Reduction of Alleles by Natural Selection (Faith and ZenMonkey Only)

First off, you are overusing the word “assumption”: an assumption is something that cannot be based on anything. Since the idea of beneficial mutations is based on the observation that mutations occur, it is not an assumption.

Wow, bluejay, let's not quibble at this level. I'm simply trying to be clear. Dr. A defined on some thread a while back how evolutionists believe in positive mutaitons as an "assumption." An assumption based on the theory. I bet there are lots of evolutionists who use the term that way. There's really nothing wrong with my use of it. As a matter of fact I'm sure you're wrong. We all get our assumptions from something we've observed. Nothing comes straight out of the blue.

A hypothetical scenario is not even remotely similar to an assumption. Please stop flinging the word “assumption” around.

OK I'll toe your line on this for the sake of peace though you are completely wrong. Shall I call it a hypothesis then? Same difference to me. I still say exactly what I said already only I substitute hypothesis for assumption.

Faith writes: For reasons said above, can't accept "default conclusion," need an actual allele for an actual phenotypic effect that's an interesting variation and not a deformity. Then you are asking for evolutionists to provide a level of proof that you would never ask of anybody else for any other claim! If I could prove to you that humans can walk, would you then demand additional evidence that shows that humans can walk to a water hole to get water? You would not demand this, because you know that the destination has no relevance whatsoever for the mechanism of getting there. If I can walk, I can walk to water. Period.

Now YOU're getting testy and it seems to be as soon as I make a point against evollution.

You haven't proved anything similar to your example here, that humans can walk. Mutations that cause disease or do nothing or maybe sometimes do something in a trade-off with another diseae process are hardly to be compared with a positive function like walking.

Bluejay, this is typical evolutionist thinking and I can hardly blame you for it, but it ought to be a patently ridiculous comparison even to you.

Dawkins is always saying that since there are observable new species in nature we can anticipate the endless development of further new species given enough time. This is false if the whole process depends on reduced genetic diversity as I am trying to argue. And I'm willing to argue it even WITH mutation in the mix because mutation is going to get reduced same as built-in alleles would and you still aren't going to get a new species without reduced genetic diversity.

No this comparison is ridiculous. You are claiming something crucially important to the argument between evolution and creaitonism. Evolutionists talk about mutations all the time as if they were observed reality. You do this when you flatly state that there is a lot of increase in genetic diversity in the seal population. All you really know is that there are probably mutations there; what you do not know is whether these contribute in any way at all to the health of the species or its ability to further vary (in healthy ways). You ASSUME this part of it, and it's quite fair to describe it in such terms.

You want me to accept something as a reality that is a flat-out empty assertion. That is what evolutionists do, treat as reality something that cannot be demonstrated but is based only on the theory. You want me to accept evolution though my whole reason to be here is to argue against it. Wow. Talk about begging the question.

YOU believe the theory of evolution. I do not. And the actual observable empirical evidence for mutations supports creationism, not evolution. You MUST produce a mutation that created a normal alele to overthrow my contention. That's what true science would require of you. Many mutations have been observed in that study you linked. Those doing the study should be working to show that any one of those 70 mutations are of the sort needed to make the constant reification of a nonexistent healthy allele an actual physical reality.

That is why I had to get this clear, get you to show that there is no observed reality behind the kind of alleles that are needed for evolution. I wasn't entirely sure myself because the way evolutionists talk you'd think they could dangle this normal allele in front of my eyes. They can't. The ONLY actual observable empirical evidence that actually exists is of mutations that cause disease or do nothing as far as anyone knows.

My point is quite reasonable. You have thousands of such observed mutations -- in all that observation you OUGHT to have at least ONE that demonstrates what you are continually treating as if it were a fact based on the theory but isn't.

But, in the case of mutations, you’ve totally flip-flopped your position, and are demanding that, after we have proven the proverbial ability to walk, we still have to prove the proverbial ability to walk to water.

BS, bluejay, BS. Ability to walk isn't comparable to thousands of disease-causing or nothing-causing mutations.

Out of all that you can't produce ONE true allele, can you?

The functionality of the allele has absolutely nothing to do with whether or not the mutation that would create the allele can happen. So, if I can show you that a new allele can be produced (and I have done so), then I have shown you the ability to make a beneficial mutation. No assumptions are involved at all in this conclusion: every step of the process is supported by evidence. If a gene can change, it can change into something functional. Period.

Nonsense. You have to have positive evidence and you have none. Evolutionists apparently bamboozle generation after generation of students with this pure fantasy they treat as reality. Wake up bluejay.

