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Author Topic:   About New Lamarckian Synthesis Theory
Taq
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Message 227 of 264 (679907)
11-16-2012 10:12 AM
Reply to: Message 226 by zi ko
11-16-2012 1:07 AM


Re: The ubsurdity of "classic" elolution Theory.
Koonin EV, Wolf YI (2009). "Is evolution Darwinian or/and Lamarckian?". Biol Direct 4: 42. doi:10.1186/1745-6150-4-42. PMC 2781790. PMID 19906303. //Is evolution Darwinian or/and Lamarckian? - PMC.
As you can see scientists have quite different ideas from you about evolution.
How so? Can you cite specifics from the paper and how it contradicts what we have been saying?

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 Message 226 by zi ko, posted 11-16-2012 1:07 AM zi ko has replied

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Taq
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Posts: 9972
Joined: 03-06-2009
Member Rating: 5.5


Message 232 of 264 (680366)
11-19-2012 9:49 AM
Reply to: Message 230 by zi ko
11-18-2012 11:08 AM


Re: The ubsurdity of "classic" elolution Theory.
"Both Darwinian and Lamarckian modalities of evolution appear to be important, and reflect different aspects of the interaction between populations and the environment."
Aren't they enough?
What are these modalities, and how do they demonstrated guided mutations in eukaryotes?

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 Message 233 by zi ko, posted 11-20-2012 12:45 AM Taq has replied

  
Taq
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Posts: 9972
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Member Rating: 5.5


Message 236 of 264 (680605)
11-20-2012 10:36 AM
Reply to: Message 233 by zi ko
11-20-2012 12:45 AM


Re:
In the rest of this article we discuss the recent studies of several phenomena that seem to call for resurrection of the Lamarckian scenario of evolution.
What are those phenomena and how do they fit into your model?

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Taq
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Posts: 9972
Joined: 03-06-2009
Member Rating: 5.5


Message 237 of 264 (680607)
11-20-2012 10:48 AM
Reply to: Message 235 by Dr Jack
11-20-2012 8:04 AM


Re: General commentary on the Koonin and Wolf paper
The first of these is the CRISPR-Cas system and it is probably their strongest example but, as we shall see, even it is only questionable Lamarckian and utterly limited in its scope.
I am more than willing to classify the CRISPR system as a Lamarckian system with guided mutations. It is exactly what I have in mind when I think of such a system. The only problem is that the CRISPR system, as you mentioned, is limited to phage resistance and phage resistance only. It is not involved in any other phenotypic changes, as far as I am aware, and it is also limited to prokaryotes while zi ko is arguing for guided mutations in eukaryotes.
Oh dear. This is, at best, poorly phrased and on the face of it simply wrong. One interpretation is that the environment referred to here is the plasmid itself but if we're to allow such an understanding there's no reason not to go further and argue that sexual partners are part of the environment and thus all sexual reproduction in Lamarckian - clearly rendering the concept meaningless. It seems they instead are suggesting that the environment (antibiotic) causes the uptake of the correct plasmid to resist the antibiotic but this is not the case. Plasmid uptake is not triggered by the antibiotic and is not selective.
Yes and no. Phage induction can occur with LexA dependent SOS type mechanisms. These phage can carry antibiotic resistance genes as well as toxins (the Panton-Valentine leukocidin in S. aureus being a good example). I wouldn't be surprised if sex pilli were upregulated in harsh conditions. There is some merit in the claim that cellular damage can trigger mechanisms that increase HGT.
Next up, they move on to what they call "quasi-Lamarckian" processes and begin by bumbling a description of stress-induced mutagenesis.
"Quasi-Lamarckian" is better known as adaptive mutation. Like you note, it is nothing more than changing the random mutation rate. This is akin to poor people buying more lottery tickets. This is definitely their poorest argument, and has been dealt with extensively in other threads.
Most importantly, the authors focus on prokaryotes while zi ko is focusing on eukaryotes, so I am not sure why zi ko is going with this paper.

