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Author Topic:   Does the Darwinian theory require modification or replacement?
AZPaul3
Member
Posts: 8513
From: Phoenix
Joined: 11-06-2006
Member Rating: 5.3


Message 266 of 760 (611880)
04-11-2011 8:45 PM
Reply to: Message 265 by shadow71
04-11-2011 8:19 PM


Re: LURIA & DELBRUCK random mutation experiment
it this scientist is correct, we may have no proof of random mutations.
shadow, do you know what a "null hypothesis" is in science?
BTW, did you spend the $45 to actually read the paper? I didn't have to.

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 Message 265 by shadow71, posted 04-11-2011 8:19 PM shadow71 has replied

Replies to this message:
 Message 279 by shadow71, posted 04-13-2011 11:25 AM AZPaul3 has replied

AZPaul3
Member
Posts: 8513
From: Phoenix
Joined: 11-06-2006
Member Rating: 5.3


(1)
Message 296 of 760 (612204)
04-13-2011 7:20 PM
Reply to: Message 279 by shadow71
04-13-2011 11:25 AM


Re: LURIA & DELBRUCK random mutation experiment
By this definition would you agree that the hypothesis of random mutation is neither true or false. ie. not proven.
Good God, no, I would not agree to such a stupid proposition especially in light of the way you see "true", "false" and "proven."
If I were speaking to another scientist I wouldn't have to answer since such a silly question would never be broached.
You have been here for a few months now. Have you not yet learned that Science never "proves" anything?
Have you not yet learned the reason for this philosophy?
In this case the data does not contradict the null hypothesis. This is but another point of evidence that the hypothesis holds. It does not leave you an opening for any rectally ejected alternative that comes along.
Now make the null hypothesis "directed mutations are the source of genotypic variation" and re-test. All the data contradicts this and thus this null hypotesis is rejected.
"Hypothesis testing" is but one weapon in the science arsenal. There also are the preponderance of the evidence and the self-consistant model able to make testable verifiable predictions. All of which we have for the role of random mutations in genotypic variation. None of which lend any support or efficacy to directed mutations (directed by what, by whom, how) as the source of genotypic variation.
You should know better by now, shadow.

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AZPaul3
Member
Posts: 8513
From: Phoenix
Joined: 11-06-2006
Member Rating: 5.3


Message 311 of 760 (612313)
04-14-2011 5:26 PM
Reply to: Message 302 by shadow71
04-14-2011 12:20 PM


Re: Cairns and directed mutation
Reference my Message 296
shadow - Message 299
A null hypothesis is not a proven hypothesis.
shadow - Message 302
he said random mutations is a null hypotheisis, ie it may be the default hypothesis, but it is not proven.
I note you acknowledged my message 296. Then you continue with this same "Null hypothesis = not proven" BS.
I must assume one of the following:
1. You acknowledged my message without reading it.
2. You read my message but did not comprehend its content.
3. You read and comprehended but choose to ignore its content.
Which is it?
I think this community deserves an answer so we know what kind of person we're dealing with here.
Edited by AZPaul3, : mechanics. Mom whould really be PO'd if she saw that.

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Replies to this message:
 Message 313 by shadow71, posted 04-15-2011 4:37 PM AZPaul3 has replied

AZPaul3
Member
Posts: 8513
From: Phoenix
Joined: 11-06-2006
Member Rating: 5.3


Message 319 of 760 (612445)
04-15-2011 5:41 PM
Reply to: Message 313 by shadow71
04-15-2011 4:37 PM


Re: Cairns and directed mutation
When you use language such as "rectally ejected" I just refuse to reply to that type of nonsense.
Fair enough.
Now, do you understand why calling something the "null hypothesis" does not call the hypothesis into doubt?
That hypothesis testing does not, never was meant to, "prove" a hypothesis but is a tool to eliminate false ones?
That in designing an experiment to test for "directed" mutations it is useful to assign "random mutations are the cause of genotypic variation" as the null hypothesis to which you compare the data?
Do you comprehend any of this at all?