Faith writes: Again, there's no need for a special mechanism [to prevent beneficial mutations] if what mutations really are is simply mistakes in the coding system, that is, a pathology of the reproductive system, that aren't desirable for the organism -- in a general sense at least if not always an obvious specific sense -- which is what the evidence so far seems to show. Once again, desirability has nothing to do with the mechanisms of allele production. What part of that is so hard to understand?

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Nothing at all. YOu have something that looks like an allele that you can show has been caused by a mistake in gene replication.

Is it really an allele? So far they all look like deformities, not alleles.

What part don't you understand of the fact that you have to PROVE that desirable alleles occur in reality or all you've proved is a pathological process that occurs that changes one healthy allele into something unhealthy or simply destroys its function altogether? You MUST prove desirability. And by all rights, given the numbers of mutations you know about you should have been able to come up with hundreds or thousands if the theory is right that mutations are the source of normal alleles.

No evidence is no evidence. Hypothesis can't substitute for evidence.

Faith writes: ...from this study it doesn't appear that you know anything about [the mutations] that would validate the assumption that all alleles originated with this kind of event, which IS the assumption of evolution, right? Okay, now you’re moving the goalposts. Why do I have to demonstrate that all alleles emerged this way? If I demonstrate that one alleles emerged this way (which I have done), I am vindicated, because it then falls on you to show that other alleles are somehow different from that allele.

Yes, if you could produce one normally coding allele for something recognizable along Mendelian lines and not disease and not the half-baked disease-for-disease version, that would be vindication. Producing sick or dead alleles is not evidence.

Besides, you’re reading everything we do in science backwards from the way it actually happens. Scientists started with the observation that mutations produce new alleles, and extrapolated that backwards to hypothesize that all alleles emerged this way. Since no one has produced evidence for any other mechanism by which alleles are generated, mutation is currently the only demonstrated way to explain the origin of alleles.

Fine, it's a reasonable hypothesis but that doesn't give you the right to treat it as reality, and that's the way you ALL treat it. You talk about increased genetic diversity as if you could actually see it and demonstrate it when it's nothing but the product of your hypothesis. You talk about all normally occurring functioning alleles AS IF they were the product of mutations as if this were established reality.

In what science is it valid to treat a hypothesis as a reality before actual evidence has been produced to demonstrate it?

And again, by this time, after you have thousands of REAL disease-producing alleles and who knows how many you can't show any function for at all, you OUGHT to be able to produce a REAL desirable one. Really, bluejay, THAT would be how science really works. You can't go on building on a hypothesis forever that cannot be proved in reality. At some point you have to abandon it.

I believe the evidence that is actually in hand demonstrates that mutations are a pathological occurence. That's the reasonable interpretation of the actual evidence you have that you yourself have shown.

And I didn't know this with so much certainty before this post of yours either. Now I know beyond a doubt that evolutionists are reifying their hypotheses and calling them facts when they are no such thing.

Until somebody presents something better, this is what we have to work with to explain the genetic diversity of life. So, that’s what we use to construct our current model of life and its history. If you disagree with this model, the onus is on you to demonstrate that reality deviates from the model, not on us to provide better proof of what we have already demonstrated to be accurate.

Your own actual evidence has disproved your hypothesis by now. If you don't have an alternative, that's no justification for going on with one that has been so soundly disproved as this one with all those thousands of sick mutations.

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Hi, Faith.

I’m as frustrated as you are: my points are also being ignored, misunderstood and misrepresented. But, from my perspective, it does not feel like you’re making a good-faith effort to understand what I’m saying to you. I have addressed your points, but my addressing them seemingly has no effect on how your next post is going to be composed.

At any rate, your last post seemed like a lot of quasi-controlled ranting. You started talking about things that don’t make any sense at all (for instance, what is a “normal allele”?), and you seemed to have started thinking that alleles that cause deformities or other debilitations are not “alleles,” which is false and may have been a source of confusion about my arguments.

I’m not going to respond directly to any comments you made, because I don’t think I have the maturity to handle that appropriately. Instead, I’m going to try to summarize the main thrust of my argument.

I have been trying to get you to see that you are looking at this situation in an entirely inappropriate light. I have uncovered the two major points of contention that you have with the evolutionist argument, and I will now provide what I think are accurate rebuttals to those two points:

1. The difference between beneficial and deleterious mutations.

   There is no difference between beneficial and deleterious mutations. At least, not for the molecules that cause them. At the molecular scale, a mutation is only a switch from an A to a T, or something akin to that. To the molecules, there is no “beneficial” or “deleterious”: they do not directly experience either one.

