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Author Topic:   The origin of new genes
Faith 
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Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 3 of 164 (351220)
09-22-2006 4:28 AM
Reply to: Message 1 by bernd
09-21-2006 5:32 PM


Nobody has doubted that new alleles, genes, are formed by mutation FROM TIME TO TIME. At least in bacteria and perhaps fruit flies this has been shown. It has NOT been actually demonstrated in mammals which is where most of the discussion is. All the mechanisms you have listed may in fact bring about a new gene / allele, but at what rate? How often is it useful or does it actually contribute to variation? Considering how many alleles already exist in most populations of sexually reproducing animalia how on earth would you know if the occasional mutation contributed anything whatever to the processes that lead to variation, as opposed to the usual shuffling of gene frequencies among those already in existence?

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Faith 
Suspended Member (Idle past 1466 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 7 of 164 (351311)
09-22-2006 1:10 PM
Reply to: Message 6 by sidelined
09-22-2006 12:40 PM


Nobody has doubted that new alleles, genes, are formed by mutation FROM TIME TO TIME. At least in bacteria and perhaps fruit flies this has been shown. It has NOT been actually demonstrated in mammals which is where most of the discussion is
You must be living in the dark ages. You are aware that cancer is caused by mutations don't you? Being that it is the second leading cause of death in human mammalsthen we can hardly state that it has not been demonstrated to be shown. It is not merely shown it is demonstratably widespread.
Oh yes, I certainly know that DISEASES are caused by mutations. Diseases and deformities and miseries galore are caused by mutations. This is one of the reasons why mutations hardly seem like an engine that could power life at all.
Again, of course mutations OCCUR, the doubt is whether they could possibly do what the ToE requires them to do, and I have not seen any actual facts that demonstrate that they could or do, merely speculations and assumptions.

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Faith 
Suspended Member (Idle past 1466 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 8 of 164 (351313)
09-22-2006 1:16 PM
Reply to: Message 4 by NosyNed
09-22-2006 4:40 AM


Re: Rate of Mutation
There have been specific studies referenced which show that there are billions of mutations in the human gene pool in each generation. Billions with a "B".
You have ignored what you've been told.
Oh I have not ignored this at all. It is part of my argument that mutations can't do what the ToE requires them to do. I don't know that "billions" of mutations have been "shown" to exist in the human gene pool, since claims about mutations are often asserted but rarely actually demonstrated, but perhaps there are that many; I know there are a lot. However, most of them wipe out useful alleles apparently, since they have no function, or bring about disease, and some minuscule number can said VERY IFFILY to confer a benefit, usually in exchange for a downside. Not the sort of mechanism that could power evolution.
Edited by Faith, : No reason given.

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Faith 
Suspended Member (Idle past 1466 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 11 of 164 (351374)
09-22-2006 3:31 PM
Reply to: Message 9 by Dr Adequate
09-22-2006 1:34 PM


One nice example of a beneficial mutation in mammals is the origin of "three-color vision" in Old World primates, which involved duplication of a gene followed by mutation of one of the copies.
I would really like to know how you think you KNOW that a mutation was involved. This is all typical speculative thinking. I can't look at the link because my computer doesn't like switching websites these days, and it's probably more time-consuming technicalities than I'm up for anyway, which I'd appreciate your explaining in your own words.
Hence, whereas most mammals see only in "two-color" vision, with "red" and "blue" receptors, we and our cousins also have a "green" receptor which is almost, but not quite, identical to the "red" one.
Design differences explain this just fine; no need to postulate mutation from one to the other.
Interestingly, reptiles see in seven colors (imagine how expensive a TV would be if you were a lizard). But the primitive mammal-like reptiles, you wil recall, were nocturnal, and developed rods at the expense of cones.
Design difference explain all this just fine; no need to postulate mutation from one to another.
For our diurnal fruit-eating ancestors, however, the ability to tell red from green is clearly an adaptive trait.
Design, etc.
Here's a paper on the genetics of vision in primates.
Please explain briefly and clearly in your own words how mutation is *known* to have anything to do with these differences between creatures. Thank you.

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Faith 
Suspended Member (Idle past 1466 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 13 of 164 (351393)
09-22-2006 4:31 PM
Reply to: Message 12 by bernd
09-22-2006 4:28 PM


I cannot read links right now.

