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Author Topic:   Does the Darwinian theory require modification or replacement?
molbiogirl
Member (Idle past 2671 days)
Posts: 1909
From: MO
Joined: 06-06-2007


(1)
Message 331 of 760 (612499)
04-16-2011 11:06 AM
Reply to: Message 321 by shadow71
04-15-2011 7:47 PM


Wright and directed mutation
Let's look at what Wright says.
Evolution depends upon events that enhance mutation rates, thus increasing the supply of variants from which the fittest are selected.
Hm. Sounds an awful lot like random mutation.
Let's look further.
That any DNA-destabilizing event will increase mutation rates is axiomatic.
OK. Same old, same old. Transcription rates go up, mutation rates go up.
As discussed above, the mutations are sequence directed and not random in the sense that they occur in bases made vulnerable by virtue of their particular location within specific DNA sequences, such as tandem repeats, or the unpaired and mispaired bases of stem-loop structures.
Notice that careful wording? NOT RANDOM IN THE SENSE THAT.
In other words, non random in ONLY ONE WAY (the location).
Which base will mutate? At what position in the gene? In a coding or noncoding section?
Huh. Still sounds random with respect to fitness.
Let's keep looking.
In higher organisms, environmental conditions of stress do not have direct access to the cells involved in reproduction, and different mechanisms resulting in hypervariation have evolved. ... These mechanisms are also random. ... its hypermutability per se is undirected, since it is unrelated to those selective conditions and to the function of the gene.
Now look at that.
Completely random, undirected mutation is responsible for the evolution of higher organisms.
Golly gee.
Looks like this paper doesn't say what you want it to say.
You think directed mutation means a tailor made genetic solution for an environmental problem. (That's not how Wright understands it, btw. Only you.)
Can you cite a paper that shows directed mutation as you understand it?
Let me get real specific for you.
"Directed mutation" in something OTHER than a bacteria or a yeast?

This message is a reply to:
 Message 321 by shadow71, posted 04-15-2011 7:47 PM shadow71 has replied

Replies to this message:
 Message 340 by shadow71, posted 04-16-2011 8:09 PM molbiogirl has replied

AZPaul3
Member
Posts: 8564
From: Phoenix
Joined: 11-06-2006
Member Rating: 4.7


Message 332 of 760 (612503)
04-16-2011 12:49 PM
Reply to: Message 330 by Wounded King
04-16-2011 4:03 AM


Re: Sped-up in a specfic locus arguably is "Directed".
I stand corrected. Thank you.

This message is a reply to:
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shadow71
Member (Idle past 2963 days)
Posts: 706
From: Joliet, il, USA
Joined: 08-31-2010


Message 333 of 760 (612533)
04-16-2011 7:06 PM
Reply to: Message 324 by NoNukes
04-15-2011 9:15 PM


Re: Directed mutations.
NoNukes writes:
I don't think there is evidence that of mechanism where a stimulus generates the perfect fix so that natural selection is out of the picture. But the directed mechanisms might decrease the amount of time needed to hit a beneficial mechanism and reduce the genetic damage inflicted by mutations over a completely random approach.
I think the mechanisms discussed in Wright's paper are real, but of course I haven't had a formal class in biology since high school.
The way I read Shapiro and apply it to Dr. Wright is that there may be "directed" mutations, ie mutations that are beneficial, and that "purilfying selection" a selection that destroys deleterious mutations takes over so the benefical mutations provide the beneficial apparatus.
I may be totally wrong, and I am sure the scientific experts on this board will correct me if I am wrong.

