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Author Topic:   Is there really such a thing as a beneficial mutation?
Faith 
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From: Nevada, USA
Joined: 10-06-2001


Message 1 of 223 (342855)
08-23-2006 9:07 PM


On the thread Natural Limitation to Evolutionary Processes, discussion came up at the end about the nature of mutations and I would like this thread to be all about mutations.
In trying to write this PNT I think I've figured out that there are two main areas of questions I have.
I hope the questions are clear. I will discuss them a bit below.
Since I always get in trouble on science threads and there is no place for this topic to be BUT a science thread I hope I can keep my participation to the role of asking questions.
For starters:
The definition of Mutation at Wikipedia
Mutations are considered the driving force of evolution, where less favorable (or deleterious) mutations are removed from the gene pool by natural selection, while more favorable (beneficial or advantageous) ones tend to accumulate. Neutral mutations are defined as mutations whose effects do not influence the fitness of either the species or the individuals who make up the species. These can accumulate over time. The overwhelming majority of mutations have no significant effect, since DNA repair is able to revert most changes before they become permanent mutations, and many organisms have mechanisms for eliminating otherwise permanently mutated somatic cells.
This definition is clear: Mutations are the DRIVING FORCE OF EVOLUTION.
Here is another definition:
In the living cell, DNA undergoes frequent chemical change, especially when it is being replicated (in S phase of the eukaryotic cell cycle). Most of these changes are quickly repaired. Those that are not result in a mutation. Thus, mutation is a failure of DNA repair.
Mutations are a failure of some sort, or a mistake.
So, mutations are both the driving force of evolution AND mistakes.
A number of posts on the old thread Natural Limitation to Evolutionary Processes might be relevant or at least give context from the earlier discussion:
======================================
Percy's 295 and some earlier ones of his I didn't track down, around the 180s. In this post he is mainly complaining about my failure to grasp certain things, and I suppose that will come up here too. I would only like to answer one point: I KNOW that there are no proteins in DNA; the proteins are "coded for" by the sequences of chemicals on the DNA, and I don't know how I gave a different impression but I suppose my language was ambiguous.
======================================
Crash's 296 in which he explains what a gene is. In the process he confirms that pseudogenes are formerly functioning genes, and I think I at least should refer back to this post for orientation from time to time, and maybe his #170 too. He is very good at giving homely analogies to make a point. His 170 got a deserved POTM for its clarity, another one to check out.
======================================
Wounded's 279 about the Solid Gold mutant ram, in which he is showing me that I'm wrong about my guess that this may merely be a variation thrown up from low-frequency alleles in the population. He describes its mosaicism, or the fact that the mutation only shows up in some of the somatic cells. This is a whole area I have hardly any understanding of, and Crash also said, I think in his post #170, that all of us get both our parents' alleles in different cells throughout our bodies -- if I got that right. I thought all our cells were some kind of package of both that defines us. But maybe I have this wrong and I'm not sure how relevant it is to this PNT anyway, but the mutant ram is certainly an interesting case of an apparently beneficial mutation.
======================================
Nosy's 277 He says:
But this is exactly what mutations are. They are changes that produce novel sequences. One may label them mistakes if we think that the gene reproducing process MUST produce perfect copies. It is clear that this would be a VERY BAD thing. These "mistakes" are what makes it possible for ongoing populations of organisms to deal with environmental changes (of all types).
And I'll take off from Nosy's comments into my main concerns about mutations for the purposes of this thread:
BENEFICIAL MUTATIONS?
From the point of view of the ToE, which is that mutations are its driving force, the origin of everything living, of course it must be true that these mistakes are essential, and perfect replication would be a disaster, as Nosy says.
But if the ToE is NOT true, then mutations really probably are mistakes, whose supposed benefits are an illusion, and really simply evidence of the gradual deterioration of all life since the Fall. In this case the fact that most of them have no effect at all just underscores the gradualness of the deterioration process, and the occasional apparently beneficial mutation is a mere anomaly that occurs in the nature of the chemistry involved.
The examples so far given on that thread of supposedly beneficial mutations are to my mind highly questionable.
But of course I was taken to task for my definition of "beneficial" which is too strict apparently as I can't accept most of the examples given as beneficial.
I dunno. We're talking about THE supposed "driving force" of evolution, the system that brought us the eye and the hand and the human brain and in fact the whole stupefyingly elegant system of genetic coding -- it makes your jaw drop to begin to appreciate the mathematical precision involved in the coding process that creates proteins that actually do things in the cells of living things that make all functions possible -- except for those "mistakes" of course. So I have a hard time accepting that whatever produced the incredible coordinated functions and variations of living things has to resort to such trade-offs in dealing with disease, or explaining how so many genetic diseases keep occurring, if the ToE is correct, and evolution really is the amazing system that brought about all the amazing perfections that are obvious despite the errors.
OK, that's my view of the examples of supposed beneficial mutations.
POSSIBLE NON-MISTAKE MUTATION? (as per YEC assumptions as opposed to ToE assumptions I mean)
But there is this other question about mutations for a creationist who believes in the Biblical Flood. What sort of genetic situation could conceivably account for the development of all the observed variation in living things from the few individuals of each Kind that were on the Ark?
ON the old thread I think it was Percy but I may be misremembering, maybe it was Wounded, who said that even if mutations are predictable they are still random the way the six sides of a die come up randomly and yet there are only those six possibilities. My answer to that is that genetic variation is random in THAT sense anyway, as in the linking up of various possible alleles from a large array in the population, and from the options in the combining of germ cells from two parents.
So it is still a possibility in my mind that there is a method to the madness of SOME so-called "mutations" that is really part of the normal reproductive system rather than merely a mistake and could somehow be part of the explanation for (micro) evolution since the ark.
All this could easily get bogged down in context because of the different basic assumptions, the ToE vs YEC, or simply because genetics is too complex and the varieties of mutations complex enough to choke a dinosaur let alone get digested by the likes of me.
So, I hope it is possible to make a thread out of this stuff.
Edited by Faith, : No reason given.
Edited by Faith, : Various organizational changes, titles, lists etc.
Edited by Faith, : Made another list