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Faith 
Suspended Member (Idle past 1466 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 20 of 164 (351512)
09-23-2006 12:15 AM
Reply to: Message 19 by sidelined
09-22-2006 10:39 PM


I do not understand what you assume TOE requires them to do. If you understand that mutations can occur that are detrimental to macroevolution why do you seem to misunderstand that it is to be expected that detrimental effects outway beneficial ones? Since a complex organization of cells {which is what animals are} requires conditions to be met it should be obvious that there are more ways in which things can go "wrong "in the development of living animals than there are ways for it to go "right".
What you don't get is that this kind of thinking is nothing but ingenious rationalization. There isn't a fact in the whole thing.
If the animal has an advantage provided by a mutation that produces , say, a longer stride capabilty in an animal that is prey for another, then it is obvious that this particular animal would be more likely to live and reproduce.
If if if. That's all true except the part about mutation being the cause of the advantageous variation, which is purely speculation. Many advantageous variations are selected but their SOURCE is what is in doubt.
Now ,since we can examine the animal genome and determine that,yes, certain genes express different characteristics such as stride length through longer leg bones that in turn are selected by the enviroment we can see that mutations such as this are indeed beneficial.
BUT NOBODY IS DENYING THAT THIS SORT OF SELECTION OCCURS. It's the SOURCE of these variations we are questioning. You do not know that these are MUTATIONS as opposed to normally occurring alleles.
What exactly is it about TOE that fails to account for life as it is?
It's all theory, all speculative guesswork! Why don't you see that? You can't actually prove those are mutations, track those supposed mutations to their origin point that you credit with bringing about all this change, you are simply ASSUMING they do so. You don't know if they are mutations, something novel, or simply a normally occurring allele that got selected in the recombination lottery.
Edited by Faith, : No reason given.

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Faith 
Suspended Member (Idle past 1466 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 21 of 164 (351513)
09-23-2006 12:19 AM
Reply to: Message 16 by Dr Adequate
09-22-2006 7:35 PM


All circumstantial evidence, Dr. A, thickly stuffed with assumptions. No hard evidence.
Edited by Faith, : No reason given.

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Faith 
Suspended Member (Idle past 1466 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 23 of 164 (351515)
09-23-2006 12:30 AM
Reply to: Message 12 by bernd
09-22-2006 4:28 PM


you seem to accept that new genes are formed by mutation in bacteria and drosophila, but you ask for evidence that the same holds true for mammals.
I don't know why it is so hard to get this across, but I DO NOT DENY THAT NEW ALLELES ARE FORMED BY MUTATION. I don't know about genes. Genes are specific loci as I understand it, which are occupied by whatever number of alleles are available for that locus in a given population. I'm not aware that actual new genes are said to be created by mutation, merely alleles for that function.
But the problem is that the evidence for a particular allele's being really the product of a mutation and yet also beneficial, truly novel and truly functional as well, is pretty scant. But of course I still can't read links so I may have missed THE evidence. Most of the new links I try cause my computer to freeze up.
Most mutations don't do anything good, right?
22 examples of novel genes within drosophila, primates, rodents, fish, plants and protozoa (each with references to the relevant primary literature). You’ll find 11 examples of mammalian genes, one - named FOXP2 - is a transcription factor which controls language and speech related functions in homo sapiens.
How do you know it's a mutation as opposed to a normally occurring alternative allele? If it's a mutation, how sure are you that it is not contributing something the organism would be better off without?
Another example of an "useful" mammalian gene would be GLUD2, a gene, which probably affects higher cognitive functions. It has been formed by retrotransposition from the household gene GLUD1 in the hominoid line about 23 million years BP. It is expressed in human nerve and testis tissue and seems to positively influence cognitive functions by enhancing the flux of a neurotransmiter.
How do you know it's a mutation as opposed to a normally occurring alternative allele? If it's a mutation, how sure are you that it is not contributing something the organism would be better off without?
Please quote whatever you want me to read from the links, please explain it in your own words, and please don't use technical jargon. Thank you.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.

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Faith 
Suspended Member (Idle past 1466 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 24 of 164 (351516)
09-23-2006 12:36 AM
Reply to: Message 17 by Philip
09-22-2006 9:26 PM


Re: New Genes?
Faith may presently buy into prokaryotes and fruit-flies somehow mutating "new genes" that enhance survival.
But random mutation of genes that enhance survival never really occurs in any viral or prokaryote scenario either ... at all ... with any statistical validation. Any true "newness" must eventually cascade into extinction.
Well, digesting nylon and surviving antibiotics DO sound like survival-enhancing variations. I just don't feel like fighting this battle on the level of bacteria and fruit flies. But if you have a good argument or some evidence that it all cascades into extinction, that would certainly fit with my overall expectations.
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 1466 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 34 of 164 (351690)
09-23-2006 10:23 PM
Reply to: Message 25 by Hawks
09-23-2006 4:53 AM


Oh yes, I certainly know that DISEASES are caused by mutations. Diseases and deformities and miseries galore are caused by mutations. This is one of the reasons why mutations hardly seem like an engine that could power life at all.
How can you know that for sure? How do you know that you not really seeing allelic shuffling or evidence of design? Seems to me like you are trying to eat your cake and have it.
Well, I know this because God wouldn't DESIGN in disease and death; It is the deterioration or disintegration of the design, the result of sin.
I've agreed that it's possible that beneficial mutations may play a part in the processes of life, but the evidence so far is not very convincing. Variations are merely CALLED mutations without any evidence whatever that they are in fact mutations. Whatever it would take to prove that they are truly novel, never existing before in the population, is what is needed.

