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Author Topic:   Is there really such a thing as a beneficial mutation?
Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 121 of 223 (343258)
08-25-2006 9:59 AM
Reply to: Message 120 by Percy
08-25-2006 9:54 AM


Re: Trade-offs
I myself have complained about the turn this thread took, and have blamed it on the way I ended up writing my OP. There is no denial involved. The thread started going back in the old direction and there seemed to be no way to rescue it and I just started answering people according to their arguments. If those arguments stop coming up, all will be well. If you have a way to rescue the thread, then do so.
However, my intention was not to understand how evolution views anything, but what science has to say about mutations.

This message is a reply to:
 Message 120 by Percy, posted 08-25-2006 9:54 AM Percy has replied

Replies to this message:
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nator
Member (Idle past 2169 days)
Posts: 12961
From: Ann Arbor
Joined: 12-09-2001


Message 122 of 223 (343259)
08-25-2006 10:02 AM
Reply to: Message 112 by Faith
08-25-2006 7:16 AM


Re: Trade-offs
quote:
But it is not anthropomorphizing anything to suspect that what is observed of what IS healthy could not possibly have come about by a system that pits disease against disease, and that calling that "beneficial" flies in the face of reason. Such a system is not a viable system even for survival let alone evolution.
Which is a more viable population;
One which is wiped out by malaria, or one that spans several continents and numbers in the millions?
Edited by schrafinator, : No reason given.

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ramoss
Member (Idle past 612 days)
Posts: 3228
Joined: 08-11-2004


Message 123 of 223 (343261)
08-25-2006 10:12 AM
Reply to: Message 116 by Faith
08-25-2006 8:24 AM


Re: Beneficial mutation
No, you are quite wrong on that.
The fossil evidence shows that the ear developed from the jaw bone of a dinosaur.
Here is a bit more information.
29+ Evidences for Macroevolution: Part 1

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nator
Member (Idle past 2169 days)
Posts: 12961
From: Ann Arbor
Joined: 12-09-2001


Message 124 of 223 (343262)
08-25-2006 10:13 AM
Reply to: Message 121 by Faith
08-25-2006 9:59 AM


Re: Trade-offs
quote:
However, my intention was not to understand how evolution views anything, but what science has to say about mutations.
Here's what science says about the CCR5 mutation.
What do you have to say about what science says about it?

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Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 125 of 223 (343263)
08-25-2006 10:16 AM
Reply to: Message 117 by Percy
08-25-2006 9:03 AM