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Replies to this message:
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shadow71
Member (Idle past 2963 days)
Posts: 706
From: Joliet, il, USA
Joined: 08-31-2010


Message 334 of 760 (612534)
04-16-2011 7:10 PM
Reply to: Message 325 by NoNukes
04-15-2011 9:22 PM


Re: Cairns and directed mutation
NoNukes writes:
Do you understand Shapiro to state that random mutations do not occur and that natural selection is not an important or relevant part of the evolutionary theory?
You talk about random vs non-random as if it were one or the other. I don't believe Shapiro or any other non-kook biologist shares that opinion.
I am torn as to whether there can be random mutations, but not convinced they do not occur. I do not rule out selection, but what I have a problem with is that this whole process of evolution is toatally random, accidential and w/o purpose.
--------------------------------------------------------------------------------

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jar
Member (Idle past 423 days)
Posts: 34026
From: Texas!!
Joined: 04-20-2004


Message 335 of 760 (612535)
04-16-2011 7:18 PM
Reply to: Message 334 by shadow71
04-16-2011 7:10 PM


Re: Cairns and directed mutation
shadow71 writes:
NoNukes writes:
Do you understand Shapiro to state that random mutations do not occur and that natural selection is not an important or relevant part of the evolutionary theory?
You talk about random vs non-random as if it were one or the other. I don't believe Shapiro or any other non-kook biologist shares that opinion.
I am torn as to whether there can be random mutations, but not convinced they do not occur. I do not rule out selection, but what I have a problem with is that this whole process of evolution is toatally random, accidential and w/o purpose.
--------------------------------------------------------------------------------
And that is the big difference between Science and the Law; in science there is no desired outcome.

Anyone so limited that they can only spell a word one way is severely handicapped!

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 Message 334 by shadow71, posted 04-16-2011 7:10 PM shadow71 has replied

Replies to this message:
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shadow71
Member (Idle past 2963 days)
Posts: 706
From: Joliet, il, USA
Joined: 08-31-2010


Message 336 of 760 (612536)
04-16-2011 7:22 PM
Reply to: Message 326 by NoNukes
04-15-2011 9:30 PM


Re: Is phenotypic plasticity magic?
NoNukes writes:
Yes, we know how you interpret Shapiro.
Why didn't Shapiro answer your question with a "Yes"? Instead, he gave you a quite carefully worded response that was completely consistent with what he says in his paper. What do you think the word "potential" means in his response? What did "certain changes" mean?
Shapiro in his paper of 2010 wrote:
Shapiro writes:
This regulatory/cognitive view of genome restructuring helps us to formulate reasonable hypotheses about two unresolved questions in evolutionary theory: (i) the connections between evolutionary change and ecological disruption; and (ii) the origins of complex adaptive novelties at moments of macroevolutionary change.
So Shapiro is not stating that Natural Genetic Engineering is a fact, but it is a hypothesis on evolutionary change, the enviroment, and sentience in cells, and the origins of macroevolution. He does not believe the modern synthesis explains these issues completely.
He discusses a regulatory/cognitive view of evolution, which is a far cry from random mutation and accidential changes.
I tend to agree with him.
I cannot speak for him but I think as a scientist he knows that he may be right or he may be wrong, so he will not answer with a yes or no. Rather he is saying this is what I opine from my research and is throwing it out to the scientific community or debate.

This message is a reply to:
 Message 326 by NoNukes, posted 04-15-2011 9:30 PM NoNukes has replied

Replies to this message:
 Message 337 by jar, posted 04-16-2011 7:30 PM shadow71 has replied
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jar
Member (Idle past 423 days)
Posts: 34026
From: Texas!!
Joined: 04-20-2004


Message 337 of 760 (612537)
04-16-2011 7:30 PM
Reply to: Message 336 by shadow71
04-16-2011 7:22 PM


