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Author Topic:   Does the Darwinian theory require modification or replacement?
molbiogirl
Member (Idle past 2669 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 294 of 760 (612185)
04-13-2011 5:54 PM
Reply to: Message 265 by shadow71
04-11-2011 8:19 PM


Cairns and directed mutation
I know Cairns and others have challenged the Luria & Delbuck experiment...
First, Cairns et al refuted directed mutation.
Fairly early on in our studies, Cairns and I ELIMINATED the hypothesis that mutations were directed toward a useful goal.
The second piece of evidence AGAINST directed mutation was obtained by putting a second revertible allele, a +1 frameshift in the tetA gene, close to the Lac− allele in FC40.
Emphasis added.
Source.
Second, you misunderstood Zheng. Just admit it.
He said the evidence for directed mutation is weak.

This message is a reply to:
 Message 265 by shadow71, posted 04-11-2011 8:19 PM shadow71 has replied

Replies to this message:
 Message 302 by shadow71, posted 04-14-2011 12:20 PM molbiogirl has replied

molbiogirl
Member (Idle past 2669 days)
Posts: 1909
From: MO
Joined: 06-06-2007


(1)
Message 310 of 760 (612309)
04-14-2011 5:13 PM
Reply to: Message 302 by shadow71
04-14-2011 12:20 PM


Re: Cairns and directed mutation
I never claimed Cairns claimed directed mutation...
Cairns' "challenge" to Luria & Delbeck WAS directed mutation.
These are the unexpected findings that led John Cairns and colleagues (10) to suggest that "bacteria, in stationary phase, have some way of producing (or selectively retaining) only the most appropriate mutations."
10. Cairns, J., J. Overbaugh, and S. Miller. 1988. The origin of
mutants. Nature (London) 335:142-145.
Source.
The title of his paper that followed his 1988 Origins of Mutants in 1992 is THE MECHANISMS OF DIRECTED MUTATION.
Unfortunately for Cairns, a bunch of labs jumped on his directed mutation idea and tried to replicate it. And guess what?
The hypothesis did not fare well, however, for a number of reasons. First, several groups quickly proposed alternative explanations that could account for Cairns' data without requiring directed mutation [5]. Second, follow-up experiments that included additional controls, as well as more careful accounting of population dynamics, demonstrated that some studies supporting directed mutation were fatally flawed [6 and 7]. Third, no one could demonstrate a molecular mechanism for any case of directed mutation, despite numerous proposals, and some proposed mechanisms were tested and found wanting [7 and 8].
Source.
And then guess what happened?
Cairns had to walk back his directed mutation bullshit.
Hence the quote I provided earlier.
The only reason I mentioned Zheng, is that he said random mutations is a null hypotheisis, ie it may be the default hypothesis, but it is not proven.
You continue to misunderstand null hypothesis.
Would legalese help?
wiki writes:
In most legal systems, the presumption that a defendant is innocent ("until proven guilty") can be interpreted as saying that his or her innocence is the null hypothesis.
Would you say that when the null hypothesis is confirmed by a jury it has been proven?
Look at it this way.
The goal is to DISPROVE the null hypothesis (that the accused is innocent).
If you do not DISPROVE the null hypothesis (convince the jury that the accused is guilty) then the null hypothesis (that the accused is innocent) is PROVEN.
Zheng did not DISPROVE the null hypothesis; therefore, random mutation is PROVEN.
Edited by molbiogirl, : No reason given.
Edited by molbiogirl, : No reason given.

This message is a reply to:
 Message 302 by shadow71, posted 04-14-2011 12:20 PM shadow71 has replied

Replies to this message:
 Message 317 by shadow71, posted 04-15-2011 5:12 PM molbiogirl has replied

molbiogirl
Member (Idle past 2669 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 312 of 760 (612316)
04-14-2011 5:43 PM
Reply to: Message 302 by shadow71
04-14-2011 12:20 PM


Zheng and the null hypothesis
One more thought on your difficulty understanding the null hypothesis.
Would it help if Zheng used the word "proven"? Cause he did.
Thus, a mutation mediated by a newfound mechanism does not automatically qualify as a directed mutation, for the existence of an undocumented mutational mechanism itself is not a deviation from the random mutation hypothesis. However, if this mutation can be PROVEN to occur only under some specific environmental conditions that favor the survival of the resulting mutants, then that mutation can be a possible example of directed mutation.
Emphasis added.
For instance, LENSKI et al. 1989 cited differential growth rates as a cause, which has been mathematically PROVEN (PAKES 1993 Down; ZHENG 2002).
Source.
FYI, Lenski was challenging Cairns' directed mutation bullshit.
And it was mathematically proven.

