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Author Topic:   About New Lamarckian Synthesis Theory
zi ko
Member (Idle past 1547 days)
Posts: 578
Joined: 01-18-2011


Message 226 of 264 (679833)
11-16-2012 1:07 AM
Reply to: Message 225 by Dr Jack
11-14-2012 2:18 PM


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. //www.ncbi.nlm.nih.gov/pmc/articles/PMC2781790/.
As you can see scientists have quite different ideas from you about evolution.


This message is a reply to:
 Message 225 by Dr Jack, posted 11-14-2012 2:18 PM Dr Jack has responded

Replies to this message:
 Message 227 by Taq, posted 11-16-2012 10:12 AM zi ko has responded
 Message 228 by Dr Jack, posted 11-17-2012 4:26 AM zi ko has responded
 Message 235 by Dr Jack, posted 11-20-2012 8:04 AM zi ko has responded

    
Taq
Member
Posts: 7577
Joined: 03-06-2009
Member Rating: 3.6


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. //www.ncbi.nlm.nih.gov/pmc/articles/PMC2781790/.
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?


This message is a reply to:
 Message 226 by zi ko, posted 11-16-2012 1:07 AM zi ko has responded

Replies to this message:
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Dr Jack
Member (Idle past 32 days)
Posts: 3507
From: Leicester, England
Joined: 07-14-2003


Message 228 of 264 (680008)
11-17-2012 4:26 AM
Reply to: Message 226 by zi ko
11-16-2012 1:07 AM


Re: The ubsurdity of "classic" elolution Theory.
Nothing in that paper supports your assertions or contradicts anything I wrote.
This message is a reply to:
 Message 226 by zi ko, posted 11-16-2012 1:07 AM zi ko has responded

Replies to this message:
 Message 230 by zi ko, posted 11-18-2012 11:08 AM Dr Jack has responded

  
zi ko
Member (Idle past 1547 days)
Posts: 578
Joined: 01-18-2011


Message 229 of 264 (680189)
11-18-2012 11:01 AM
Reply to: Message 227 by Taq
11-16-2012 10:12 AM


Re: The ubsurdity of "classic" elolution Theory.
Can you cite specifics from the paper and how it contradicts what we have been saying?

I quote
However, various evolutionary phenomena that came to fore in the last few years, seem to fit a more broadly interpreted (quasi)Lamarckian paradigm. The prokaryotic CRISPR-Cas system of defense against mobile elements seems to function via a bona fide Lamarckian mechanism, namely, by integrating small segments of viral or plasmid DNA into specific loci in the host prokaryote genome and then utilizing the respective transcripts to destroy the cognate mobile element DNA (or RNA). A similar principle seems to be employed in the piRNA branch of RNA interference which is involved in defense against transposable elements in the animal germ line. Horizontal gene transfer (HGT), a dominant evolutionary process, at least, in prokaryotes, appears to be a form of (quasi)Lamarckian inheritance. The rate of HGT and the nature of acquired genes depend on the environment of the recipient organism and, in some cases, the transferred genes confer a selective advantage for growth in that environment, meeting the Lamarckian criteria. Various forms of stress-induced mutagenesis are tightly regulated and comprise a universal adaptive response to environmental stress in cellular life forms. Stress-induced mutagenesis can be construed as a quasi-Lamarckian phenomenon because the induced genomic changes, although random, are triggered by environmental factors and are beneficial to the organism.

Conclusion
Both Darwinian and Lamarckian modalities of evolution appear to be important, and reflect different aspects of the interaction between populations and the environment.



This message is a reply to:
 Message 227 by Taq, posted 11-16-2012 10:12 AM Taq has not yet responded

    
zi ko
Member (Idle past 1547 days)
Posts: 578
Joined: 01-18-2011


Message 230 of 264 (680192)
11-18-2012 11:08 AM
Reply to: Message 228 by Dr Jack
11-17-2012 4:26 AM


Re: The ubsurdity of "classic" elolution Theory.
Nothing in that paper supports your assertions or contradicts anything I wrote.