Re: Is phenotypic plasticity magic?
shadow71 writes:
NoNukes writes:
Yes, we know how you interpret Shapiro.
Why didn't Shapiro answer your question with a "Yes"? Instead, he gave you a quite carefully worded response that was completely consistent with what he says in his paper. What do you think the word "potential" means in his response? What did "certain changes" mean?
Shapiro in his paper of 2010 wrote:
Shapiro writes:
This regulatory/cognitive view of genome restructuring helps us to formulate reasonable hypotheses about two unresolved questions in evolutionary theory: (i) the connections between evolutionary change and ecological disruption; and (ii) the origins of complex adaptive novelties at moments of macroevolutionary change.
So Shapiro is not stating that Natural Genetic Engineering is a fact, but it is a hypothesis on evolutionary change, the enviroment, and sentience in cells, and the origins of macroevolution. He does not believe the modern synthesis explains these issues completely.
He discusses a regulatory/cognitive view of evolution, which is a far cry from random mutation and accidential changes.
I tend to agree with him.
I cannot speak for him but I think as a scientist he knows that he may be right or he may be wrong, so he will not answer with a yes or no. Rather he is saying this is what I opine from my research and is throwing it out to the scientific community or debate.
That you tend to agree with him is why you will ultimately fail.
Stop and think.
What will a cell use for cognition?
What will a cell use for sentience?
Sorry but there is simply nothing available to think with.
The most that can be said is that there might be some response (chemical and physical) to specific stimuli.
But there is no thought, no direction, no design.

Anyone so limited that they can only spell a word one way is severely handicapped!

This message is a reply to:
 Message 336 by shadow71, posted 04-16-2011 7:22 PM shadow71 has replied

Replies to this message:
 Message 344 by shadow71, posted 04-16-2011 8:19 PM jar has replied

shadow71
Member (Idle past 2963 days)
Posts: 706
From: Joliet, il, USA
Joined: 08-31-2010


Message 338 of 760 (612538)
04-16-2011 7:48 PM
Reply to: Message 329 by AZPaul3
04-16-2011 2:07 AM


Re: Cairns and directed mutation
AZPaul3 writes:
All are talking about "directed mutations" as a cascade of natural chemical events leading to the increased retention of randomly generated mutations within the genes. Some speculate that some of these cascades could be "targeted" to specific genes or suites of genes and only come into play when some other chemical cascades, responding in a completely natural non-intelligent way to some environmental change, kick them into action.
These scientific papers I have cited and others I will cite in the future on this thread, reinforce my belief that there is more to life than natural accidential occurrences.
The controversy here is not about some intelligent agent specifically causing some specific mutation with the intent of creating some specific change. It is about whether these natural chemical cascades responding to the environment really exist and whether they can affect the rate of retained random mutations in the genome.
There is nothing here for any religionist or ID advocate or woo-woo believer to point to as proof of god or magic or inter-dimensional intelligence. There is only real work for real biologists and some fodder for charlatans to pick stupid peoples' pockets.
But you miss my point with your last paragraph. I am not a "woo believer" whatever that means. I am a person who believes in creation in some manner by a supernatural being, and a person who, after trying many medical and product liabilty cases knows that scientists do not have all the answers and are not always correct.
The controversy, as I see it, is whether there is something more than accidential, natural causation of the eloquent evolution we see in this world.
The symmetry of the Universe, the complex wonderful life forms, the physists who say but for one change in the chemical makeup of the beginning of the universe, we would not be here.
You believe in "natual creation", I do not.
So when a scientist discusses directed, non random causes, it reinforces my belief that the universe and life are not random accidents.
That in fact there is a plan that is being carried out in our universe.
You may laugh at me, that is your right, but every day scientists who are not as you say creationists are putting forth new studies that lead to the conclusion of some planned, "engineered, if you will" program.
--------------------------------------------------------------------------------

This message is a reply to:
 Message 329 by AZPaul3, posted 04-16-2011 2:07 AM AZPaul3 has replied

Replies to this message:
 Message 341 by NoNukes, posted 04-16-2011 8:10 PM shadow71 has replied
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Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 339 of 760 (612540)
04-16-2011 8:01 PM
Reply to: Message 333 by shadow71
04-16-2011 7:06 PM