This message is a reply to:
 Message 302 by shadow71, posted 04-14-2011 12:20 PM shadow71 has seen this message but not replied

molbiogirl
Member (Idle past 2669 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 320 of 760 (612447)
04-15-2011 5:49 PM
Reply to: Message 317 by shadow71
04-15-2011 5:12 PM


Re: Cairns and directed mutation
Are you referring to random mutation as "proven" in re "directed mutations" or it is proven, end of story?
Given that you've chosen to ignore nearly my entire post, I will restate my objections.
Here is your original claim.
I know Cairns and others have challenged the Luria & Delbuck experiment, but it this scientist is correct, we may have no proof of random mutations.
When I pointed out that Cairns backpedalled his "challenge" as fast as he could, you resorted to backpedalling too.
I never claimed Cairns claimed directed mutation, I merely pointed out his paper casts doubts on the Luria & Delbeck expertiment allegedly showing random mutations.
What, praytell, was Cairns' "challenge" to random mutation if not directed mutation?
When you first mentioned Zheng, you said:
I have just been reading some papers on "directed mutations" and one very qualified researcher QI Zheng states as follows: This paper calls attention to an overlooked logical difficulty that has impeded the directed mutation debate for over half a century. It further suggests that the random mutation hypothesis be regarded at present as a null hypothesis in evolutionary biology.
When it was pointed out that you misunderstood "null hypothesis", you repeatedly stated:
That random mutation for fitness is not a proven hypothesis. That directed and adapative mutations do occur.
He [Zheng] is saying, in re the debated about, random, directed, adapative mutations, that there is no proof that random mutation is true.
Do you, or do you not understand, that if the null hypothesis is NOT DISPROVEN the null hypothesis is considered, for all intents and purposes, PROVEN?
Zheng is a mathematician. In the paper I presume you read, Mathematical Issues Arising From the Directed Mutation Controversy, Zheng set out to untangle the math used by Cairns.
Zheng writes:
Interpretation of some of the evidence depends on mathematical reasoning, which can be subtler than it appears at first sight. This article attempts to clarify some of the mathematical issues arising from the directed mutation controversy, thereby offering alternative interpretations of some of the evidence.
Zheng is offering ALTERNATIVE explanations to directed mutation. NOT supporting directed mutation.
Here's the bottom line.
You misunderstood Zheng as supporting directed mutation. He didn't.
You picked a REALLY bad paper by Cairns to support your claim of directed mutation. Even Cairns doesn't support directed mutation these days (after getting his ass handed to him by other labs).
Can you cite any papers that support directed mutation?

This message is a reply to:
 Message 317 by shadow71, posted 04-15-2011 5:12 PM shadow71 has replied

Replies to this message:
 Message 321 by shadow71, posted 04-15-2011 7:47 PM molbiogirl has replied

molbiogirl
Member (Idle past 2669 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

molbiogirl
Member (Idle past 2669 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 351 of 760 (612580)
04-17-2011 10:59 AM
Reply to: Message 340 by shadow71
04-16-2011 8:09 PM


Re: Wright and directed mutation
Wrights paper says it is possible "MANY MUTATIONS ARE TO SOME EXTENT DIRECTED..."
She's talking about "microorganisms, from phage to fungi".
I was quoting her passage on "higher organisms".
See? In the passage you quoted?
Completely random, undirected mutation is responsible for the evolution of higher organisms.
You do understand that there are 2 million species on this planet, only 9000 of which are microorganisms, right?
Wright claims that for 99.5% of the extant species on earth, mutation is completely random and undirected.
Care to dispute Dr. Wright's findings?
Cite a paper that supports directed mutation in something other than a microorganism.
I see Wounded King is handling your continued misunderstanding of "directed" but I would like to repeat:
Wright writes:
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...
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?
Do you, or do you not, understand what is being directed? THE LOCATION ONLY.
Don't ignore my question this time.
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.
Since, as you insist, there's an abundance of creo research, let's see some.
In fact, why don't you dig up a creo paper on directed mutation in something other than a microorganism?
Edited by molbiogirl, : No reason given.
Edited by molbiogirl, : No reason given.