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 Message 235 by Dr Jack, posted 11-20-2012 8:04 AM Dr Jack has replied

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Taq
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Posts: 9972
Joined: 03-06-2009
Member Rating: 5.5


Message 240 of 264 (681583)
11-26-2012 3:13 PM
Reply to: Message 239 by zi ko
11-22-2012 9:15 AM


Re: General commentary on the Koonin and Wolf paper
Coonin accepts the possibility of coexistance of random and guided mechanisms.So what?
Where is the evidence that mutations are guided?
Moreover there is no evidence of plasmids picking up is random. It is your own assumption.
It is. The mechanisms that move DNA from one bacteria to another do not read the DNA before taking in the DNA. The bacteria have no idea what the sequence of the plasmids are before it enters the bacteria.
Of course randomness can explain evolution (some aspects of it), but that does not exclude, as there is not any evidence, other explanations as well( e.g guided evolution).
Why should we include these other explanations when there is no evidence for them?

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 Message 239 by zi ko, posted 11-22-2012 9:15 AM zi ko has replied

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 Message 241 by zi ko, posted 12-02-2012 9:38 AM Taq has replied

  
Taq
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Posts: 9972
Joined: 03-06-2009
Member Rating: 5.5


Message 243 of 264 (682507)
12-03-2012 11:39 AM
Reply to: Message 241 by zi ko
12-02-2012 9:38 AM


Re: General commentary on the Koonin and Wolf paper
Of course bacteria don't know.But environment ,as you are suggesting by your first sentence, can fascilitate HGT (why not and other mechanisms as well ?)
However, the bacteria have no way of knowing if the DNA will be helpful, detrimental, or make no difference. In other words, it is random with respect to fitness.
Coonin at all have brought quite a lot of evidence, enough to convince themselves and others as well, or at least to make some to rethink about their fixed and uninevidenced ideas
Their "quasi-Lamarckian" mechanisms are random mutations. They are not guided.

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Taq
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Posts: 9972
Joined: 03-06-2009
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Message 248 of 264 (682665)
12-04-2012 12:44 PM
Reply to: Message 244 by dayalanand roy
12-04-2012 12:25 AM


Re: A fresh look at Lamarckism is needed
I also have great expectations from data coming out from Epigenetic research.
Epigenetics does not involve a change in DNA sequence. The differences between species is due to a difference in DNA sequence. Epigenetics can not be the cause of divergence between species.
When I consider the erect posture of humans, my conscience refuses to accept that it was simply due to some mutations followed by natural selection, and the efforts of humans themselves had nothing to do.
There were those whose conscience refused to accept that the Earth moved about the Sun, and yet it was so.
Why did random mutation did not create a nervous system in even a single plant?
Lineage specific adaptations are a hallmark of random mutations.

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Taq
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Posts: 9972
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Message 250 of 264 (682816)
12-05-2012 2:39 PM
Reply to: Message 249 by zi ko
12-05-2012 11:15 AM


Re: science versus opinions
It is so strange to me that this type of authoritarian remark, so many times repeated on this forum, in spite of, many times at least by me, questioning about the evidence that supports this authoritative opinion, the responce was very poor, regarding metazoans.
The only one making authoritarian remarks is you. You are arguing that mutations are not guided because you think they do. You do not offer evidence. All you offer is your insistence that you have to be right because you say so.
Your entire argument in an authoritarian argument.
One would expect on such crucial matter(random vs guided+random mutations) the amount and quality of such evidence to be overwhelming in the favor of randomness.
And it is. You just refuse to look at the evidence. Instead, you fall back to your authoritarian argument where the world has to be a certain way because you say so.