Re: Directed mutations.
I may be totally wrong, and I am sure the scientific experts on this board will correct me if I am wrong.
Well we try, but it gets tedious when you continually ignore our corrections and repeat the same mistaken arguments again and again.
For instance your description of 'purifying selection' is nonsense. Purifying selection doesn't take over, it is simply one result of ongoing natural selection, and by acknowledging its role in this situation you are conceding that your fabulous "directed mutation" mechanisms are producing deleterious mutations which need to be weeded out.
Which is essentially what everyone has been telling you all along when we point out that there is still a whole spectrum of beneficial and deleterious mutations being produced. The spectrum of mutations after selection is a completely different issue and we would expect it to be strongly weighted towards beneficial mutations.
I think you need to realise that Wright's "direction" is regardless of the fitness benefits of the resultant mutation. The "direction" is simply to a specific genetic locus. Wright makes a reasonable argument that this will give an increased chance of a beneficial mutation occurring at that locus since it has an increased chance of all mutations associated with its transcriptional state. We can easily point out that this will also produce an increased chance of deleterious mutations at this locus, and this is where selection plays its part by favouring the proliferation of the beneficial mutations and tending to eliminate the deleterious ones.
I do not rule out selection, but what I have a problem with is that this whole process of evolution is toatally random, accidential and w/o purpose.
Again, simply wrong. The whole point of acknowledging the role of selection is that it means that evolution is not totally random or accidental. Evolution is a feedback between the genomes of organisms and their environment with the environment constraining and filtering the form of the evolving genome.
You may laugh at me, that is your right, but every day scientists who are not as you say creationists are putting forth new studies that lead to the conclusion of some planned, "engineered, if you will" program.
Really? Excellent! Can you provide us references for 5 papers published in the last month which lead to this conclusion? So far you have managed a handful, mostly review papers, covering about a decade.
It seems that you are slipping into hyperbole here.
Perhaps what you meant was that every day scientists are putting forth new studies which you insist on fitting into your preconceived notions of how things should be. Which would explain why you are throwing Cairns' name around even though he has produced several papers which have effectively shown that the phenomenon he observed was not directed mutation.
TTFN,
WK
Edited by Wounded King, : No reason given.

This message is a reply to:
 Message 333 by shadow71, posted 04-16-2011 7:06 PM shadow71 has replied

Replies to this message:
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shadow71
Member (Idle past 2963 days)
Posts: 706
From: Joliet, il, USA
Joined: 08-31-2010


Message 340 of 760 (612541)
04-16-2011 8:09 PM
Reply to: Message 331 by molbiogirl
04-16-2011 11:06 AM


Re: Wright and directed mutation
Wright writes:
In contrast, hypermutation that is the consequence of starvation-induced derepression and transcriptional activation represents a very rapid and specific response to each adverse circumstance. 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.
molbiogirl writes:
Now look at that.
Completely random, undirected mutation is responsible for the evolution of higher organisms.
Golly gee.
Looks like this paper doesn't say what you want it to say.
You think directed mutation means a tailor made genetic solution for an environmental problem. (That's not how Wright understands it, btw. Only you.)
Can you cite a paper that shows directed mutation as you understand it?
Let me get real specific for you.
"Directed mutation" in something OTHER than a bacteria or a yeast?
Wrights paper says it is possible "MANY MUTATIONS ARE TO SOME EXTENT DIRECTED..."
That is a start to further development of the hypothesis of directed mutations in some manner and in some way.
Because it is not fully proven today, does not mean it won't be in the future.
You close your mind molbiogirl too quickly.

This message is a reply to:
 Message 331 by molbiogirl, posted 04-16-2011 11:06 AM molbiogirl has replied

Replies to this message:
 Message 351 by molbiogirl, posted 04-17-2011 10:59 AM shadow71 has replied

NoNukes
Inactive Member


Message 341 of 760 (612542)
04-16-2011 8:10 PM
Reply to: Message 338 by shadow71
04-16-2011 7:48 PM


Re: Cairns and directed mutation
I'm guessing you wrote the following sentence and accidentally attributed said sentence to AZPaul3
quote:
These scientific papers I have cited and others I will cite in the future on this thread, reinforce my belief that there is more to life than natural accidential occurrences.
shadow71 writes:
You may laugh at me, that is your right, but every day scientists who are not as you say creationists are putting forth new studies that lead to the conclusion of some planned, "engineered, if you will" program.
Looking forward to the next paper.