This message is a reply to:
 Message 340 by shadow71, posted 04-16-2011 8:09 PM shadow71 has replied

Replies to this message:
 Message 352 by OliverChant, posted 04-17-2011 2:05 PM molbiogirl has not replied
 Message 364 by shadow71, posted 04-17-2011 3:16 PM molbiogirl has replied

molbiogirl
Member (Idle past 2669 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 390 of 760 (612704)
04-17-2011 7:08 PM
Reply to: Message 364 by shadow71
04-17-2011 3:16 PM


Re: Wright and directed mutation
Is the above statement;" Completely random..." a quote from Wright?
Yes.
Now. Since Wright contends that 99.5% of all mutations are random and undirected, let's see you cite a paper that supports directed mutation in something other than a microorganism.
And, once again, don't ignore the question. Just provide a cite.
I understand that the beneficial mutations are being directed to a locus only, along with deleterious mutations, and purfyilng selection eliminates the deleterious mutations, thereby allowing only the beneficial mutations to proceded.
Here's a definition of directed.
A definition of adaptive mutation is that only useful, not deleterious or neutral, mutations occur during selection (7, 12, 29).
Source.
However, that's not what happens.
Neutral mutations accumulate.
To date, two cases of neutral mutations occurring at higher frequencies than expected among selected mutants have been published.
Source.
Deleterious mutations accumulate too.
First, lethal mutations remove cells from the mutagenized population and reduce the potential yield of individuals with a beneficial mutation.
Second, even genomes that acquire a beneficial mutation (without suffering a lethal mutation) are likely to acquire deleterious nonlethal mutations.
Source.
In the words of an author who collaborates with Cairns.
The controversy surrounding adaptive mutation originally centered on whether and how selected mutations could arise when neutral or deleterious mutations did not.
The two criteria for this selectivity were: (a) nonselected mutations did not occur during selection; and (b) the selected mutations did not arise under nonspecific stress, such as starvation.
As discussed above, several prominent examples of adaptive mutation have failed one or the other of these tests.
FAILED.
Source.
Guess what it's called when beneficial, neutral and deleterious mutations accumulate and are sorted out by natural selection?
Random mutation! (Just in case it needs to be said again, random with respect to fitness.)
You know who claimed that only beneficial mutations accumulate?
Cairns!
And you know in which paper?
The one he had to refute in a later paper!
Remember?
Fairly early on in our studies, Cairns and I eliminated the hypothesis that mutations were directed toward a useful goal.
(This) allowed us to dismiss the hypothesis that the selective conditions instructed the cell to make appropriate mutations.
Source.
Tell you what.
How about you provide a cite for directed mutation in a microorganism in which only beneficial mutations are produced?
And make it after 2004. After Cairns tucked his tail in between his legs and admitted he had failed.
Hey. Here's a thought. Show me where in Wright's paper she claims that only beneficial mutations were produced!

This message is a reply to:
 Message 364 by shadow71, posted 04-17-2011 3:16 PM shadow71 has replied

Replies to this message:
 Message 393 by shadow71, posted 04-19-2011 1:12 PM molbiogirl has replied

molbiogirl
Member (Idle past 2669 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 397 of 760 (612868)
04-19-2011 4:03 PM
Reply to: Message 393 by shadow71
04-19-2011 1:12 PM


Ho? Really??? HO?
You can't find an example of directed mutation in something other than a microorganism, so you change the subject?
Fabulous.
You cite Cairns.
Cairns refuted his paper.
You cite Zheng.
You get his findings exactly backwards.
You cite Wright.
Wright claims mutation is random and undirected in 99.5% of all extant species.
And now you're trying to cite that nutbag Ho.
Antivaxer Ho. Source.
Homeopathy Ho. Source.
Miracle water Ho. Source.
Quantum medicine Ho. Source.
And to top it off, you "cite" an opinion piece she wrote for an interest group she founded!
Get real.
Cite a paper in the research literature that supports your contention of directed evolution in higher organisms.
Directed evolution.
Got it?
That's your claim.
Back it up.
Edited by molbiogirl, : No reason given.

This message is a reply to:
 Message 393 by shadow71, posted 04-19-2011 1:12 PM shadow71 has replied

Replies to this message:
 Message 406 by shadow71, posted 04-20-2011 12:14 PM molbiogirl has replied

molbiogirl
Member (Idle past 2669 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 398 of 760 (612869)
04-19-2011 4:15 PM
Reply to: Message 396 by AZPaul3
04-19-2011 3:56 PM


Re: 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.
I have a hard time with scientists who buy into woo and try to support it with "research".
Here's what I mean:
Ho writes:
That’s why the quantum jazz of the organism is so fantastic; its antennae are tuned to signals from many frequencies, even those from faraway galaxies, and will respond to them with new music.
Source.
Ho is getting signals from outer space!
Agree to disagree, AZ?