Re: Trade-offs
Perhaps the confusion is related to the definition of beneficial. There's definitely a component of your approach to to thinking this that seems to be saying, "How could a mistake ever be beneficial? This is obviously impossible!"
A beneficial mutation is one that confers differential reproductive success upon the organism. Differential reproductive success means that the organism with the mutation is differently successful than other organisms without the mutation at producing offspring. If the mutation causes the organism to become better at producing offspring, then to a degree governed by the laws of genetics and the details of the organism's reproductive process its offspring inherit the mutation, and it spreads throughout the population because of the greater ability to produce offspring.
But if the mutation causes the organism to become less successful at producing offspring, then the mutation tends not to spread through the population because the organism produces less offspring than other individuals. In the worst case the mutation causes death before the organism reaches sexual maturity, the organism produces no offspring at all, and the mutation dies out in a single generation.
What's most important about a mutation is its effect on an organism's ability to produce offspring. If the mutation enables it to produce more offspring, then it is beneficial. If the mutation makes the organism less able to produce offspring, then it is harmful.
Another restatement of the evo definition. I understand it already. I've understood it all along. Let's get the thread off the creo-evo argument and this will not be a problem any more. As long as that argument is alive I'm going to continue to challenge this tunnel-visioned definition as simply obscuring the fact that evolution can't happen. Drop it now and let's get on with the actual science of mutations.
Another component to your approach to thinking about beneficial mutations seems related not to single mutations during single reproductive events, but multiple beneficial mutations over long periods of time and many reproductive events. But once you've accepted the possibility of a beneficial mutation in a single reproductive event, since the probability of a beneficial mutation is largely independent of past reproductive events, future reproductive events are about as likely to produce beneficial mutations as ones in the past. Just like a throw in dice of boxcars (6 on each of two die) does not affect the likelihood of the next throw being boxcars, a reproductive event resulting in a beneficial mutation does not affect the likelihood of another beneficial mutation in the next reproductive event.
I never said it did and I already answered your die analogy.
You have to be somehow dismissing the implications of the enormous preponderance of deleterious mutations and supposedly functionless mutations that simply snuff out alleles right and left to who-knows-what ultimate end.
I thought you said you were going to try and understand things this time. Where did you get the idea that functionless mutations snuff out alleles?
Perhaps a misunderstanding. I don't remember where. From something Crashfrog said I think. If false, then let it be corrected.
Yes, I know selection supposedly weeds all this out, but but that's just theory, not actual fact.
It's not fact, but it *is* theory supported by massive piles of evidence.
Let me reword it. I gave examples of how it doesn't appear that enough weeding is going on.
You're now denying a process that is so well established that students in biology programs observe this very process experimentally when they do their genetics labs. This is why people keep mentioning bacterial experiments to you. The bacterial experiments aren't popular because the process only happens in bacteria. They're popular because they can be done in less than a week. The same kind of reproductive errors and selection observed with bacteria are observed with other organisms, both in the lab and in the wild, but over much longer time periods.
I'm not sure what this proves. I've accepted the bacteria examples. I simply don't like the human examples. They aren't of the same sort of thing.
There's a lot of useless junk and various less-than-desirable mutations in all our genomes so obviously a lot didn't get weeded out.
I guarantee you that no one living in the world today possesses a fatal mutation that is dominant expressive. That's because they're filtered (selected against) very well. In other words, 100% of fatal mutations are filtered. Mutations that are less than 100% fatal or that have recessive qualities so they can easily hide in the genome are of course filtered to a lesser degree. But since they do not contribute positively to people's differential reproductive success and because they can, under conditions that cause them to be expressed, contribute negatively to differential reproductive success, they cannot help but be filtered to some degree from the population because the affected individuals produce fewer offspring.
I don't have a problem understanding this. I simply see it as a system that can't work for what it's supposed to account for. BUT I DO NOT WANT TO ARGUE THIS ANY MORE. In fact why are YOU arguing it since you want to get this thread back onto science?
Well, this is where I'd like to see a really comprehensive list of these so-called novel traits you have actually seen develop de novo that are viable or beneficial. I'm not impressed with the short list so far.
I've seen no indication that you've understood anything on the short list so far, though that hasn't stopped you from saying you're unimpressed and rejecting them. You seem to believe it's valid to conclude that that which you don't yet understand is false.
I understand it just fine. I don't see why you think I don't. I disagree with the role it is given to play in being the driving force of evolution. BUT AGAIN, if you really want to get this thread off this argument and onto a simple discussion of the scientific facts, then stop arguing this.
I suppose I should rewrite the OP because it is only going to invite more of same.

This message is a reply to:
 Message 117 by Percy, posted 08-25-2006 9:03 AM Percy has replied

Replies to this message:
 Message 131 by Percy, posted 08-25-2006 10:56 AM Faith has replied

  
Percy
Member
Posts: 22391
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


Message 126 of 223 (343264)
08-25-2006 10:22 AM
Reply to: Message 121 by Faith
08-25-2006 9:59 AM


Re: Trade-offs
Faith writes:
However, my intention was not to understand how evolution views anything, but what science has to say about mutations.
You've drawn a distinction without any meaning. The field of science that deals with mutations is genetics, which is part of the modern synthesis of evolutionary theory. Evolution *is* science, so science and evolution will say the same thing about mutations.
--Percy

This message is a reply to:
 Message 121 by Faith, posted 08-25-2006 9:59 AM Faith has replied

Replies to this message:
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Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 127 of 223 (343265)
08-25-2006 10:24 AM
Reply to: Message 126 by Percy
08-25-2006 10:22 AM


Re: Trade-offs
Science is phenomena, is facts. Evolution is theory, is interpretation.