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Faith 
Suspended Member (Idle past 1557 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 12 of 223 (342944)
08-24-2006 10:32 AM


Sorry, I got busy for a bit
Just so you all know, I'm watching this thread and Wounded's thread on mutation, but I have other things demanding my attention right now, AND the threads are picking up quite a bit of extraneous stuff to sort through later when I have more time. These threads could take quite a bit of commitment.
Thanks to Frog, though, yes, that's the basic idea I have in mind.
Edited by Faith, : No reason given.

  
Faith 
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From: Nevada, USA
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Message 14 of 223 (342959)
08-24-2006 11:34 AM
Reply to: Message 13 by ikabod
08-24-2006 11:27 AM


I think we creationists understand that quite well, that is, we understand that evolution is blind, not purposeful, has no interest in WHAT survives and propagates, only that it does.
But this is precisely what we are questioning, that such a system could produce the amazing stuff of life that we see all around us, that a system which only produces degrees of disease and deformity could ever have come up with the functioning precision and elegance in so many living things, most of which functions without the compromises and trade-offs accepted as beneficial mutations.
It would help if it were understood that we don't have a problem understanding the definitions, we are questioning that any system that operated by such principles could produce any of what actually exists, let alone provide the material for future useful changes.
Yes, I get it, I get it, all of you who are giving examples of how it supposedly works. I get that mutations do happen that have a beneficial function although they also have destructive properties.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.

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Faith 
Suspended Member (Idle past 1557 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 17 of 223 (342969)
08-24-2006 12:00 PM
Reply to: Message 15 by Wounded King
08-24-2006 11:51 AM


This seems to suggest that any beneficial mutation must also have a downside, there is no reason this need be the case. In fact this seems to be rather jumping the gun and making what should be what you are trying to show into one of your initial assumptions.
Really, no, I simply have not seen any convincing evidence yet.
The process of mutation can produce both beneficial and detrimental mutations, and which is which may depend on the environmental context.
Again, this is definitional, and again it is very hard to see how such a principle could produce what is actually observed of living things. I understand that such a process is very difficult to prove or provide evidence for, but it is so far only a definition, or working hypothesis if you prefer -- and the evidence for its ability to drive evolution is really just not there for whatever reason.
The concept of 'destructive properties' is not a biological one and seems wrapped up in this creationist view of organisms as having some sort of platonically ideal complement of genes from which any change can only be downhill.
Don't get too hung up on my terminology; I'm always reaching for terms to convey what I have in mind, there's nothing hard and fast about them. I consider the creationist view to be a working hypothesis. We all have those, nothing wrong with that.

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Faith 
Suspended Member (Idle past 1557 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 19 of 223 (342971)
08-24-2006 12:06 PM
Reply to: Message 18 by Archer Opteryx
08-24-2006 12:02 PM


Re: Beneficial mutation
Your 'questioning' is an argument from incredulity.
Questioning is what one does about a theory that isn't making sense. Dismissing it as an argument from incredulity is just a convenient way of ignoring that it is in fact a reasonable objection to the principle.
Your counterproposal is aesthetic (elegance), not scientific (research).
That is not a counterproposal, it is an observation that brings the definition of evolution into doubt. "Elegance" as in "elegance of function" or "the elegant mathematical precision of the way the DNA chemistry works" is not so easily dismissed as *mere* aesthetics. It describes something that exists, that had to come about by evolution if evolution is true, but appears to be something evolution couldn't have brought about even by accident.
I do get that mutations do happen that have a beneficial function
Progress.
I'm simply getting around to protesting that I get it, it's not a new thing that I get it. I got it from the beginning, but every time I raise a question about its efficacy I'm accused of not getting it. I get it already.
Edited by Faith, : No reason given.