This message is a reply to:
 Message 396 by AZPaul3, posted 04-19-2011 3:56 PM AZPaul3 has replied

Replies to this message:
 Message 399 by AZPaul3, posted 04-19-2011 4:36 PM molbiogirl has replied

molbiogirl
Member (Idle past 2669 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 400 of 760 (612875)
04-19-2011 5:28 PM
Reply to: Message 399 by AZPaul3
04-19-2011 4:36 PM


Re: Ho, Ho, Ho
The very least shadow can do, then, is cite her work, not her loony tune musings on ISIS.
I looked, btw, and she hasn't published anything on directed evolution or directed mutation.

This message is a reply to:
 Message 399 by AZPaul3, posted 04-19-2011 4:36 PM AZPaul3 has replied

Replies to this message:
 Message 401 by AZPaul3, posted 04-19-2011 5:48 PM molbiogirl has not replied

molbiogirl
Member (Idle past 2669 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 405 of 760 (612882)
04-19-2011 7:37 PM
Reply to: Message 404 by shadow71
04-19-2011 7:31 PM


Ho & epigenetics
Ho has written one paper on epigenetics.
In 1978.
How about discussing the paper and not her wackadoo crap from ISIS?

This message is a reply to:
 Message 404 by shadow71, posted 04-19-2011 7:31 PM shadow71 has replied

Replies to this message:
 Message 414 by shadow71, posted 04-20-2011 7:23 PM molbiogirl has replied

molbiogirl
Member (Idle past 2669 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 407 of 760 (612943)
04-20-2011 12:17 PM
Reply to: Message 406 by shadow71
04-20-2011 12:14 PM


For the fourth time, answer the question.
I am discussing Ho.
Ho is a nutbag.
Provide evidence of directed evolution in higher organisms.
Or admit defeat.

This message is a reply to:
 Message 406 by shadow71, posted 04-20-2011 12:14 PM shadow71 has replied

Replies to this message:
 Message 408 by shadow71, posted 04-20-2011 12:26 PM molbiogirl has replied
 Message 458 by shadow71, posted 04-26-2011 11:28 AM molbiogirl has replied

molbiogirl
Member (Idle past 2669 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 409 of 760 (612947)
04-20-2011 12:30 PM
Reply to: Message 406 by shadow71
04-20-2011 12:14 PM


Ho pubmed search
Mae-wan Ho, presented this paper, which is a review of the many papers she published with P.T. Saunders on epigenetics
Here's a pubmed search of Mae-wan Ho.
Care to show me the "many" papers on epigenetics?

This message is a reply to:
 Message 406 by shadow71, posted 04-20-2011 12:14 PM shadow71 has replied

Replies to this message:
 Message 451 by shadow71, posted 04-25-2011 4:40 PM molbiogirl has replied

molbiogirl
Member (Idle past 2669 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 410 of 760 (612951)
04-20-2011 12:38 PM
Reply to: Message 408 by shadow71
04-20-2011 12:26 PM


Re: For the fourth time, answer the question.
I am reading the paper and her prior papers and will post later on them.
Papers published in the research literature I hope.
I provided a pubmed search in my prior post in case you need a little help finding them.
You should read her papers and then let me know if she is a "nutbag."
I read plenty of this woman's addled rambling yesterday.
Here's a taste:
Highly polarized multiple layers of liquid crystalline water molecules form dynamically coherent units with the macromolecules, enabling them to function as quantum molecular energy machines that transform and transfer energy with close to 100 percent efficiency.
The quantum coherent organism is a macroscopic quantum being with an ever-evolving wave function spread throughout the entire universe, entangling the wave functions of other quantum beings.
Ooooooooo!

This message is a reply to:
 Message 408 by shadow71, posted 04-20-2011 12:26 PM shadow71 has replied

Replies to this message:
 Message 411 by Coragyps, posted 04-20-2011 1:52 PM molbiogirl has replied
 Message 429 by shadow71, posted 04-22-2011 3:17 PM molbiogirl has replied
 Message 459 by shadow71, posted 04-26-2011 11:33 AM molbiogirl has replied

molbiogirl
Member (Idle past 2669 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 413 of 760 (612961)
04-20-2011 2:54 PM
Reply to: Message 411 by Coragyps
04-20-2011 1:52 PM


Ho woo
We're talking Rupert Sheldrake levels of delusion here. Morphogenic fields, biophotons, etc.
Take a look at the talk she gave for the Radionic Association.
Just a taste.
The putative memory of the water invoked for homeopathic activity, in the form of specific electromagnetic signals, can be clearly and independently detected.
A science of homeopathy has the potential to revolutionize biology and put all forms of energy medicine, including radionics on the map.
What's "radionics"? So glad you asked.
Radionics is a healing technique in which our natural intuitive faculties are used both to discover the energetic disturbances underlying illness and to encourage the return of a normal energetic field that supports health.
The woo is strong with this one.

This message is a reply to:
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