   So, the monikers “beneficial” and “deleterious” do not apply to the mechanism of mutation. They only apply to the phenotype of the resulting allele. So, arguments about the mechanism of the mutation apply equally as well to mutations that would have a beneficial effect and to mutations that would have a deleterious effect. There is no mechanistic distinction between beneficial and deleterious mutations, so classifying them as "beneficial" and "deleterious" when discussing if and how they happen is meaningless: rather, we should be categorizing them mechanistically: i.e., "point mutations," "insertions," "deletions," etc.

   This was where the walking analogy came in. Walking is walking. There is no mechanistic difference between walking to the store and walking to the park: in both cases, the same mechanism is used to get there.

   Likewise for mutations. Mutations are mutations. There is no mechanistic difference between mutating into a beneficial allele and mutating into a deleterious allele: in both cases, the same mechanism is used to get there.

   A beneficial mutation is just a specific case of a mutation, just as walking to the watering hole is just a specific case of walking. There's no reason to think it is somehow different from every other case of mutation/walking. That was the point of the analogy.

   Do you understand what I’m saying?

   For the record, I also feel like I am being made to cross all the t’s and dot all the i’s for you: you come off as an idiot to me as much as I come off as an idiot to you. We can solve this by (1) repeatedly libeling each other and calling each other idiots or (2) trying to understand each other in the hope that understanding will cure each other’s idiocy.

2. What is based on what?

   You think our argument unfolds as follows:

   (1) Assume that all alleles come from mutations.
   (2) Observe an allele that we have never seen before.
   (3) Conclude that the allele came from mutation.

   In actuality, our argument unfolds as follows:

   (1) Demonstrate that mutations create new alleles.
   (2) Observe that no other means of creating alleles has been demonstrated.
   (3) Disregard these undemonstrated means of creating alleles.
   (4) Conclude that, to the best of our knowledge, all alleles come from mutations.

   Then, only after that, we tack on two more steps:

   (5) Observe an allele that we have never seen before.
   (6) Conclude that the allele came from mutation.

   Your argument is that the first three steps never happened. This is simply false.

   I’ll grant that some of us may get overzealous about our conclusion, and may not treat it with the proper air of tentativity, but it really is the only conclusion that can be arrived at by only using processes that have been demonstrated to happen. I don't see how logic could allow any other progression of thought on the subject.

   The only remedy for this is to demonstrate that some other process that produces alleles is happening (e.g. an Intelligent Designer). In the absence of that, we literally have no choice but to fall back on mutation as the only possible explanation.

   There is no sense in demanding that I prove that mutations could have caused situation X when it has already been shown that mutations have caused things that are mechanistically indistinguishable from situation X, and when nobody has been able to demonstrate that a suitable alternative explanation is viable.

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I believe I have accurately represented your views here, and have provided solid rebuttals that should clear up your misgivings about the reasons we support mutation as the primary source of genetic diversity.

I don't expect that this will change your mind about whether alleles arise by mutation, but I hope it will at least put an end to your inaccurate portrayals of our arguments and methods of reasoning.

If you take these points under consideration, I think we're prepared to discuss the role of mutation in the processes of speciation and diversification.

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-Bluejay (a.k.a. Mantis, Thylacosmilus)

Darwin loves you.

(Yes, I know you aren't claiming to make healthy alleles out of unhealthy ones so please don't try to claim I mean the title that literally. It's meant to be a play on the proverb you can't make a silk purse out of a sow's ear. But of course the full message would be that you can't get healthy alleles out of a system that produces sick mutations. At the very least you haven't proven that you can.)

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I think we're going to have to change direction here.

I have answered your posts completely honestly. I am not even close to "ranting." I may repeat myself because of having been misunderstood so much, but that shouldn't be more than boring if you're getting what I'm saying.

Yes, you are insisting that even if it's a sick allele it's still an allele and yes I'm coming to realize that it probably doesn't deserve the term, but OK I'll call it an allele too, with the usual qualifiers, "deleterious" and so on. That's why I started using the term "normal" -- just another way to contrast with "deleterious" that seems to me to make the point better -- an allele that produces all the traits that are talked about when adaptations are being discussed, which is a normal healthy process as opposed to a genetic disease.

There is a great deal of difference between genetic disease and normal adaptational alleles, same difference as between going from a disease of the legs that requires braces or crutches for walking to normal walking. There is no normal progression from one to another as in your erroneous example of going from walking at all to walking a distance. Simple traits such as eye color and hair color and body type come from normal genes; genetic diseases come from diseased genes. I'm sure this is clear enough.

