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Author Topic:   Does the Darwinian theory require modification or replacement?
NoNukes
Inactive Member


Message 166 of 760 (609978)
03-25-2011 7:42 AM
Reply to: Message 136 by shadow71
03-23-2011 3:52 PM


Re: Dr. Wright's conclusion
shadow71 writes:
The last sentence in this quote from Wrights paper on p.7 seem to be saying that these mutations that are non-random would surely be beneficial and therefor selected. I read that as saying that the mutations would be SELECTED, mutations that are non-random and beneficial.
Am I wrong?
Yes, you are wrong. I'll repeat that last sentence with emphasis added by me.
quote:
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.
Wright says that the mechanism for generating non-random mutations is beneficial. In other words, the presence of mechanisms for non-random mutations is itself a product of mutation and selection (and most likely evolution of the neo-Darwinist type). She definitely does not say that the generated mutations would be surely beneficial.
You are reading a paper describing natural processes. If something "seems to saying" otherwise, you need to dig harder to be sure. I'll admit to having understood the paragraph as you did the first time I read it.

This message is a reply to:
 Message 136 by shadow71, posted 03-23-2011 3:52 PM shadow71 has replied

Replies to this message:
 Message 169 by bluegenes, posted 03-25-2011 10:27 AM NoNukes has seen this message but not replied
 Message 176 by shadow71, posted 03-25-2011 12:34 PM NoNukes has replied

jar
Member (Idle past 393 days)
Posts: 34026
From: Texas!!
Joined: 04-20-2004


Message 167 of 760 (609982)
03-25-2011 9:37 AM
Reply to: Message 163 by NoNukes
03-24-2011 11:48 PM


Re: Cart/Horse
So Shadow is once again just blowing smoke?

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

This message is a reply to:
 Message 163 by NoNukes, posted 03-24-2011 11:48 PM NoNukes has replied

Replies to this message:
 Message 193 by NoNukes, posted 03-28-2011 9:19 AM jar has seen this message but not replied

Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


Message 168 of 760 (609987)
03-25-2011 10:13 AM
Reply to: Message 165 by Wounded King
03-25-2011 5:38 AM


Re: Cart/Horse
That is a bit unfair, he has done quite a bit of work on Mu bacteriophage transposable elements, and that also seems to be the principle basis for most of his claims.
Is there anything special about his pet transposable elements that makes them different from all the others? If there is, shouldn't they have been mentioned more often on this thread?

This message is a reply to:
 Message 165 by Wounded King, posted 03-25-2011 5:38 AM Wounded King has replied

Replies to this message:
 Message 170 by Wounded King, posted 03-25-2011 11:36 AM Dr Adequate has not replied

bluegenes
Member (Idle past 2477 days)
Posts: 3119
From: U.K.
Joined: 01-24-2007


Message 169 of 760 (609988)
03-25-2011 10:27 AM
Reply to: Message 166 by NoNukes
03-25-2011 7:42 AM


Re: Dr. Wright's conclusion
I can't be the only one on this thread getting a deja vu impression from the Wright paper. Message 25
Yes, she concludes that the mechanism would have faced positive selection.

This message is a reply to:
 Message 166 by NoNukes, posted 03-25-2011 7:42 AM NoNukes has seen this message but not replied

Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 170 of 760 (609998)
03-25-2011 11:36 AM
Reply to: Message 168 by Dr Adequate
03-25-2011 10:13 AM


Re: Cart/Horse
Mainly that it is one with a long history, having been characterised in the early 70s. There are also engineered strains which have a Lac operon, which makes for a very useful experimental system for identifying when insertions have occurred producing fusion proteins.
If there is, shouldn't they have been mentioned more often on this thread?
As to that, you must have noticed that whenever IDists bring up these arguments they never care about the actual mechanisms involved, only that they can quote someone saying that adaptive mutations are non-random or directed.
TTFN,
WK

This message is a reply to:
 Message 168 by Dr Adequate, posted 03-25-2011 10:13 AM Dr Adequate has not replied

shadow71
Member (Idle past 2933 days)
Posts: 706
From: Joliet, il, USA
Joined: 08-31-2010