I quote:
"However, various evolutionary phenomena that came to fore in the last few years, seem to fit a more broadly interpreted (quasi)Lamarckian paradigm. The prokaryotic CRISPR-Cas system of defense against mobile elements seems to function via a bona fide Lamarckian mechanism, namely, by integrating small segments of viral or plasmid DNA into specific loci in the host prokaryote genome and then utilizing the respective transcripts to destroy the cognate mobile element DNA (or RNA). A similar principle seems to be employed in the piRNA branch of RNA interference which is involved in defense against transposable elements in the animal germ line. Horizontal gene transfer (HGT), a dominant evolutionary process, at least, in prokaryotes, appears to be a form of (quasi)Lamarckian inheritance. The rate of HGT and the nature of acquired genes depend on the environment of the recipient organism and, in some cases, the transferred genes confer a selective advantage for growth in that environment, meeting the Lamarckian criteria. Various forms of stress-induced mutagenesis are tightly regulated and comprise a universal adaptive response to environmental stress in cellular life forms. Stress-induced mutagenesis can be construed as a quasi-Lamarckian phenomenon because the induced genomic changes, although random, are triggered by environmental factors and are beneficial to the organism.
Conclusion
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?



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 Message 228 by Dr Jack, posted 11-17-2012 4:26 AM Dr Jack has responded

Replies to this message:
 Message 231 by Dr Jack, posted 11-19-2012 5:21 AM zi ko has not yet responded
 Message 232 by Taq, posted 11-19-2012 9:49 AM zi ko has responded

    
Dr Jack
Member (Idle past 32 days)
Posts: 3507
From: Leicester, England
Joined: 07-14-2003


Message 231 of 264 (680327)
11-19-2012 5:21 AM
Reply to: Message 230 by zi ko
11-18-2012 11:08 AM


Re: The ubsurdity of "classic" elolution Theory.
What does any of that have to do with giraffe's necks? If you want to concede on megafauna and move on to discussing prokaryotes we can do that? Otherwise you will need to post something relevant to our long necked friends.
This message is a reply to:
 Message 230 by zi ko, posted 11-18-2012 11:08 AM zi ko has not yet responded

  
Taq
Member
Posts: 7577
Joined: 03-06-2009
Member Rating: 3.6


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?


This message is a reply to:
 Message 230 by zi ko, posted 11-18-2012 11:08 AM zi ko has responded

Replies to this message:
 Message 233 by zi ko, posted 11-20-2012 12:45 AM Taq has responded

  
zi ko
Member (Idle past 1547 days)
Posts: 578
Joined: 01-18-2011


Message 233 of 264 (680552)
11-20-2012 12:45 AM
Reply to: Message 232 by Taq
11-19-2012 9:49 AM


Re:
Can you cite specifics from the paper and how it contradicts what we have been saying?

What are these modalities, and how do they demonstrated guided mutations in eukaryotes?

--------------------------------------------------------------------------------
//www.ncbi.nlm.nih.gov/pmc/articles/PMC2781790/.

quote:
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.



This message is a reply to:
 Message 232 by Taq, posted 11-19-2012 9:49 AM Taq has responded

Replies to this message:
 Message 234 by Dr Jack, posted 11-20-2012 6:37 AM zi ko has not yet responded
 Message 236 by Taq, posted 11-20-2012 10:36 AM zi ko has not yet responded

    
Dr Jack
Member (Idle past 32 days)
Posts: 3507
From: Leicester, England
Joined: 07-14-2003


Message 234 of 264 (680572)
11-20-2012 6:37 AM
Reply to: Message 233 by zi ko
11-20-2012 12:45 AM


Re:
Taq is quite capable of reading, Zi Ko, as am I. We're asking you to make your own argument and present the relevant points you wish to discuss. Simply linking to the Koonin and Wolf paper again doesn't do that.
This message is a reply to:
 Message 233 by zi ko, posted 11-20-2012 12:45 AM zi ko has not yet responded

  
Dr Jack
Member (Idle past 32 days)
Posts: 3507
From: Leicester, England
Joined: 07-14-2003


(2)
Message 235 of 264 (680582)
11-20-2012 8:04 AM
Reply to: Message 226 by zi ko
11-16-2012 1:07 AM


General commentary on the Koonin and Wolf paper
In their paper (Is Evolution Darwinian or/and Lamarckian), Koonin and Wolf argue that recently discovered mechanism of change constitute Lamarckian mechanisms for evolutionary change. Let's go through the paper and see what their arguments are.

The paper begins with a historical perspective on Lamarck's ideas. There's nothing here we need to discuss, I'll just note that they draw particular attention to the point made by Lamarckists that his scheme suggests the inheritance of adaptive features only not any and all acquired traits and insist that Lamarckism needs to be more than mere "inheritance of acquired characteristics".

