promoter. This indicates that the increase in the beneficial mutation rate is tied to gene regulation, that is the ssDNA condition of that part of the genome. This means that any gene that is being actively transcribed is going to see an increase in the mutation rate. This includes vital housekeeping genes.
I cited DNA gyrase as one of those genes, and it serves as a good example. In the experiment, the DNA gyrase gene worked just fine. There was no environmental pressure for the gyrase gene to change. From my own work, I know that any living cell is always actively copying this gene from DNA to RNA. That is why they call it a housekeeping gene. This means that this gene is always incurring more mutations than genes that are not actively being transcribed from DNA to RNA. The only result of mutating this gene in an environment that does not need a change in DNA gyrase activity is either a neutral change or a detrimental change (i.e. a lethal frame shift mutation that takes away the vital gyrase activity).
So, the very mechanism that increases the rate of beneficial mutations in the lueB gene also increases the neutral and lethal mutations in vital housekeeping genes. By definition, this is random mutation. It is an increase in changes that are random with respect to fitness.

This message is a reply to:
 Message 225 by herebedragons, posted 12-22-2011 8:12 PM herebedragons has replied

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Taq
Member
Posts: 9944
Joined: 03-06-2009
Member Rating: 4.8


Message 233 of 296 (645125)
12-23-2011 1:26 PM
Reply to: Message 231 by zi ko
12-23-2011 11:59 AM


Re: Are there RANDOM MUTATIONS?
Yes mutations are random to fitness but not random to life's preservation.
Those are the same thing.
At the bacteria level they more or less are random, but not at metazoa with neural system, which provides the mechanism to let organisms to know what is about "the right mutation" for them.
Humans are born with mutations that cause lethal diseases that kill children before they ever reach adulthood. You are clearly wrong.
Maybe becouse they are enough for life to continue to exist.Mutations here are really random to fitness; nature (universal laws) can allow randomness to play a role and this is done quite often.
The 2 out of 1 billion is the same rate whether there are a billion bacteria or just 10. Again, you are clearly wrong.

This message is a reply to:
 Message 231 by zi ko, posted 12-23-2011 11:59 AM zi ko has replied

Replies to this message:
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