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Replies to this message:
 Message 322 by shadow71, posted 04-15-2011 7:55 PM AZPaul3 has replied

AZPaul3
Member
Posts: 8513
From: Phoenix
Joined: 11-06-2006
Member Rating: 5.3


(2)
Message 328 of 760 (612464)
04-15-2011 9:47 PM
Reply to: Message 322 by shadow71
04-15-2011 7:55 PM


Sped-up is "Directed".
What is your position. Is random mutation a fact? or is it a hypothesis that may in the future possibly be falsified?
Yes, random mutation is the major vector of genotypic variation. This is fact.
Where you may be confusing things is that biologists, like Dr. Wright, have identified some possible mechanisms that cause an organism to "derepress" (lessen the mechanisms that repress or fix mutations) thus allowing hypermutation to occur.
There may even be derepression mechanisms that have been selected and preserved through evolution that target specific suites of genes (metabolism or respiration) that get activated by environmental conditions (in times of food shortage or atmosphere change). And there may be others yet unidentified influencing other capabilities.
But the point is that the individual mutations themselves are random. There just happens to be whole lot of them going on in a very short period of time.
These derepression mechanisms (if they actually exist) may have been preserved by natural selection because they often hit on novel sets of (random) mutations that allow adaption to the new environmental conditions in shorter order then the natural rate of mutation could achieve.
The language used within these papers is intended for the scientifically astute and (all too) often use word choices (like "directed") that are open to misunderstanding. Dr. Wright's use of the word is, I contend, used to convey the idea that the environment "directs" (affects) the mechanisms that speed up or slow down the mutation repression mechanisms.
She did not intend to imply that any individual mutation was directly intended as known or planned before hand.
Edited by AZPaul3, : No reason given.

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 Message 330 by Wounded King, posted 04-16-2011 4:03 AM AZPaul3 has replied

AZPaul3
Member
Posts: 8513
From: Phoenix
Joined: 11-06-2006
Member Rating: 5.3


(1)
Message 329 of 760 (612476)
04-16-2011 2:07 AM
Reply to: Message 322 by shadow71
04-15-2011 7:55 PM


Re: Cairns and directed mutation
Sorry to have cut that first response short. Other lives sometimes interfere.
Now let's take this whole shebang and put it into some perspective.
Cairns and company were talking the same kind of "directed" mutation Wright was using. His experiments sought to show some "derepress" mechanisms in bacteria. Meaning a mechanism that would shut down the normal processes used to fix the randomly generated mutations in the DNA. He was not looking for some intelligent hand directing specific mutations with foreknowledge of a specified outcome. He was just looking for the mechanisms that would allow copious mutations to remain thus increasing the chances that some beneficial random mutations would come along.
As noted, other labs, duplicating his work, found some anomalies and posited other reasons for the data.
In comes Zheng and takes the more philosophical approach. Cairn's, and other biologist's, data on "directed mutations" appeared to support the contention that some mechanism of "directed mutation" (again meaning allowing large numbers of random mutations to remain unfixed) existed. What Zheng showed through the use of the "null hypothesis" tool was this:
If the null hypothesis of these studies were "random mutation" instead of "directed mutation" (keeping in mind the scientific 'directed' here) then the data generated by those studies did not conflict with the "random" null hypothesis either. In other words the studies showed absolutely nothing!
You misunderstood Zheng's use of the null hypothesis. You misunderstood Cairn's and Wright's use of the word "directed" as applied to their studies. I suspect (though I cannot be certain since I do not know Shapiro's work) you misunderstand Shapiro and misunderstand his responses to your e-mails.
Nowhere in any of this is anyone suggesting that "directed mutations" are intelligently directed with foreknowledge of a specified outcome.
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.
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.

This message is a reply to:
 Message 322 by shadow71, posted 04-15-2011 7:55 PM shadow71 has replied

Replies to this message:
 Message 338 by shadow71, posted 04-16-2011 7:48 PM AZPaul3 has replied

AZPaul3
Member
Posts: 8513
From: Phoenix
Joined: 11-06-2006
Member Rating: 5.3


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.