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Faith 
Suspended Member (Idle past 1466 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 35 of 164 (351695)
09-23-2006 10:30 PM
Reply to: Message 26 by Dr Adequate
09-23-2006 7:20 AM


Reciting this does not make it true
Recitation doesn't make anything true, but thinking it through ought to show that this really is just circumstantial speculative reasoning with no actual facts involved:
Dr. A writes:
How do I know a mutation was involved? Because this form of three-color vision is confined within a group of animals known to be a clade. How do I know this, I hear you ask? By comparing the predictions of this theory to the data in morphology, genetics, and the fossil record, of course.
Because this form occurs within a certain group is not evidence for your claim. You are assuming descent from one to another, but this is not proved, merely assumed. Similarity of design accounts just as well for the facts. Morphology and genetics and the fossil record are equally well accounted for by this other explanation. You are arguing from theory through association and comparison. There is no actual proof here. Mere analogizing.

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Faith 
Suspended Member (Idle past 1466 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 36 of 164 (351697)
09-23-2006 10:44 PM
Reply to: Message 27 by jerker77
09-23-2006 7:41 AM


Re: New Genes?
... there is no such thing as nonsense DNA, in the qualified meaning of the word. All possible combinations within the triplet actually say something. Either it is any of the 20 something amino acids or start or stop. So any given combination will say something. If that something that is said is beneficial for the survivability and proliferation of the gene is a different question.
OK, this sounds like a topic I may want to take to the mutation discussion threads eventually.
It IS a different question, yes, but WHAT the DNA "says" has to be the most important thing.
A gene is a very very long string of these amino acids, right? That codes for a specific protein, right? The 20 amino acids do combine into triplets that say something quite definite, but when strung out along a gene into the hundreds and thousands, are you claiming there are that many coherent/articulate proteins?
But of course I think from the perspective of God's designing it all, and in that case all the codes MUST code for something beneficial to life -- regardless of environment. Sickle cell is beneficial with respect to malaria but in itself it is deadly in ALL environments. And this one example, or maybe there are two or three by now, that is brought out as supposedly typical of mutation, is just not a convincing argument.

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Faith 
Suspended Member (Idle past 1466 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 39 of 164 (351705)
09-23-2006 11:04 PM
Reply to: Message 37 by Dr Adequate
09-23-2006 10:45 PM


Seems to me what I said is a fair representation of the implications of what you said, but if I'm wrong you need to show how, not just keep saying it over and over. As you yourself said, merely reciting something doesn't make it true.

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Faith 
Suspended Member (Idle past 1466 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 54 of 164 (352721)
09-27-2006 9:57 PM
Reply to: Message 53 by Brad McFall
09-27-2006 6:41 PM


Side issue
Brad, sometimes you sound like you may have some creationist views or at least sympathies -- not in this post but I thought I'd ask. Do you?
Edited by Faith, : No reason given.

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Faith 
Suspended Member (Idle past 1466 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 58 of 164 (352833)
09-28-2006 1:00 PM
Reply to: Message 56 by Equinox
09-28-2006 12:17 PM


Re: New Genes?
Faith, are you saying that there is only one example, or "maybe two or three by now" of a mutation which adds a trait? You and I discussed over a dozen on a thread here just the other day - some included my beautiful buttocks, the Apo person, whale legs, babies with tails, copper tolerant monkey flowers, conquistador algae, and more. You aren't claiming you forgot, are you?
Yeah I forgot some of them. What's your point now, it's not two or three but six or seven? And what are they supposed to prove? I thought the tail example wasn't supposed to be a mutation. What would be the point in that case? Isn't it supposed to prove we're related to apes? A novel trait wouldn't prove that.
As we discussed, for most of them there are reasons to know that we aren't talking about reshuffled already-present alleles. For instance, the algae is asexual - so you don't reshuffle anything. Similar reasons hold for the others.
There are some mutations. I've acknowledged that. They're an odd bunch these you list. Pretty pathetic evidence that mutation could possibly account for all the variety of life.

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