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Author Topic:   How novel features evolve #2
New Cat's Eye
Inactive Member


Message 136 of 402 (671621)
08-28-2012 1:18 PM
Reply to: Message 134 by zi ko
08-28-2012 12:32 PM


Re: Meaningless controvercy.
It had proved beyond any doupt that stress causes genes mutations.
...which are still random with respect to fitness. So therefore, the environment is not driving evolution by directly affecting any mutations.
So the mechanism for it exists in metazoa.
But its not a mechanism for what you are proposing.

This message is a reply to:
 Message 134 by zi ko, posted 08-28-2012 12:32 PM zi ko has not replied

  
zi ko
Member (Idle past 3648 days)
Posts: 578
Joined: 01-18-2011


Message 137 of 402 (671906)
08-31-2012 11:06 AM
Reply to: Message 132 by New Cat's Eye
08-27-2012 10:20 AM


Re: DNA sequences and Phenotype selection
The article you suggested is very interesting.
I quote from it:
"Although most mutations are believed to be caused by replication errors, they can also be caused by various environmentally induced and spontaneous changes to DNA that occur prior to replication but are perpetuated in the same way as unfixed replication errors. As with replication errors, most environmentally induced DNA damage is repaired, resulting in fewer than 1 out of every 1,000 chemically induced lesions actually becoming permanent mutations. The same is true of so-called spontaneous mutations. "Spontaneous" refers to the fact that the changes occur in the absence of chemical, radiation, or other environmental damage. Rather, they are usually caused by normal chemical reactions that go on in cells, such as hydrolysis. These types of errors include depurination, which occurs when the bond connecting a purine to its deoxyribose sugar is broken by a molecule of water, resulting in a purine-free nucleotide that can't act as a template during DNA replication, and deamination, which results in the loss of an amino group from a nucleotide, again by reaction with water. Again, most of these spontaneous errors are corrected by DNA repair processes. But if this does not occur, a nucleotide that is added to the newly synthesized strand can become a permanent mutation."
So environment causes gene mutations! I can add stress as an environmental factor causing gene mutations.
But i think there is a serious omission on this work. There isn't any relation as to if the error repairing actions are directed to special types of mutations, leaving others to perpatuate.
In that case we would have a serious evidence or not of guided mutations.
Edited by zi ko, : No reason given.
Edited by zi ko, : No reason given.


This message is a reply to:
 Message 132 by New Cat's Eye, posted 08-27-2012 10:20 AM New Cat's Eye has replied

Replies to this message:
 Message 139 by New Cat's Eye, posted 08-31-2012 11:23 AM zi ko has not replied
 Message 140 by Percy, posted 08-31-2012 11:26 AM zi ko has replied
 Message 145 by Taq, posted 08-31-2012 12:53 PM zi ko has replied

  
zi ko
Member (Idle past 3648 days)
Posts: 578
Joined: 01-18-2011


Message 138 of 402 (671908)
08-31-2012 11:14 AM
Reply to: Message 135 by Taq
08-28-2012 12:42 PM


Re: Meaningless controvercy.
I see a lot of vague claims but zero evidence.
--------------------------------------------------------------------------------
Read please my message 137 to Catholic Scientist.
Edited by zi ko, : No reason given.


This message is a reply to:
 Message 135 by Taq, posted 08-28-2012 12:42 PM Taq has not replied

  
New Cat's Eye
Inactive Member


Message 139 of 402 (671911)
08-31-2012 11:23 AM
Reply to: Message 137 by zi ko
08-31-2012 11:06 AM


Re: DNA sequences and Phenotype selection
So environment causes gene mutations!
Sure, but it really doesn't have any impact on the evolution of species. Its negligible. It doesn't really matter.
You just have your pet idea and are doing anything you can to confirm your preconceived suspicions. Far be it from me to try to convince you to do otherwise.
In that case we would have a serious evidence or not of guided mutations.
But damn do you have to be grasping at straws to even come close to thinking that!