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AZPaul3
Member
Posts: 8513
From: Phoenix
Joined: 11-06-2006
Member Rating: 5.3


Message 349 of 760 (612563)
04-17-2011 2:24 AM
Reply to: Message 338 by shadow71
04-16-2011 7:48 PM


Re: Cairns and directed mutation
I am not a "woo believer" whatever that means.
.
.
.
(snip)
.
.
.
I am a person who believes in creation in some manner by a supernatural being ...
That is a very good description of a woo believer.
You believe in "natual creation", I do not.
I do not believe. I know only what the present facts and observations tell us and the direction they point.
Only imagination and blind desire can manufacture from nothing, in the face of all the contrary evidence, the kind of universe you wish we lived it. It is a delusion that just will not yield up its proof. So at every turn you misunderstand, you misinterpret and you mis-frame the words and works of others attempting to justify your personal desires and confirm your delusion.
You spend all your time in your fantasy. You deny the true beauty of a natural universe that made stars by purely natural means, which made atoms by purely natural means, that made planets and molecules and orchids and thunderstorms and puppies all on its own, not by accident but by nature, without any overseer or plan or magic.
That is the real miracle of this universe and tragically, since you will pass this way but once, you are missing it.
Edited by AZPaul3, : No reason given.

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 Message 338 by shadow71, posted 04-16-2011 7:48 PM shadow71 has replied

Replies to this message:
 Message 357 by shadow71, posted 04-17-2011 2:56 PM AZPaul3 has replied

AZPaul3
Member
Posts: 8513
From: Phoenix
Joined: 11-06-2006
Member Rating: 5.3


Message 388 of 760 (612695)
04-17-2011 6:08 PM
Reply to: Message 357 by shadow71
04-17-2011 2:56 PM


Imperfect Knowledge
Edited by Adminnemooseus, : Hide and off-topic banner.

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AZPaul3
Member
Posts: 8513
From: Phoenix
Joined: 11-06-2006
Member Rating: 5.3


Message 394 of 760 (612851)
04-19-2011 1:19 PM
Reply to: Message 392 by shadow71
04-19-2011 11:42 AM


Shapiro Answers
"Selection is unavoidable, but in my view it is a purifying rather than a creative process."
Selection has always been a purifying process. That is its function; to weed out (purify) the most egregious genomes from the population.
I also note that Shapiro's response clearly distances himself from your "creative" bent. I suspect the tone of your communication with him let him know you are a creationist/IDist and he is running away as fast as he can.
"The genome sequence databases are full of examples, and I cite many of them in my papers."
And we can cite a number of vectors of genetic change here, like viral insertion, gene flow, etc. to which I suspect Shapiro refers. No one here ever said random mutation is the only vector of change in the genome.
"The neo-Darwinian Modern Synthesis could not account for the evolution of antibiotic resistance in the latter 20th Century. It also does not explain much in the genome sequence record"
How is he defining "neo-Darwinian Modern Synthesis"? If he is referring to the 1930's version, which is the usual definition of that term, then he is correct. A whole lot of evolutionary and genetic knowledge has accumulated into the Theory of Evolution over the last 70-80 years.
I think Shapiro saw you coming. He probably gets a lot of this from creationists/IDists and I suspect he is being very careful in avoiding direct explanatory answers. Why, I could not say.
But here, again, shadow, you see the words and misinterpret the meanings to fit your preconceptions. "Purifying" vs "creative" selection should have been a big clue that Shapiro was not saying what you had hoped he would have said.

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AZPaul3
Member
Posts: 8513
From: Phoenix
Joined: 11-06-2006
Member Rating: 5.3


Message 396 of 760 (612867)
04-19-2011 3:56 PM
Reply to: Message 393 by shadow71
04-19-2011 1:12 PM


Ho, Ho, Ho
OK, Mae-Wan Ho I do know. Her warnings on the dangers of DNA tinkering with our present lack of knowledge are to be given much weight. A lot of respect for that lady.
On epigenetics her data was a bit sketchy and still needs a lot of verification and refinement, and she and her fellow geneticists may be on to something. But it is not "intelligently directed evolution" as I hear you mean. It is Lamarckian with some modern epigenetic twists.
Epigenetics is well known in evolution through cell differentiation, developmental plasticity, homoplasy, all that Evo-Devo stuff, so nothing new or spooky there.
Her view that macro evolutionary change is epigenetic-driven with some yet unknown mechanism that will encode this change into the genome needs a considerable amount of work and evidence and may yet be shown deficient. If not, then just like Punctuated Equilibrium, it will be appended to the body of the Theory of Evolution, not replace it.
the answer that "micro evolution" may not direct mutations, but rather keeps organisms as they are and "macro evolution" directs the changes per Shapiro and Ho's theories.
Not at all what either of these folks said. Re-read and re-think, shadow.
The OP in this thread "Does the Darwinian theory require modification or replacement?"
When there is a considerable body of evidence that some specific mechanisms impact the Theory of Evolution then they will be incorporated. You are looking, I think, to totally overturn the Theory of Evolution. There is nothing on the horizon that looks promising in that regard. You certainly haven't found it in here anywhere.
Edited by AZPaul3, : spln errer