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Aegist
Member (Idle past 3699 days)
Posts: 23
From: Sydney NSW Australia
Joined: 08-21-2006


Message 128 of 223 (343268)
08-25-2006 10:30 AM
Reply to: Message 119 by Faith
08-25-2006 9:14 AM


Re: Trade-offs
I just want to take a moment to show my respect to Fatih. Never before have I seen someone who clearly doesn't believe in Evolution seriously trying to come to understand the science around it. Honestly, I am impressed with your efforts, and I will do my best to understand where you are coming from and sort out the differences.
Faith said:
Traits are simply the selected product of the variety of alleles already present in a population, which were designed into the creature, not created by mutation.
So I was not talking about traits, but only about the supposedly beneficial mutations that are currently claimed to have been observed, more than one of which is like the Sickle Cell genetic disease which is strongly selected because of its protection against malaria.
OK, I am trying to work from your point of view, and hopefully I understand what you are trying to establish. We are assuming that all species have been created as they are. Lets suppose for the sake of argument that the Earth was created by the Magratheans 1000 years ago ala Hitch Hikers Guide to the galaxy. They created humans and all other species with a degree of variety there so that sexual reproduction could continue to mix alleles and continue to maintain variety in the species.
Have any mutations created new improvements in humans since that time?
Would this premise and question be somewhat in line with what you are trying to understand?
I need to understand exactly what you want to be shown. I am from a Molecular Biology background, so the mechanisms of mutation and the affects on the DNA -> Protein -> Phenotype process arising from a mutation is rather familiar to me. However it is very difficutl for me to name a "Beneficial Mutation" to you which is 1. In humans, 2. Not related to a disease 3. Not only beneficial given specific circumstances. If you want those criteria then the only beneficial mutations possible are ones which we simply can't detect and ones which you can easily argue as "Pre-existing traits" and hence not mutations.
This last point is really the catch 22. Anything which has happened could be argued as a pre-existing trait which has been repressed or ressesive until now. And anything which hasn't happened we can't assume will happen. And thus, we have no examples of beneficial mutations in humans.
I hope you can see how restrictive this criteria would be, and I hope you don't intentionally impose it. Particularly since this thread was supposed to be about whether any mutation could be beneficial.
Also, this article looked to be of interest
When more is less: Study into Human Genome vs Chimpanzee genome. Loss of function = improvement
http://biology.plosjournals.org/perlserv/?request=get-doc...

----------------------------------
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http://www.sportsarbitrageguide.com

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 Message 119 by Faith, posted 08-25-2006 9:14 AM Faith has replied

Replies to this message:
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RickJB
Member (Idle past 4990 days)
Posts: 917
From: London, UK
Joined: 04-14-2006


Message 129 of 223 (343275)
08-25-2006 10:44 AM
Reply to: Message 127 by Faith
08-25-2006 10:24 AM


Re: Trade-offs
faith writes:
Science is phenomena, is facts. Evolution is theory, is interpretation.
How long have you been posting here, Faith? Again and again the same old "not a fact but a theory" canard.
ALL science is based on theories that are used to explain observed facts. Evolution IS science. The fact that you think otherwise is of absolutely no consequence.
Edited by RickJB, : No reason given.

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 Message 127 by Faith, posted 08-25-2006 10:24 AM Faith has replied

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Brad McFall
Member (Idle past 5032 days)
Posts: 3428
From: Ithaca,NY, USA
Joined: 12-20-2001


Message 130 of 223 (343278)
08-25-2006 10:55 AM
Reply to: Message 126 by Percy
08-25-2006 10:22 AM


Re: Trade-remarks
There can be ignorance of science that is different than ignoring how the so-called modern synthesis contains structurally mutations as a part of genetics.
quote:
Kant "Introduction to Logic"
It seems simply the lack of the genetic measure of the general science information collected from various divisions possible of "mutations" in the QUALITATIVE nature of the mutations (?qualia?)
(which also according to Kant can not have an intuition (as read by me)(hence why I considered it more probable to have a intution of body plans rather than organs interthread alia)) is responsible (Gould supplied a conceptual nexus to think this)because it is hard to find the inutition for adventious tissue between two nodes on a stem for instance (cellulose just in case
sense was had)where Kant was want to write out the Newton of a "blade of grass" IN A JUDGMENT.
Is this a mutation?
Is it benefical??