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Faith 
Suspended Member (Idle past 1557 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 21 of 223 (342978)
08-24-2006 12:21 PM
Reply to: Message 20 by crashfrog
08-24-2006 12:06 PM


Well, those are some good answers there. I'll have to think about them.

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Faith 
Suspended Member (Idle past 1557 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 25 of 223 (342994)
08-24-2006 1:27 PM
Reply to: Message 23 by Wounded King
08-24-2006 12:31 PM


If you do 'get' the idea of mutation and evolution then you would not expect to see experimentally observed examples of the evolution of the sorts of complex traits which take great spans of time to evolve. What we might expect to see with the resources we have available we do see.
Yes, I understand that it's a practical problem, and I don't expect it, I'm simply spelling out what I see as some implications of the basic principle.
However, I think this is going to take the thread in a wrong direction in which we just exchange opinions that can't be supported, so I'll try to get back to the strictly scientific points.

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Faith 
Suspended Member (Idle past 1557 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 74 of 223 (343109)
08-24-2006 7:18 PM
Reply to: Message 73 by Jazzns
08-24-2006 7:06 PM


Re: Trying to steer the past sub-thread back on topic
... seems that in order for a creationist to agree that a mutation is "beneficial" that is must do something drastic...
My reasoning is simply that it seems that good examples of beneficial mutations are being overlooked for this pie-in-the-sky expectation of lizard evolving before our eyes.
Yes, you were saying that early on, and WK said something similar, but it certainly does not characterize anything I said or believe. It seems to be something you think you get from what I've said but I don't see how. Really a confusing straw man I'd say.
This thread seems to have gone very wrong while I've been busy and I'm still busy and may not get back to it for a day or so. Too bad.
{edit:
All I wanted to point out is that any creationists wanting to discuss if a mutation is beneficial may need to adjust their expectations to what the ToE actually says is possible.
This is ridiculous. In other words you are saying we have to accept evolution, period.
No, what you mean is not what EVOLUTION says is possible but what SCIENCE says is possible. And I for one am responding to that when I question that what science says is possible could actually produce the changes over billennia that evolved everything living, or in other words question the evolutionist idea of a beneficial mutation.
However, I think it's too easy for this thread to wander too many places. I hope we can drop this particular line of thought for now and just focus down on the particulars of the claims about what a beneficial mutation is}
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.

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Faith 
Suspended Member (Idle past 1557 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 78 of 223 (343120)
08-24-2006 7:42 PM
Reply to: Message 77 by Jazzns
08-24-2006 7:37 PM


Re: Trying to steer the past sub-thread back on topic
Faith, please do not jump to conclusions. Please take what I said in context. It is silly to attempt to discredit a beneficial mutation by referencing the oft straw-man character of evolution based on the hopeful monster. That is all I am saying.
But your accusation that we are discrediting beneficial mutation by this hopeful monster idea is false. I am not doing that and I haven't seen anyone else doing that. I believe this is a misreading on your part, and it amounts to a very confusing straw man misrepresentation of our argument.
No one is saying that you have to accept evolution. What I am simply pointing out is that you shouldn't use a false characture of evolution to define what is and is not considered beneficial or the mechanism for change within evolution.
Again this is your misreading. I absolutely do not recognize it and do not know where you are getting it.

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Faith 
Suspended Member (Idle past 1557 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 80 of 223 (343126)
08-24-2006 7:47 PM
Reply to: Message 76 by Wounded King
08-24-2006 7:35 PM


Re: Trying to steer the past sub-thread back on topic
It isn't that you have to accept evolution per se but that you should accept evolutionary theories own estimations as to what could reasonably be expected to be experimentally observed arising in terms of mutation in line with that theory. This is in contrast to just picking your own arbitrary standard for what constitutes a beneficial mutation and insisting that evolutionary theory toes the line if it is to be credible.
I know my OP invited this discussion but now I'm rather regretting it because I think we need to cover a lot more examples of supposed beneficial mutations first.
However, nobody is picking some arbitary standard. I am actually THINKING ABOUT "what could reasonably be expected to be experimentally observed arising in terms of mutation in line with that theory" and finding it very questionable that such phenomena could be the driving force of evolution. If most mutations are of this form of compromises or tradeoffs between something useful in the prevention of disease with some other form of disease, that's like saying you ought to be able to run a car on gasoline mixed with water.
I think it's a logical train of thought.
But I also would rather drop it at this point if that is possible, and try to focus down on the particulars of what beneficial mutations are claimed to be.
Edited by Faith, : No reason given.