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 Message 393 by shadow71, posted 04-19-2011 1:12 PM shadow71 has replied

Replies to this message:
 Message 398 by molbiogirl, posted 04-19-2011 4:15 PM AZPaul3 has replied
 Message 404 by shadow71, posted 04-19-2011 7:31 PM AZPaul3 has replied

AZPaul3
Member
Posts: 8513
From: Phoenix
Joined: 11-06-2006
Member Rating: 5.3


Message 399 of 760 (612870)
04-19-2011 4:36 PM
Reply to: Message 398 by molbiogirl
04-19-2011 4:15 PM


Re: Ho, Ho, Ho
Ho is getting signals from outer space!
... er ... Ho, ho, ho. That's good.
No, Mae-Wan is not suggesting signals from space. "Quantum Jazz" is her analogy for the complex inter-relationships among all the processes, sub-atomic, molecular, intra-cellular, inter-cellular and on thru to environment (which includes th Universe) that she sees as shaping all life and evolution. A "Life Symphony" if you will. She's a jazz fan.
Though she does have a bit of the "woo" side to some of her more aggressive holistic views, I will grant you that.
I can respect the lady's science and intellect, if not all of her views. She is one smart cookie if a little "sideways" sometimes.
Edited by AZPaul3, : clarification

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 Message 398 by molbiogirl, posted 04-19-2011 4:15 PM molbiogirl has replied

Replies to this message:
 Message 400 by molbiogirl, posted 04-19-2011 5:28 PM AZPaul3 has replied

AZPaul3
Member
Posts: 8513
From: Phoenix
Joined: 11-06-2006
Member Rating: 5.3


Message 401 of 760 (612877)
04-19-2011 5:48 PM
Reply to: Message 400 by molbiogirl
04-19-2011 5:28 PM


Re: Ho, Ho, Ho
I looked, btw, and she hasn't published anything on directed evolution or directed mutation.
Nor will she. She's retired now and has that other gig dissing Genetic Modified anything. She makes a lot of good points there, but seems to get politically strident, which, IMHO, detracts from her base message which in essence is ... we have to be extra careful here because we do not yet understand the full relationships we are screwing with.
But this is off topic and I've already crossed the Moose once this week. Bye.
Edited by AZPaul3, : No reason given.
Edited by AZPaul3, : proofread then submit. proofread then submit. proofread then submit.

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AZPaul3
Member
Posts: 8513
From: Phoenix
Joined: 11-06-2006
Member Rating: 5.3


Message 619 of 760 (621433)
06-25-2011 10:15 PM
Reply to: Message 616 by shadow71
06-25-2011 4:21 PM


Natural Engineering
Shapiro's natural genetic engineering is based upon a process that cannot be completely random.
Shapiro's natural genetic engineering is based upon a process that relies on escalating random mutation at the genome based upon a biochemical cascade from an outside stimulus to a specific locus in the genome developed over billions of years of intra-cellular trial-and-error (read mutation and selection).
Shapiro's natural genetic engineering is based upon a process that you seem hell-bent to misrepresent.
If Shapiro and Wright and Pigliucci are right then these unplanned natural mechanisms will become additional vectors of hereditary change within the Theory of Evolution. Descent with modification, random mutation and natural selection, will not have been overturned.
Edited by AZPaul3, : No reason given.
Edited by AZPaul3, : No reason given.

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AZPaul3
Member
Posts: 8513
From: Phoenix
Joined: 11-06-2006
Member Rating: 5.3


Message 620 of 760 (621436)
06-25-2011 10:40 PM
Reply to: Message 404 by shadow71
04-19-2011 7:31 PM


Re: Ho, Ho, Ho
while "macro" in a non Darwinian sense determines the evolution of organisms for major changes and those changes are not random and natural selection, but mostly enviromentally driven.
Then you mis-understand their positions and the mechanisms they propose.
Try again.

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