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Percy
Member
Posts: 22391
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


Message 131 of 223 (343280)
08-25-2006 10:56 AM
Reply to: Message 125 by Faith
08-25-2006 10:16 AM


Re: Trade-offs
Faith writes:
Another restatement of the evo definition [of beneficial mutations]. I understand it already. I've understood it all along. Let's get the thread off the creo-evo argument and this will not be a problem any more. As long as that argument is alive I'm going to continue to challenge this tunnel-visioned definition as simply obscuring the fact that evolution can't happen. Drop it now and let's get on with the actual science of mutations.
This is a dismissal, not a continuation of a discussion. Understanding what a beneficial mutation is fundamental to having sufficient common ground for a meaningful discussion to take place. Understanding this is fundamental to pursuing the topic of this thread, which is whether there is any such thing as a beneficial mutation.
So if you understand the explanation I provided (and you claim you do), and if you don't accept it, then the next step is to explain why. By explaining why, I mean by referencing parts of the explanation about beneficial mutations, and not by dismissals like references to "this tunnel-visioned definition" and statements like "evolution can't happen."
I never said it did [past random events affecting the likelihood of future random events] and I already answered your die analogy.
The only thing my argument using the dice had in common with my earlier argument using a die is dice. They were two completely different arguments. The early one made a point that the effect of random events on something cannot be considered some inherent part of the original objects. It was made in reply to your argument that mutations should be considered part of the original genome.
This time I used dice for a completely different argument, that random events are independent. You say you don't dispute this. Good.
But you ignored the rest of the argument, that part of the reason you don't accept the possibility of beneficial mutations is because you don't believe a chain of them is possible. Did I get that wrong? Do you accept that a beneficial mutation occurring in one generation does not affect the possibility of a beneficial mutation occurring in the next generation?
Perhaps a misunderstanding. I don't remember where. From something Crashfrog said I think. If false, then let it be corrected.
That's what we're trying to remedy, remember? Your misunderstandings? A mutation cannot "snuff out" alleles. One organism of a population losing an allele because of a mutation that transforms it to a new allele cannot affect all the other individuals in the population that possess the old allele.
But it can happen over time that a new allele out competes other alleles of the same gene, even to the point of extinction for those alleles. This involves differential reproductive success and selection. If the new allele allows organisms possessing it to produce more offspring and more competitive offspring, then it could actually, over time, "snuff out" some other alleles.
Let me reword it. I gave examples of how it doesn't appear that enough weeding is going on.
I think your only example was human beings, and I agreed with you. The comforts of modern civilization and the benefits of modern medicine insulate us from traditional selection factors. But if WW-III sends us back to the stone age then you'll see plenty of selection going on.
I'm not sure what this proves. I've accepted the bacteria examples. I simply don't like the human examples. They aren't of the same sort of thing.
But they are "of the same sort of thing". The time scales are longer and the reproduction is sexual, but it is still mutations and selection. If you don't think it is "of the same sort of thing", then you have to explain why.
I simply see it as a system that can't work for what it's supposed to account for. BUT I DO NOT WANT TO ARGUE THIS ANY MORE. In fact why are YOU arguing it since you want to get this thread back onto science?
This *is* science, Faith. Evolution *is* science. And if I've been sufficiently careful, then most of this post is about the topic of this thread, beneficial mutations. If you don't want to talk about beneficial mutations, then don't reply.
I understand it [the examples of beneficial mutations] just fine.
No, I don't think you do. I think you're just claiming that you do so you won't have to face them anymore. If you understood them then you'd be able to explain, at a technical level, why you don't accept that, for example, the wisdom tooth mutation is beneficial, something you have yet to do.
--Percy

This message is a reply to:
 Message 125 by Faith, posted 08-25-2006 10:16 AM Faith has replied

Replies to this message:
 Message 134 by Faith, posted 08-25-2006 11:07 AM Percy has replied
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Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 132 of 223 (343281)
08-25-2006 10:57 AM
Reply to: Message 129 by RickJB
08-25-2006 10:44 AM


Re: Trade-offs
How long have YOU been posting here? The same old canard about how the theory of evolution IS science. Fine, it's science the way any working interpretation of the data is science in some sense. The ToE is under debate here, remember? This habit of treating the ToE as the open and shut explanation of the data is offensive in this context. The scientific facts are open to other interpretations and keeping some degree of an open mind about that is what SHOULD be going on here.