This message is a reply to:
 Message 137 by zi ko, posted 08-31-2012 11:06 AM zi ko has not replied

Replies to this message:
 Message 141 by Percy, posted 08-31-2012 11:29 AM New Cat's Eye has replied

  
Percy
Member
Posts: 22502
From: New Hampshire
Joined: 12-23-2000
Member Rating: 4.9


Message 140 of 402 (671912)
08-31-2012 11:26 AM
Reply to: Message 137 by zi ko
08-31-2012 11:06 AM


Re: DNA sequences and Phenotype selection
Hi Zi Ko,
There has never been any doubt in anyone's mind that both the environment and stress (which need not be referenced separately since it is actually induced by the environment) can cause mutations, but these mutations are random with respect to fitness.
zi ko writes:
In that case we would have a serious evidence or not of guided mutations.
Not.
What has this to do with how novel features evolve?
--Percy

This message is a reply to:
 Message 137 by zi ko, posted 08-31-2012 11:06 AM zi ko has replied

Replies to this message:
 Message 147 by zi ko, posted 09-03-2012 10:19 AM Percy has replied
 Message 164 by zi ko, posted 09-05-2012 9:16 AM Percy has replied

  
Percy
Member
Posts: 22502
From: New Hampshire
Joined: 12-23-2000
Member Rating: 4.9


Message 141 of 402 (671913)
08-31-2012 11:29 AM
Reply to: Message 139 by New Cat's Eye
08-31-2012 11:23 AM


Re: DNA sequences and Phenotype selection
Catholic Scientist writes:
So environment causes gene mutations!
Sure, but it really doesn't have any impact on the evolution of species.
I'm guessing you really meant to something about guided evolution since any mutation, regardless of ultimate cause, can have an impact on evolution.
--Percy

This message is a reply to:
 Message 139 by New Cat's Eye, posted 08-31-2012 11:23 AM New Cat's Eye has replied

Replies to this message:
 Message 142 by New Cat's Eye, posted 08-31-2012 11:39 AM Percy has replied

  
New Cat's Eye
Inactive Member


Message 142 of 402 (671916)
08-31-2012 11:39 AM
Reply to: Message 141 by Percy
08-31-2012 11:29 AM


Re: DNA sequences and Phenotype selection
Catholic Scientist writes:
So environment causes gene mutations!
Sure, but it really doesn't have any impact on the evolution of species.
I'm guessing you really meant to something about guided evolution since any mutation, regardless of ultimate cause, can have an impact on evolution.
Your right. What I meant was that environment caused mutations aren't really that important when we're considering the evolution of speices. Sure, they aren't non-existant, but do they really matter? Meh, not so much. They don't really (read: an appreciable amount) affect evolution.
Especially, that is, compared to the extent that zi ko wants to use them to claim that it opens up an avenue for there to be guided mutations through the environment. That's why I said they're negligible.
But its obvious what he's doing. He wants there to be an intelligent designer. He likes that idea that mutation are guided through the environment. So what does he do? He points to every instance of there being any affect on mutation by the environment and then wants to think that that gives room for his favorite idea... but it doesn't.

This message is a reply to:
 Message 141 by Percy, posted 08-31-2012 11:29 AM Percy has replied

Replies to this message:
 Message 143 by Percy, posted 08-31-2012 12:04 PM New Cat's Eye has replied

  
Percy
Member
Posts: 22502
From: New Hampshire
Joined: 12-23-2000
Member Rating: 4.9


Message 143 of 402 (671917)
08-31-2012 12:04 PM
Reply to: Message 142 by New Cat's Eye
08-31-2012 11:39 AM


Re: DNA sequences and Phenotype selection
Catholic Scientist writes:
Your right. What I meant was that environment caused mutations aren't really that important when we're considering the evolution of speices. Sure, they aren't non-existant, but do they really matter? Meh, not so much. They don't really (read: an appreciable amount) affect evolution.
You may be unduly minimizing the impact of environmentally caused mutations on evolution. Environmental stress can increase mutation rates. A population under environmental stress and possibly facing eventual extinction has a better chance of evolving it's way out of its predicament if it has a higher mutation rate. I think the current understanding is that environmentally caused mutations can matter a great deal.
--Percy

This message is a reply to:
 Message 142 by New Cat's Eye, posted 08-31-2012 11:39 AM New Cat's Eye has replied