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 Message 249 by zi ko, posted 12-05-2012 11:15 AM zi ko has replied

Replies to this message:
 Message 251 by zi ko, posted 12-07-2012 10:40 AM Taq has replied

  
Taq
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Posts: 9972
Joined: 03-06-2009
Member Rating: 5.5


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Message 252 of 264 (683078)
12-07-2012 10:52 AM
Reply to: Message 251 by zi ko
12-07-2012 10:40 AM


Re: Who is authoritarian?
Lamarckism had been so unjustly neglected for centuries,
Why? Because you say so?
and now that serious scientists try with evidence to put it on the right place, you accuse their advocates as being authoritarian!
No, I am accusing YOU of being authoritarian. You are trying to claim that mutations are guided simply because you want it to be true. You offer no evidence. The papers you have cited involve random mutations, not guided mutations, and yet you still insist that mutations are guided? Why? Because you say so.

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Taq
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Posts: 9972
Joined: 03-06-2009
Member Rating: 5.5


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Message 255 of 264 (683424)
12-10-2012 1:22 PM
Reply to: Message 254 by zi ko
12-09-2012 10:40 AM


Re: science versus opinions
Yes, randomness of mutations in relation to fitness is well established and accepted , and it could well be the only explanation for evolution, but it was not well evidenced for the part of metazoans. and it is not falsifiable.
It is falsifiable. If mutations are not random then we would expect a large portion of a single generation to share the de novo beneficial mutation. IOW, their parents would not have this mutation, but a large portion of the subsequent generation would have this mutation, and it would be shown to be triggered by an environmental cue.
So what do we observe? We do not observe the environment triggering the same beneficial mutation in multiple individuals at a rate beyond that expected from random mutations. What we do observe is the same mechanism of mutation producing mutations throughout the genome, including detrimental mutations that lead to genetic diseases such as achondroplasia and hemophilia. We observe that these mechanisms produce mutations in junk DNA where it has no effect on fitness.
Mind you, i don't say that guided mutations are necessarily related to fitness.
Then what are they related to?
As for the "extraordinary" evidence needed for my ideas, i have to insist again that current theory can work equally perfectly well, without any change, using either the notion of random mutations , or that of guided mutations.
So guided mutations are indistinguishable from random mutations? And here you are accusing random mutations of being unfalsifiable. It appears that it is guided mutations that are unfalsifiable.

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 Message 254 by zi ko, posted 12-09-2012 10:40 AM zi ko has replied

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 Message 256 by zi ko, posted 12-12-2012 11:39 AM Taq has replied

  
Taq
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Posts: 9972
Joined: 03-06-2009
Member Rating: 5.5


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Message 258 of 264 (683700)
12-12-2012 4:00 PM
Reply to: Message 256 by zi ko
12-12-2012 11:39 AM


Re: science versus opinions
We have in front of us the reality of life.This is what they are related to.
So mutations are guided with respect to life? What does that even mean?
Random and guided mutations are equally unfalsifiable.
I spent an entire paragraph demonstrating that random mutations (with respect to fitness) are falsifiable. Perhaps you could do the honest thing and actually address what I said? Are are you saying that random mutations are unfalsifiable simply because you say so?
Your example of falcification of random mutatations could easily be used to falsify guided mutations as well,
Why? Because you say so?
unless you could bring reliable works favoring randomness about time needed to have the present life diversity.
Already did that in multiple posts. I discussed the Luria-Delbruck flucutation test, the Lederberg's plate replica experiment, and the pocket mice. You ignored all of it and just kept claiming that mutations are guided without ever addressing the points that I made.
Your entire argument boils down to "mutations are guided because zi ko says so".