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Aegist
Member (Idle past 3699 days)
Posts: 23
From: Sydney NSW Australia
Joined: 08-21-2006


Message 133 of 223 (343282)
08-25-2006 10:58 AM
Reply to: Message 121 by Faith
08-25-2006 9:59 AM


Re: Trade-offs
I spent probably over an hour on my last post (mostly surfing looking for examples, so sorry it was a little late and much has been said in between.
However, my intention was not to understand how evolution views anything, but what science has to say about mutations
Oh, well in that case, let me tell you all about mutations.
There are MANY types of mutations, and MANY causes of mutation. Attempted to list all of the causes of mutations would be futile, but breifly some of the more obvious causes are errors during copying and no correction, radiation, retroviral insertion, transposon insertion or removal, recombination and oxidative damage.
Much more interestingly are the TYPES of mutations. I think the Wikipedia entry covers it sufficiently well. Mutation - Wikipedia
Read that entry, and read any of the entries that are linked from terms you don't understand.
When you understand exactly what mutations are, you can see it is simply a changing of genetic material. Changing a base pair, inverting a sequence, moving a sequence, deleting a sequence, adding a sequence, copying a sequence.... Shuffling DNA in one form or another. Since DNA is directly translated into proteins, and proteins tend to have functions in cells and directly or inadvertantrly affect phenotypes, it is obviously possible for mutations to have beneficial outcomes.

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This message is a reply to:
 Message 121 by Faith, posted 08-25-2006 9:59 AM Faith has replied

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Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 134 of 223 (343289)
08-25-2006 11:07 AM
Reply to: Message 131 by Percy
08-25-2006 10:56 AM


Re: Trade-offs
No, I don't think you do. I think you're just claiming that you do so you won't have to face them anymore. If you understood them then you'd be able to explain, at a technical level, why you don't accept that, for example, the wisdom tooth mutation is beneficial, something you have yet to do.
For crying out loud, Percy, do you regard the explanations of its supposed benefits that have been put forward here as being on a TECHNICAL level? You mean those wild imaginative hypotheses about how it is good for small jaws, and because they get impacted a lot and so on?
What sort of technical answer could there be to that anyway? I'm sure there are lots of things we can do without that once had a function. The appendix probably once had a function. We probably had all kinds of disease protections we no longer have. How could I guess the probable role of wisdom teeth in our ancestry? Just because losing them is no felt loss now, and in some cases (how many? Nobody has said) may be a relief from crowded teeth and other ills, doesn't mean it isn't REALLY a deleterious mutation, perhaps accommodating to who-knows-how-many previous losses by mutation. Is that technical enough for you? It's at least equivalent to the imaginative ideas about how it's a benefit.
{edit: OK, here's my theory. It's not evo theory for sure. EVEN IF it spreads in the population, by my theory it may still be deleterious. Evo theory DEFINES it as beneficial if it spreads in the population, but this is why the definition is a problem. That's how you get the definition of sickle cells as a beneficial mutation. The loss of wisdom teeth may be positive in relation to previous deleterious mutations that brought about the smaller jaw perhaps. Evolution theory doesn't care. Evolution theory is optimistic about everything that gets spread in the population. That's supposedly how evolution came about. But what if Biblical creationism is true instead? Then everything is deteriorating, human beings are deteriorating, and we may get adaptations TO our deteriorated condition but the overall effect is still deterioration. This is why the nicely streamlined evolutionist definition of survival and propagation of a trait just doesn't cut it. It hides the possibility that devolution may be in fact what is happening.
Edited by Faith, : No reason given.

This message is a reply to:
 Message 131 by Percy, posted 08-25-2006 10:56 AM Percy has replied

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Jazzns
Member (Idle past 3911 days)
Posts: 2657
From: A Better America
Joined: 07-23-2004


Message 135 of 223 (343291)
08-25-2006 11:12 AM
Reply to: Message 78 by Faith
08-24-2006 7:42 PM


Evolutionary constraints
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.
Well I HAVE seen it. It is par for the course for these types of discussion. In fact in this very thread MJ was asking for the very thing you claim is a straw man. He wanted a recent example of a mutation that changed the body plan of an organism.
I am coming from the perspective of having both read and participated in many of these discussion about beneficial mutations and the one area where most creationists fail at is simply the basic understanding that evolution is about co-option.
The best analogy I can think of is that evolution is like water trickling down a hill. The only place the water can go is dependent on where it has been.
I am not saying that you DONT get this. I know MJ was having a hard time with it. I was just simply trying to get this POTENTIAL confusion out of the way from the beginning because I have seen it destroy good conversations about beneficial mutations.

Of course, biblical creationists are committed to belief in God's written Word, the Bible, which forbids bearing false witness; --AIG (lest they forget)

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