Replies to this message:
 Message 144 by New Cat's Eye, posted 08-31-2012 12:30 PM Percy has seen this message but not replied
 Message 149 by zi ko, posted 09-03-2012 11:09 AM Percy has replied

  
New Cat's Eye
Inactive Member


Message 144 of 402 (671919)
08-31-2012 12:30 PM
Reply to: Message 143 by Percy
08-31-2012 12:04 PM


Re: DNA sequences and Phenotype selection
You may be unduly minimizing the impact of environmentally caused mutations on evolution.
I may be. Hey, maybe I'll learn something!
Environmental stress can increase mutation rates.
How's that work? What's the mechanism?
A population under environmental stress and possibly facing eventual extinction has a better chance of evolving it's way out of its predicament if it has a higher mutation rate.
See, I'm under the impression that zi ko is talking about the environment directly causeing a particular mutation... not that environmental stress can increase the rate of mutations in general.
I think the current understanding is that environmentally caused mutations can matter a great deal.
But a particular mutation isn't caused by the enivronment in these cases, is it? I know it is possible for the evnironment to directly cause a mutation, but that's not the same thing as the environment increasing mutation rates. And an environmentally increased mutation rate doesn't have anything to do with guided evolution.

This message is a reply to:
 Message 143 by Percy, posted 08-31-2012 12:04 PM Percy has seen this message but not replied

Replies to this message:
 Message 146 by Taq, posted 08-31-2012 1:03 PM New Cat's Eye has not replied

  
Taq
Member
Posts: 10084
Joined: 03-06-2009
Member Rating: 5.1


Message 145 of 402 (671925)
08-31-2012 12:53 PM
Reply to: Message 137 by zi ko
08-31-2012 11:06 AM


Re: DNA sequences and Phenotype selection
So environment causes gene mutations!
Yes, and those mutations are random with respect to fitness. We are all aware that chemical mutagens and radiation cause mutations. We are also aware of things like the SOS response in E. coli. In each case, the mutations that are produced are random with respect to fitness.
There isn't any relation as to if the error repairing actions are directed to special types of mutations, leaving others to perpatuate.
DNA repair mechanisms are not specific to any sequence. These repair mechanisms can not tell if the repair will result in a decrease or increase in fitness, nor are they gene specific.
Going back to my lottery analogy, a poor person buying more lottery tickets than a rich person does not make the lottery non-random. In the same way, a bacteria producing more random mutations while under stress does not make those mutations non-random. They are still random. Increasing the random mutation rate does not make mutations non-random, it just produces more random mutations.
Edited by Taq, : No reason given.

This message is a reply to:
 Message 137 by zi ko, posted 08-31-2012 11:06 AM zi ko has replied

Replies to this message:
 Message 150 by zi ko, posted 09-03-2012 11:25 AM Taq has replied

  
Taq
Member
Posts: 10084
Joined: 03-06-2009
Member Rating: 5.1


(3)
Message 146 of 402 (671927)
08-31-2012 1:03 PM
Reply to: Message 144 by New Cat's Eye
08-31-2012 12:30 PM


Re: DNA sequences and Phenotype selection
How's that work? What's the mechanism?
Excellent question. In the case of the SOS response in E. coli it is triggered by DNA damage. The presence of ssDNA and halted replication forks activates RecA. RecA interacts with the repressor LexA which removes LexA from the upstream promoters of certain genes allowing them to be expressed. Amongst those proteins that are upregulated are error prone polymerases and DNA repair mechanisms that can result in gene duplications and other recombination events. Wiki has a decent page on it:
SOS response - Wikipedia
There is also evidence for increased transposon activity in stressed cells and just plain ol' DNA damage due to starvation conditions.
But a particular mutation isn't caused by the enivronment in these cases, is it? I know it is possible for the evnironment to directly cause a mutation, but that's not the same thing as the environment increasing mutation rates. And an environmentally increased mutation rate doesn't have anything to do with guided evolution.
Precisely. It is an increase in the random mutation rate. It is analogous to a gambler playing 10 slot machines at the same time instead of just one. This doesn't change the random nature of each result, but it does increase the chances that the gambler will hit the big jackpot.