This message is a reply to:
 Message 256 by zi ko, posted 12-12-2012 11:39 AM zi ko has replied

Replies to this message:
 Message 259 by zi ko, posted 12-14-2012 9:54 AM Taq has replied

  
Taq
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Posts: 9972
Joined: 03-06-2009
Member Rating: 5.5


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Message 260 of 264 (683891)
12-14-2012 11:51 AM
Reply to: Message 259 by zi ko
12-14-2012 9:54 AM


Re: science versus opinions
You talk about mutations not related to fitness.
No, I don't. I am saying that mutations are RANDOM relative to fitness.
I talk about mutations related to the reality of life.
What does that mean?
You just relate unsupported conlusions, taking for granted that guided mutations would lead to what you like to be.
That is not a conclusion. That is the definition of guided mutations. To reiterate what I stated before, this is what guided mutations look like:
". . .the environment triggering the same beneficial mutation in multiple individuals at a rate beyond that expected from random mutations."
You use inthe pocket mice example the highily unreliable notions of mutation rates and relative time frames to reach to your conclusions.
Why are they unreliable? Are they unreliable just because you say so?
The Luria-Delbruck flucutation test and the Lederberg's plate replica experiment are referring one cell organisms. I asked for for evidence about metazoans.
That's strange, because you then use references that mention the CRISPR system in one celled organisms as an example of guided mutations. Perhaps you should follow your own advice?
Also, the two experiments mentioned demonstrate how random mutations are falsifiable. The Luria and Delbruck paper specifically describes exactly how to falsify random mutations using specific math equations. I strongly suggest that you read the actual paper:
http://www.genetics.org/content/28/6/491.full.pdf+html
They specifically tested for Lamarckian type acquisition of immunity to bacteriophage. That is, they directly tested for guided mutations. The same ideas can be applied to all species, including metazoans.
A human corrolary to bacteriophage resistance in E. coli is human HIV resistance. People with a missing portion of their CCR5 gene are strongly resistant to HIV. Just like the Luria and Delbruck experiment, this mutation occurred independently of HIV. This mutation did not occur as a guided response to the presence of HIV. The mutation does offer a benefit to those exposed to HIV, but it came about by a random mutation before HIV even existed. This mutation was random with respect to fitness as modeled in the Luria and Delbruck experiment.
If mutations were guided, then we would expect to see this de novo mutation occuring at high rates in children born in areas with high levels of HIV infection. We don't.
Here is a work that i would like you to coment on:
You first. It is your reference, so YOU need to show how the evidence in the article supports YOUR arguments.
Edited by Taq, : No reason given.

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Taq
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Posts: 9972
Joined: 03-06-2009
Member Rating: 5.5


(2)
Message 262 of 264 (684351)
12-17-2012 10:47 AM
Reply to: Message 261 by zi ko
12-17-2012 12:42 AM


Re: comenting on the work of HO
It is clear that the wrighters believe that environmental stimuli cause
"large" evolutionary changes which are the result of canalization, which is not negated by random mutations that can follow.
Again, epigenetic changes do not explain the differences between species. The differences between humans and chimps is not due to epigenetics, it is due to a difference in the DNA SEQUENCE of their genomes. Any explanation of why species are different MUST explain how differences in sequence arise.
They talk also about mechanisms of canalization, which clearly reminds me about that "epigenetic changes pave the way to guided deep genome mutations" i had insisting of
So they are the same thing because you say so? Why don't you actually SHOW how epigenetics guides mutations instead of putting words in other peoples' mouths. After all, the paper is from 1979 well before DNA methylation and epigenetics was understood.
Edited by Taq, : No reason given.
Edited by Taq, : No reason given.

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 Message 261 by zi ko, posted 12-17-2012 12:42 AM zi ko has replied

Replies to this message:
 Message 263 by zi ko, posted 12-18-2012 11:10 AM Taq has replied

  
Taq
Member
Posts: 9972
Joined: 03-06-2009
Member Rating: 5.5


Message 264 of 264 (684799)
12-18-2012 5:05 PM
Reply to: Message 263 by zi ko
12-18-2012 11:10 AM


Re: : comenting on the work of M. MONK
Taq here you maybe find the answer of your questions to me.
Why don't YOU show me where those answers are.

This message is a reply to:
 Message 263 by zi ko, posted 12-18-2012 11:10 AM zi ko has not replied

  
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