Message 171 of 760 (609999)
03-25-2011 11:42 AM
Reply to: Message 163 by NoNukes
03-24-2011 11:48 PM


Re: Cart/Horse
NoNukes writes:
In a court of law, attorney arguments and interpretation of data are not evidence, and the trier of fact is not to give anything the attorney says evidentiary weight.
Also in a court of law, would not presenting an expert via his papers violate the Confrontation Clause?
You are right that the attorneys arguments are not evidence, but the attorney comments 0n and interprets the evidence, i.e. the data in this case and Shapiro's testimony and opinions, and the jury then makes a decision on the isssue.
In re the Expert. The evidence would be presented by the Expert under direct examination by Plaintiff's counsel and then cross examination by defendants's counsel
The data would be admitted by both the experts testimony and the admission of the papers into evidence.The jury, in some cases, may even take the actual papers with them to the jury consulation room where they reach their verdict.
There is no hearsay problem under that procedure.

This message is a reply to:
 Message 163 by NoNukes, posted 03-24-2011 11:48 PM NoNukes has replied

Replies to this message:
 Message 179 by NoNukes, posted 03-25-2011 3:44 PM shadow71 has replied
 Message 204 by Taq, posted 03-28-2011 7:06 PM shadow71 has replied

shadow71
Member (Idle past 2933 days)
Posts: 706
From: Joliet, il, USA
Joined: 08-31-2010


Message 172 of 760 (610002)
03-25-2011 11:53 AM
Reply to: Message 160 by Taq
03-24-2011 4:21 PM


Re: Just blowing smoke
Wright writes:
This minireview suggests that sensitive, directed feedback mechanisms initiated by different kinds of stress might facilitate and accelerate the adaptation of organisms to new environments.
taq writes;
Nowhere in that quote can you find the word "fitness". She mentions random mutations, but she does not mention how they are random. Like we have said many times, mutations are not random with respect to time and sequence, but they are random with respect to fitness. It's not as if skydivers acquire mutations that produce wings in their children.
I interpret the above part of the quote to mean the non-random mutations she discussed provided a benefical adapation of the organism to its new enviroment.

This message is a reply to:
 Message 160 by Taq, posted 03-24-2011 4:21 PM Taq has replied

Replies to this message:
 Message 205 by Taq, posted 03-28-2011 7:47 PM shadow71 has replied

shadow71
Member (Idle past 2933 days)
Posts: 706
From: Joliet, il, USA
Joined: 08-31-2010


Message 173 of 760 (610003)
03-25-2011 11:56 AM
Reply to: Message 159 by Taq
03-24-2011 4:18 PM


Re: Cart/Horse
taq writes:
In a court of law you also have to supply this evidence to the opposing side so that they can examine the evidence themselves. For example, any DNA evidence submitted by a procecutor must also be available to the defense so that they can do their own sequencing if they see fit. You need to supply the data.
Please see my message 171 that explains how the evidene is presented at trial.

This message is a reply to:
 Message 159 by Taq, posted 03-24-2011 4:18 PM Taq has replied

Replies to this message:
 Message 178 by Taq, posted 03-25-2011 12:48 PM shadow71 has replied

shadow71
Member (Idle past 2933 days)
Posts: 706
From: Joliet, il, USA
Joined: 08-31-2010


Message 174 of 760 (610004)
03-25-2011 12:03 PM
Reply to: Message 164 by Dr Adequate
03-25-2011 12:04 AM


Re: Cart/Horse
Wounded King writes:
That is a bit unfair, he has done quite a bit of work on Mu bacteriophage transposable elements, and that also seems to be the principle basis for most of his claims.
I agree with Wounded King.
And I haven't come across any papers that have challenged Shapiro's papers, findings or opinions.