This message is a reply to:
 Message 144 by New Cat's Eye, posted 08-31-2012 12:30 PM New Cat's Eye has not replied

  
zi ko
Member (Idle past 3648 days)
Posts: 578
Joined: 01-18-2011


Message 147 of 402 (672107)
09-03-2012 10:19 AM
Reply to: Message 140 by Percy
08-31-2012 11:26 AM


Re:meaningless controvercy
What has this to do with how novel features evolve?
If cells are directing repairing mechanisms only to some specific DNA damage and not all, then there is surely a matter of guided evolution. That is what i meant saying that this work suffered a serious ommission.
Edited by zi ko, : No reason given.


This message is a reply to:
 Message 140 by Percy, posted 08-31-2012 11:26 AM Percy has replied

Replies to this message:
 Message 148 by Percy, posted 09-03-2012 10:39 AM zi ko has not replied

  
Percy
Member
Posts: 22502
From: New Hampshire
Joined: 12-23-2000
Member Rating: 4.9


Message 148 of 402 (672108)
09-03-2012 10:39 AM
Reply to: Message 147 by zi ko
09-03-2012 10:19 AM


Re: Re:meaningless controvercy
zi ko writes:
If cells are directing repairing mechanisms only to some specific DNA damage and not all, then there is surely a matter of guided evolution.
If somewhere out there something or someone is making decisions about which DNA damage to repair then that would be guided evolution, but there's no evidence of any conscious decision making. What we observe is only cellular repair mechanisms at work. Cellular copying mechanisms are not perfect, and neither are cellular repair mechanisms. There is nothing to indicate that copying errors or lacks in repair mechanisms are the result of conscious decisions.
Again, what has this to do with how novel features evolve? You appear to be trying to turn this thread into a discussion of your favorite topic. Unless you have evidence for guided evolution causing novel features I think you're off topic.
--Percy

This message is a reply to:
 Message 147 by zi ko, posted 09-03-2012 10:19 AM zi ko has not replied

  
zi ko
Member (Idle past 3648 days)
Posts: 578
Joined: 01-18-2011


Message 149 of 402 (672112)
09-03-2012 11:09 AM
Reply to: Message 143 by Percy
08-31-2012 12:04 PM


Re: Meaningless controvercy.
I think the current understanding is that environmentally caused mutations can matter a great deal
It was a great step forward, don't you think?
Anyway accepting increased rate mutation, caused by environment is not far away from accepting guided evolution! (note: not mutation). Random mutations is a usefull mechanism not to be used by nature, in its scope to evolution, specifically in mono cell organisms. But here we reach at the main issue, the core problem we have to face: Are natural laws enough to explain life emergence and next evolution? Or we have to resort to the Supernatural?
Edited by zi ko, : No reason given.
Edited by zi ko, : No reason given.


This message is a reply to:
 Message 143 by Percy, posted 08-31-2012 12:04 PM Percy has replied

Replies to this message:
 Message 151 by Percy, posted 09-03-2012 12:02 PM zi ko has replied

  
zi ko
Member (Idle past 3648 days)
Posts: 578
Joined: 01-18-2011


Message 150 of 402 (672114)
09-03-2012 11:25 AM
Reply to: Message 145 by Taq
08-31-2012 12:53 PM


Re: Meaningless controvercy.
Yes, and those mutations are random with respect to fitness. We are all aware that chemical mutagens and radiation cause mutations. We are also aware of things like the SOS response in E. coli. In each case, the mutations that are produced are random with respect to fitness.
I have no dificulty to accept all that, with the presuppposition we had solved firstly the core question: Are natural laws enough to explain life appearance and concequently species evolution ?
In the case of positive answer we accept that natural laws are guiding evolution (not mutations!). In the other case Supernatural is doing it.
In either case it is secondary, at least philosofically, if there are only random mutations, or only guided mutations, or both of them.
Edited by zi ko, : No reason given.


This message is a reply to:
 Message 145 by Taq, posted 08-31-2012 12:53 PM Taq has replied

Replies to this message:
 Message 161 by Taq, posted 09-04-2012 1:14 PM zi ko has not replied

  
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