Following the introduction we get to a section where Koonin and Wolf attempt to recast the Lamarckian hypothesis into genetic terms so that it can be assessed in a modern light. They summarise Lamarck's hypothesis as "Lamarck's idea of heridity is based on a threefold causal chain: environment-habit-form". That is, the environment alters the organism through the alteration of behaviour and that behaviour alters form in a heritable fashion. Koonin and Wolf then reformulate that idea as:

quote:
1) environmental factors cause genomic (heritable) changes

2) the induced changes (mutations) are targeted to a specific gene(s)

3) the induced changes provide adaptation to the original causative factor


This isn't a direct reinterpretation of Lamarck's ideas but I think we can see that it entails a modern reinterpretation of a similar scheme. Since Science regularly recasts ideas as we develop greater knowledge I think this is perfectly allowable. However, if it is to retain the essence of Lamarck's idea and remain a coherent and useful framework we need to be very careful in how we allow the key concepts to be understood. As we shall see, Koonin and Wolf fail to do this throughout the rest of the paper, and their failure renders their reformulation so broad as to be meaningless. Note also that Koonin and Wolf's "Lamarckian" makes no claims about change over time. Whereas Lamarck proposed a mechanism for explaining the diversity of life, Koonin and Wolf are not even requiring that it take even a supporting role.

Having established what "Lamarckian" means to them, the authors then move on to present the examples they believe constitute Lamarckian processes. 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. Before we move on to the problems with their interpretation I should probably explain what the CRISPR-Cas system is. CRISPR is a system present in prokaryotes that functions as an adaptive protection system that limits attack by phages and the acquisition of unwanted plasmids. In a manner analogous to RNAi in eukaryotes, the CRISPR systems produces short RNA sections (crRNAs) which are complementary to the target DNA sequences and allow the cells attack mechanisms to disrupt the target DNA. Cleverly, rather than relying on random mutation to develop the sequences from which these crRNAs are transcribed the CRISPR system instead works by directly incorporating fragments of the foreign DNA into specific sites in their core DNA. (See Marraffini and Sontheimer (2010) CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea, Nature Review Genetics 11:181-190 for a fuller review)

Thus the CRISPR system is a mechanism for producing inheritable change based on environmental factors (phage and plasmid encounters). The authors would have you believe that this meets their criteria for Lamarckism; I disagree. A key feature of the Lamarckian schema is the three fold process environment-habit-form but CRISPR is not environment-habit-form it is environment-form; it's not induced change in response to the environment; it's actively incorporating some part of the environment into the genome. This, it seems to me, is a key difference. However, even if we are to accept CRISPR as Lamarckian then it stands not as a mechanism for generating iterative change (and thus a mechanism that could explain diversity) but rather a highly controlled and specialised mechanism with tightly defined limits.

Following on from CRISPR they briefly discuss similar mechanisms in other organisms, there's not much meat here and little new so I'll skip straight over it and move on to the most bizarre and false of their claims: that horizontal gene transfer is Lamarckian. I'll quote at length here:

quote:
Perhaps, the most straightforward and familiar case in point is evolution of antibiotic resistance. When a sensitive prokaryote enters an environment where an antibiotic is present, the only chance for the newcomer to survive is to acquire a resistance gene(s) by HGT, typically, via a plasmid. This common (and, of course, extremely practically important) phenomenon seems to be a clear case of Lamarckian inheritance. Indeed, a trait, in this case, the activity of the transferred gene that mediates antibiotic resistance, is acquired under a direct influence of the environment and is clearly advantageous, even essential in this particular niche.

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. It is a random, Darwinian, process. Plasmid uptake occurs at all times at random; the retention of the plasmid is then maintained in the presence of the antibiotic by selection. Cells that lose the plasmid die; cells that retain it do not. Simple, Darwinian, selection. The source of variation is now not sex or mutation but transformation but the process remains essentially Darwinian.

Next up, they move on to what they call "quasi-Lamarckian" processes and begin by bumbling a description of stress-induced mutagenesis. I'll leave as moot the question of whether stress-induced mutagenesis is actually adaptive or whether it is a simple consequence of stress limiting the ability of an organism to suppress mutation. So, a quick recap: stress-induced mutagenesis occurs when an organism (prokaryotes are the main group known to undergo this process but there is emerging evidence in other organisms) is placed under stress conditions and results in an increased mutation rate. This can be adaptive if the high mutation rate produces beneficial mutation(s). Koonin and Wolf themselves admit "(a)daptive evolution resulting from stress-induced mutagenesis is not exactly Lamarckian because the stress does not cause mutations directly and specifically in genes conferring stress resistance." I'd go further: it's not Lamarckian at all. It does not meet their criteria. There is a response to the environment, yes, but the heritable change is strictly random and Darwinian; it's mutation followed by selection. There is no targeting (it does not meet their criteria 2). If we're to consider this "quasi-Lamarckian" then it is not clear that any mutation is not "quasi-Lamarckian" since nearly all mutation are induced by the environment - whether by radiation, free radicals or carcinogenic compounds. Thus allowing stress-induced mutation as Lamarckian renders the concept meaningless.