This message is a reply to:
 Message 164 by Dr Adequate, posted 03-25-2011 12:04 AM Dr Adequate has not replied

Replies to this message:
 Message 175 by Wounded King, posted 03-25-2011 12:28 PM shadow71 has seen this message but not replied

Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 175 of 760 (610005)
03-25-2011 12:28 PM
Reply to: Message 174 by shadow71
03-25-2011 12:03 PM


Re: Cart/Horse
And I haven't come across any papers that have challenged Shapiro's papers, findings or opinions.
How have you looked?
I'm not being facetious but it is not an easy thing to identify papers with differing opinions in the literature. Even in review papers, which one might hope would be comprehensive, there is often a heavy bias towards the authors chosen interpretation of the data which may include not mentioning data they consider inconsequential.
The fact that you didn't find anyone specifically challenging his opinions can just as easily be interpreted as the result of his views being marginal rather than correct.
TTFN,
WK

This message is a reply to:
 Message 174 by shadow71, posted 03-25-2011 12:03 PM shadow71 has seen this message but not replied

shadow71
Member (Idle past 2933 days)
Posts: 706
From: Joliet, il, USA
Joined: 08-31-2010


Message 176 of 760 (610006)
03-25-2011 12:34 PM
Reply to: Message 166 by NoNukes
03-25-2011 7:42 AM


Re: Dr. Wright's conclusion
Dr. Wright writes--------------------------------------------------------------------------------
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.
NoNukes writes:
Wright says that the mechanism for generating non-random mutations is beneficial. In other words, the presence of mechanisms for non-random mutations is itself a product of mutation and selection (and most likely evolution of the neo-Darwinist type). She definitely does not say that the generated mutations would be surely beneficial.
You are reading a paper describing natural processes. If something "seems to saying" otherwise, you need to dig harder to be sure. I'll admit to having understood the paragraph as you did the first time I read it.
I interpret that to mean that a mechanism is limiting the mutation rates to non-random mutations to certain genes under stress would be beneficial to those genes and selected for evolution.
That is not a process put forth by the Modern Synthesis and goes beyond the modern synthesis.
Here is an interesting quote from Dr. Wrights paper page 4.
Dr. Wright writes:
It is noteworthy that the experiments described above on the effects of artificially induced transcription on mutation rates in growing cells are all examples of specifically directed mutations.
However, none of the researchers come to that conclusion or challenge the assumptions and implications inherent in the experiments of Luria and Delbruck (63), which reinforce neo-Darwinism.
This situation may be due to the dominance of current dogma and to the assumption that mechanisms operative during growth cannot also be critical during evolution under conditions of environmental stress.
In fact, the limited evidence now available suggests that only growing cells, or cells in transition between growth and stationary phase, have the metabolic potential required for specific, transcription-induced mutations in response to environmental challenge....
She seems to be challenging the experiments of Luria and Delbruck in re random mutations that Taq previously cited.
She is also saying that dominance of current is perhaps is having a negtative effect on scientists who may put forth critical or different views than the current dogma holds.
It surely seems some scientists are in fact challenging the modern synthesis.

This message is a reply to:
 Message 166 by NoNukes, posted 03-25-2011 7:42 AM NoNukes has replied

Replies to this message:
 Message 177 by Taq, posted 03-25-2011 12:41 PM shadow71 has replied
 Message 180 by NoNukes, posted 03-25-2011 3:59 PM shadow71 has replied
 Message 181 by Dr Adequate, posted 03-25-2011 4:51 PM shadow71 has replied

Taq
Member
Posts: 9970
Joined: 03-06-2009
Member Rating: 5.6


Message 177 of 760 (610007)
03-25-2011 12:41 PM
Reply to: Message 176 by shadow71
03-25-2011 12:34 PM


Re: Dr. Wright's conclusion
I interpret that to mean that a mechanism is limiting the mutation rates to non-random mutations to certain genes under stress would be beneficial to those genes and selected for evolution.
Your interpretation inserts "non-random". Nowhere in the quote does it speak of non-random mutations. You are not interpretting. You are projecting your own biases into the quote.
She seems to be challenging the experiments of Luria and Delbruck in re random mutations that Taq previously cited.
What data does she cite that challenges the Luria and Delbruck's conclusions?
It surely seems some scientists are in fact challenging the modern synthesis.
In order for them to mount a challenge they need data to support their challenge. What is that data?