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Faith 
Suspended Member (Idle past 1557 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 84 of 223 (343130)
08-24-2006 8:14 PM
Reply to: Message 79 by NosyNed
08-24-2006 7:45 PM


Re: What is possible...
Then perhaps you should point out just what changes are too great to have arisen this way.
What do you mean "too great?" I don't even see how you can get a viable population from Sickle Cell despite its protection against malaria, myself, for such a disease-ridden population to change further, let alone float the whole history of evolution. Sure if malaria leaves the environment then the sickle cell factor will become less frequent in the population. In other words you have to get rid of it to have a healthy population. How is that anything that could possibly further evolution? Shouldn't a "beneficial" mutation be something you can see being built upon by future beneficial mutations? If you have to get rid of it you're back to square one, you haven't taken one mutational step toward anything you could call evolution. Now if malaria remains and sickle cell remains you are going to have forever this population that is prone to die young. I GUESS this can go on indefinitely, but what kind of model is that for evolution that supposedly brought about all the HEALTHY stuff in living forms?
ABE
What you miss is the nature of the real differences. You see the external form of life but it is driven by chemical changes that are what mutations are. We have found out how some, comparitively, very small chemical changes can produce large external changes.
The subject is BENEFICIAL changes. Honestly, I have no problem with the principle of mutations in general. But the supposedly beneficial ones are a sad lot, at least the ones offered up for humans. Nothing could survive a million years of that kind of change. All life would have been extinct in a few millennia of such stuff.
Untill you understand all of that you will remain incredulous. It is astonishing! It is also real.
You balk at our being related to unicellular life. How far are we from "rats" and how far are they from a worm?
From rats to worms was 10 times a long as from rats to us. From rats to us was 10 times as long as from our common ape ancestor to us.
And the changes, chemically from worms to rats to primates to us are not so great over those times. We share a lot.
Honestly, none of my thinking has anything to do with objecting to being related to anything. What you explain as relatedness I explain as similar design. I think it's at least as viable an explanation. At least. There is no amount of time that is going to make evolution work by a system that produces disease in the process of curing disease.
You suffer from a focus on the external forms that you see. The real changes that mutations introduce are chemical. We have learned how small, comparitively small, changes there can produce profound changes in the body of an animal.
Until you understand all this you will remain incredulous. It is astonishing! It is also real.
You mean until I accept it. I understand it just fine.
I think what is needed here is a more comprehensive idea of what is accepted as a beneficial mutation in humans, some discussion of the beneficial mutations of the sort Crashfrog brought up, the one that prevents cholesterolemia for instance.

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Faith 
Suspended Member (Idle past 1557 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 85 of 223 (343136)
08-24-2006 8:34 PM
Reply to: Message 81 by Archer Opteryx
08-24-2006 8:00 PM


nylon eating bacteria
True, I'm convinced of what I'm convinced of, but don't accuse me of dishonesty -- and that's against forum guidelines too.
Aren't you the one who said you think the bacteria that eat nylon is proof enough of beneficial mutations?
I'd like to see some discussion of the nature of this population of bacteria.
Question: Are they different in any OTHER ways from those they were selected from?

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Faith 
Suspended Member (Idle past 1557 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 89 of 223 (343158)
08-24-2006 10:40 PM


You are all repeating yourselves, saying nothing I don't already know.
Perhaps this thread is dead already.

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Faith 
Suspended Member (Idle past 1557 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 91 of 223 (343176)
08-25-2006 12:45 AM
Reply to: Message 90 by Aegist
08-25-2006 12:26 AM


Seems to me that this thread is dead because your question has been answered several times over more than sufficiently. Yet every example that is given isn't the one you want to hear....
... Either way, because it is conceivable of a situation in which it would be beneficial, it is therefore a fact that beneficial mutations exist.
Obviously there is no way to discuss this, and I really don't enjoy the attitude, not that yours is particularly bad.
Perhaps we can turn this thread in another direction?

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Faith 
Suspended Member (Idle past 1557 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 93 of 223 (343183)
08-25-2006 1:13 AM
Reply to: Message 92 by Aegist
08-25-2006 12:57 AM


What is the thrill in being the tenth or twelfth evolutionist to pile on the one or two creationists, just expounding variations on the same old thing? What do you get out of it? I got the message a long time ago. I have my own opinion nevertheless, and I'm very tired of arguing it. You don't like my opinion, you don't want to consider it, you just want to bash it. You are determined to tar me as stupid. What's the thrill? Give it up. The whole lot of you.
Edited by Faith, : No reason given.

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