I have no problem at all understanding the difference between the mechanism of mutation and the product. I'm sorry, you've cleared up nothing. You've in fact strengthened my understanding that evolutionists have got themselves seriously deceived and I believe I've gone a long way to showing that in my last two posts and it is you who is not understanding and even possibly not approaching this honestly if you don't see that -- not intentionally probably but simply as a result of your solidly unyielding evolutionist bias.

You think our argument unfolds as follows: (1) Assume that all alleles come from mutations. (2) Observe an allele that we have never seen before. (3) Conclude that the allele came from mutation.

Sure looks like that as it is normally encountered.

In actuality, our argument unfolds as follows: (1) Demonstrate that mutations create new alleles.

Yes, but if the alleles being created are all disease-producing or apparently functionless they can hardly be accepted as the same as alleles that produce the traits that make for all the interesting variations in nature. They're sick and broken alleles.

(2) Observe that no other means of creating alleles has been demonstrated. (3) Disregard these undemonstrated means of creating alleles. (4) Conclude that, to the best of our knowledge, all alleles come from mutations.

You really think I've been missing this obvious progression of how you all think? It is the ToE that leads you to even have to have a means of creating alleles. And it does so to such an extent that evolutionists will even apparently accept a disease process as a normal process. That seems to me to be getting confirmed more and more as we speak.

Your conclusion is really that, to the best of your knowledge if the ToE is correct, there is no other source for alleles than mutations. But if the mutations are producing no true useful trait-making alleles but only disease or untranslatable garbage, your conclusion may continue to be an hypothesis but it should be getting harder and harder to hold onto it with all the evidence against it.

Then, only after that, we tack on two more steps: (5) Observe an allele that we have never seen before. (6) Conclude that the allele came from mutation.

I'm sure, yes. This is the part we normally encounter in evolutionist presentations, but truly, bluejay, the steps you have added to this don't make it any more reasonable. They only demonstrate your assumption of the ToE, and you simply want to MAKE me accept it. Is that debate?

AND none of this in any way justifies calling it FACT. It's all still an unconfirmed hypothesis at best. To call it FACT is really to commit a fraud. Again, true science never treats its hypotheses as fact -- the whole enterprise is toward proving or disproving them. You all insist on treating it as fact simply because, well, you don't have an alternative. How many times in the history of science do you suppose an alternative didn't appear to replace a hypothesis that wasn't working or was outright disproved? You don't hold onto it just because you don't have an alternative when all the evidence is pointing against it, as it obviously is against mutation as any kind of normal process.

Your argument is that the first three steps never happened. This is simply false.

No, that is not my argument. What's false is the idea that this is my argument. I have no problem at all accepting that those are the steps you go through. But there's a basic flaw in the reasoning, that's what I'm trying to point out.

The first three steps don't help you as I say above; they merely show how the whole system is assumed based on the ToE and remains unproven, while evidence galore has been mounting that demonstrates that mutation could not possibly be the source of genuine healthy traits and adaptations.

If you are insisting on equating disease with health and that I accept this as proof that mutations produce alleles, I'm very sorry, I consider this to be a staggeringly glaring case of where science goes wrong.

If you take these points under consideration, I think we're prepared to discuss the role of mutation in the processes of speciation and diversification.

I cannot accept any of this reasoning. But just as I started out, I can go with the common assumption that mutations produce alleles anyway for the purpose of argument, as I have been assuming that it doesn't make any difference for the argument I've been trying to make. If you want to just leave this discussion as a place where we agree to disagree that's OK with me.

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Wanna take a little decompression side trip and just talk about stuff like, oh, junk DNA or something, before we come back to the topic? Or how genes with thousands of codons can be identified with their phenotypes and so on? I'm really interested.

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I think it is important to keep the focus on mutations until a common understanding emerges.

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--	Percy
	EvC Forum Director

Hi, Faith.

I don’t really pay that much attention to subtitles (except when I want to write one of my own), and I rarely (if ever) respond to them.

Faith writes: I have no problem at all understanding the difference between the mechanism of mutation and the product... ...Simple traits such as eye color and hair color and body type come from normal genes; genetic diseases come from diseased genes... ... If you are insisting on equating disease with health and that I accept this as proof that mutations produce alleles, I'm very sorry, I consider this to be a staggeringly glaring case of where science goes wrong.

See, this shows that, despite your claims, you do not understand the difference between mechanism and phenotype.

“Diseases” and “handicaps” are phenotypes: it has not been demonstrated that such a thing as a “diseased gene” or “diseased allele” exists. For this reason, intellectual honesty requires scientists to disregard the notion of “diseased genes” until somebody steps up and shows that this is actually a meaningful way to categorize genes.