This message is a reply to:
 Message 176 by shadow71, posted 03-25-2011 12:34 PM shadow71 has replied

Replies to this message:
 Message 184 by shadow71, posted 03-25-2011 7:57 PM Taq has not replied

Taq
Member
Posts: 9970
Joined: 03-06-2009
Member Rating: 5.6


Message 178 of 760 (610008)
03-25-2011 12:48 PM
Reply to: Message 173 by shadow71
03-25-2011 11:56 AM


Re: Cart/Horse
Please see my message 171 that explains how the evidene is presented at trial.
I already read it. It is wrong. You don't get to present expert testimony even as a written affidavit. Even worse, you don't get to present your interpretation of the expert testimony as evidence. Expert witnesses have to present the data that supports their conclusion, and they have to be available for cross. That's how it works. That is how it worked in the famous Dover ID trial where ID advocates were not allowed to submit written affidavits. They had to be available for cross. You should know that.
Of the questions related directly to fitness and random mutations, Shapiro ducked them. When directly asked if mutations were random with respect to fitness HE CHANGED THE QUESTION. He changed it from "random with respect to fitness" to "probability of biological utility". These are NOT THE SAME THING. This should be a very big clue to someone not blinded by their own biases.
The fact of the matter is that the mutational mechanisms described by Shapiro produce beneficial, neutral, and detrimental phenotypes. These processes are blind to what will benefit or harm the organism. I have already shown that one of the mechanisms cited by Shapiro (the E. coli SOS response) produces mutations that are random with respect to fitness as defined by both the fluctuation and plate replica methods. For example, the SOS response increases the number of antibiotic mutants EVEN IN THE ABSENCE OF ANTIBIOTICS.
Edited by Taq, : No reason given.

This message is a reply to:
 Message 173 by shadow71, posted 03-25-2011 11:56 AM shadow71 has replied

Replies to this message:
 Message 182 by shadow71, posted 03-25-2011 5:00 PM Taq has replied

NoNukes
Inactive Member


Message 179 of 760 (610016)
03-25-2011 3:44 PM
Reply to: Message 171 by shadow71
03-25-2011 11:42 AM


Re: Cart/Horse
shadow71 writes:
The evidence would be presented by the Expert under direct examination by Plaintiff's counsel and then cross examination by defendants's counsel
The data would be admitted by both the experts testimony and the admission of the papers into evidence.The jury, in some cases, may even take the actual papers with them to the jury consulation room where they reach their verdict.
There is no hearsay problem under that procedure.
That's right. But presenting the evidence without the expert, as you are doing here, would be improper in court.
My question is, why are you trying to justify yourself by appealing to courtroom procedures when you aren't even following them?

This message is a reply to:
 Message 171 by shadow71, posted 03-25-2011 11:42 AM shadow71 has replied

Replies to this message:
 Message 224 by shadow71, posted 04-01-2011 7:08 PM NoNukes has replied

NoNukes
Inactive Member


Message 180 of 760 (610017)
03-25-2011 3:59 PM
Reply to: Message 176 by shadow71
03-25-2011 12:34 PM


Re: Dr. Wright's conclusion
shadow71 writes:
Dr. Wright writes--------------------------------------------------------------------------------
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.
shadow71 writes:
I interpret that to mean that a mechanism is limiting the mutation rates to non-random mutations to certain genes under stress would be beneficial to those genes and selected for evolution.
I know how you interpret it. But your interpretation is facially incorrect. Wright says, quite unambigously, that it is the mechanism for generating the non-random mutations that is clearly beneficial. She also says that most mutations are deleterious and does not disclaim that characterization for the mutations produced by her method.
Wright's point is instead that the deleterious effect of mutations is limited to specific portions of the genome. This is also stated unambigously in the same paragraph.
shadow71 writes:
That is not a process put forth by the Modern Synthesis and goes beyond the modern synthesis.
So what? The point of the paper is to propose an alternate naturalistic process and Wright clearly does propose exactly that.

This message is a reply to:
 Message 176 by shadow71, posted 03-25-2011 12:34 PM shadow71 has replied

Replies to this message:
 Message 225 by shadow71, posted 04-01-2011 7:37 PM NoNukes has replied

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