This message is a reply to:
 Message 338 by shadow71, posted 04-16-2011 7:48 PM shadow71 has replied

Replies to this message:
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shadow71
Member (Idle past 2963 days)
Posts: 706
From: Joliet, il, USA
Joined: 08-31-2010


Message 342 of 760 (612543)
04-16-2011 8:16 PM
Reply to: Message 335 by jar
04-16-2011 7:18 PM


Re: Cairns and directed mutation
jar writes:
And that is the big difference between Science and the Law; in science there is no desired outcome.
If you read the postings on this board in reply to the scientific papers I cite, there is a definite desired outcome that the current theory of evolution not be challenged.

This message is a reply to:
 Message 335 by jar, posted 04-16-2011 7:18 PM jar has replied

Replies to this message:
 Message 343 by jar, posted 04-16-2011 8:19 PM shadow71 has seen this message but not replied
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jar
Member (Idle past 423 days)
Posts: 34026
From: Texas!!
Joined: 04-20-2004


Message 343 of 760 (612544)
04-16-2011 8:19 PM
Reply to: Message 342 by shadow71
04-16-2011 8:16 PM


Re: Cairns and directed mutation
shadow71 writes:
jar writes:
And that is the big difference between Science and the Law; in science there is no desired outcome.
If you read the postings on this board in reply to the scientific papers I cite, there is a definite desired outcome that the current theory of evolution not be challenged.
I'm sorry but that is totally false, simply not true.
The current theory of evolution is the result of 150 years of successful challenges. That is how it has changed.
What will assure your utter failure is that you have a desired outcome.

Anyone so limited that they can only spell a word one way is severely handicapped!

This message is a reply to:
 Message 342 by shadow71, posted 04-16-2011 8:16 PM shadow71 has seen this message but not replied

shadow71
Member (Idle past 2963 days)
Posts: 706
From: Joliet, il, USA
Joined: 08-31-2010


Message 344 of 760 (612545)
04-16-2011 8:19 PM
Reply to: Message 337 by jar
04-16-2011 7:30 PM


Re: Is phenotypic plasticity magic?
jar writes:
That you tend to agree with him is why you will ultimately fail.
Stop and think.
What will a cell use for cognition?
What will a cell use for sentience?
Sorry but there is simply nothing available to think with.
The most that can be said is that there might be some response (chemical and physical) to specific stimuli.
But there is no thought, no direction, no design.
Those are the issues we may well solve in the future with unbiased scientific research.

This message is a reply to:
 Message 337 by jar, posted 04-16-2011 7:30 PM jar has replied

Replies to this message:
 Message 345 by jar, posted 04-16-2011 8:22 PM shadow71 has seen this message but not replied
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jar
Member (Idle past 423 days)
Posts: 34026
From: Texas!!
Joined: 04-20-2004


Message 345 of 760 (612546)
04-16-2011 8:22 PM
Reply to: Message 344 by shadow71
04-16-2011 8:19 PM


Re: Is phenotypic plasticity magic?
shadow71 writes:
jar writes:
That you tend to agree with him is why you will ultimately fail.
Stop and think.
What will a cell use for cognition?
What will a cell use for sentience?
Sorry but there is simply nothing available to think with.
The most that can be said is that there might be some response (chemical and physical) to specific stimuli.
But there is no thought, no direction, no design.
Those are the issues we may well solve in the future with unbiased scientific research.
Stop and think, please.
What can a cell use for cognition?
What can a cell use for sentience?

Anyone so limited that they can only spell a word one way is severely handicapped!

This message is a reply to:
 Message 344 by shadow71, posted 04-16-2011 8:19 PM shadow71 has seen this message but not replied

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