Having presented their examples - each of which we have already seen to be flawed in interpretation - they go on to try and bring their ideas together. I'll not go over what they write here in detail, it seems pointless with their examples so obviously flawed that their conclusions have no foundation, but I'd like to draw particular attention to the laughable Figure 3 in which they absurdly claim that the "Lamarckian modality" takes over from the "Darwinian modality" under conditions of increasing stress. But, as we've seen, stress-induced mutagenesis is a strictly Darwinian process! The mechanism relies on basic Darwinian principles of mutation and selection.

tl;dr: The papers examples are balls, and thus their conclusions are meaningless.


This message is a reply to:
 Message 226 by zi ko, posted 11-16-2012 1:07 AM zi ko has responded

Replies to this message:
 Message 237 by Taq, posted 11-20-2012 10:48 AM Dr Jack has responded
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Taq
Member
Posts: 7577
Joined: 03-06-2009
Member Rating: 3.6


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?


This message is a reply to:
 Message 233 by zi ko, posted 11-20-2012 12:45 AM zi ko has not yet responded

  
Taq
Member
Posts: 7577
Joined: 03-06-2009
Member Rating: 3.6


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.


This message is a reply to:
 Message 235 by Dr Jack, posted 11-20-2012 8:04 AM Dr Jack has responded

Replies to this message:
 Message 238 by Dr Jack, posted 11-20-2012 11:44 AM Taq has not yet responded

  
Dr Jack
Member (Idle past 32 days)
Posts: 3507
From: Leicester, England
Joined: 07-14-2003


Message 238 of 264 (680633)
11-20-2012 11:44 AM
Reply to: Message 237 by Taq
11-20-2012 10:48 AM


Re: General commentary on the Koonin and Wolf paper
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.

I'm not so convinced. It's not clear to me that it's anything more than a specialised form of HGT. Importantly, it's missing any kind of middle step; it's environment->adaptation not environment->habit->form. Instead what we see is a random acquisition of phage fragments followed by maintenance of those fragments only in the presence of selection. The process is unusual and targeted but I think calling it Lamarckian is pushing it.

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.

Yes, you're correct. I'm afraid I didn't phrase that very well. HGT is increased by stress conditions (hell, the standard lab procedure for transformation uses chemical conditioning and heat shock) however it (a) occurs anyway and (b) isn't targeted. The bacteria aren't responding to antibiotic presence by searching for antibiotic resistance they're still adopting a process of random uptake (variation) and selection.

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.

Indeed.


This message is a reply to:
 Message 237 by Taq, posted 11-20-2012 10:48 AM Taq has not yet responded

  
zi ko
Member (Idle past 1547 days)
Posts: 578
Joined: 01-18-2011


Message 239 of 264 (681058)
11-22-2012 9:15 AM
Reply to: Message 235 by Dr Jack
11-20-2012 8:04 AM


Re: General commentary on the Koonin and Wolf paper
Next up, they move on to what they call "quasi-Lamarckian" processes and begin by bumbling a description of stress-induced mutagenesis.... I'd go further: it's not Lamarckian at all. It does not meet their criteria. There is a response to the environment, yes, but the heritable change is strictly random and Darwinian; it's mutation followed by selection. There is no targeting (it does not meet their criteria 2). If we're to consider this "quasi-Lamarckian" then it is not clear that any mutation is not "quasi-Lamarckian" since nearly all mutation are induced by the environment - whether by radiation, free radicals or carcinogenic compounds. Thus allowing stress-induced mutation as Lamarckian renders the concept meaningless.

"There is a response to the environment, yes,... but the heritable change is strictly random and Darwinian;" So you accept there is a mechanism that communicates environment and genome.
"but the heritable change is strictly random and Darwinian": Coonin accepts the possibility of coexistance of random and guided mechanisms.So what? Moreover there is no evidence of plasmids picking up is random. It is your own assumption. 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).


This message is a reply to:
 Message 235 by Dr Jack, posted 11-20-2012 8:04 AM Dr Jack has not yet responded

Replies to this message:
 Message 240 by Taq, posted 11-26-2012 3:13 PM zi ko has responded

    
Taq
Member
Posts: 7577
Joined: 03-06-2009
Member Rating: 3.6


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?


This message is a reply to:
 Message 239 by zi ko, posted 11-22-2012 9:15 AM zi ko has responded

Replies to this message:
 Message 241 by zi ko, posted 12-02-2012 9:38 AM Taq has responded

  
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