Until such time as “diseased genes” are shown to be meaningfully distinguished from “normal genes” on grounds other than phenotype, you are making the same error you have been harping on evolutionists for making: that is, you are claiming to be talking about genotype, when, in fact, you are only talking about phenotype.

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Faith writes: Bluejay writes: (1) Demonstrate that mutations create new alleles. (2) Observe that no other means of creating alleles has been demonstrated. (3) Disregard these undemonstrated means of creating alleles. (4) Conclude that, to the best of our knowledge, all alleles come from mutations. You really think I've been missing this obvious progression of how you all think?

Yes, Faith, I do think you have been, and still are, missing it. And, you proved it when you wrote the very next sentence:

Faith writes: It is the ToE that leads you to even have to have a means of creating alleles.

When you write stuff like this, what choice do I have but to conclude that you completely missed this “obvious progression of how we all think”?

Even under creationism, there would need to be a means of creating alleles.
Otherwise, how did any of us ever end up possessing alleles?
The creationist means of creating alleles is whatever design process was used by the Designer.
Because no such process has been demonstrated to exist, scientists are required to exclude it from our models. If you want it to be considered in scientific models, demonstrate that it exists.

In science, we can only use those means of creating alleles that have been demonstrated to exist, and, so far, mutation is all we’ve got. We are literally---literally---out of options, Faith. We don’t really have a choice but to conclude that mutations are all there is. In religion, we have the luxury of tossing around indemonstrable processes, but the standards in science are such that we can only base our models on things we can demonstrate.

This is why it is up to you, the person who thinks some other means of creating alleles needs to be invoked, to demonstrate that mutation cannot explain “normal” or “beneficial” alleles, or to demonstrate that this other means of creating alleles actually exists.

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Faith writes: AND none of this in any way justifies calling it FACT. It's all still an unconfirmed hypothesis at best. To call it FACT is really to commit a fraud.

I think these are the first two times the word “fact” has appeared in this conversation.
There is no use throwing around libel about “fraud” when the conditions you cite for fraud have not been met and show no indication of being met in the near future.

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-Bluejay (a.k.a. Mantis, Thylacosmilus)

Darwin loves you.

Yeah, I had a feeling you were going to say that there is no difference between disease and health genetically speaking, it's all still gene and its phenotype. This is of course implied by what you have been saying.

The idea that there is no distinction at this level doesn't even fly with observations of nature that evolutionists make in other contexts all the time. That is, when evolutionists describe various species they describe them in terms of their adaptive healthy normal functions, and disease is regarded as something that happens occasionally to interfere with them, fortunately rare -- which is the normal way we all view these things. The preponderant recognition is of adaptive and healthy function and the logical distinction is clearly made between health and disease and deformtiy. That is you clearly and naturally distinguish between "healthy" and "diseased" at this level of discussion, like any normal person does.

Oh right, the unhealthy phenotypes were selected out. That would fly if the ratio of healthy to unhealthy were not the tiny-to-huge that exists in known mutations which would prevent any living thing from ever having existed at all if they were actually the source of all alleles.

When you get to the area of mutations then it becomes useful to evolution to discard the normal way of thinking and blur health and disease all together into gene and phenotype no matter what disease or deformity is the result. You can convince yourselves of this because of course evolution is "blind," but no evolution could possibly have ever got off the ground with predominantly disease-producing alleles, and the actual evidence you have is almost exclusively of disease-producing or nonfunctional mutations, NOT the normal proportion of health to disease that is seen in living things themselves.

Why is it so hard to come up with a real example of an actual mutation you can point to that produces a genuine normal trait in the organism? Why? If you have so many examples of mutation-caused diseases you can point to, even locate on the DNA strand, there's no reason at all why you shouldn't have examples of normal functioning alleles too if your hypothesis is correct. The fact that you have none is STRONG evidence that mutations don't do what you think they do. The EVIDENCE is that they are only a destructive event.

No, as a creationist I don't have to give a source of alleles because I assume them all to have been there from the beginning, and they are demonstrably already there in any species and in any example we discuss. There is certainly no evidence that shows this couldn't be the case.

Evolution has the task of finding a source for them, not creationists.

I'm writing this in a rush as I have to get back to work, simply wanted to get this much said. I'll be back later and see if I missed anything in your post, but I've got to say right now there's probably no hope for this debate. You're going to go on saying I don't understand things I perfectly well understand, simply because I disagree with you and explain everything through a different set of assumptions -- for which the evidence is every bit as good or better than it is for evolution. I not only disagree with you and the evidence supports my view, but I've shown that the evolutionist thinking is absurd.

You will of course refuse to accept this barring a miracle.

Back later.

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Looks to me like I pretty much answered your post but thought I might say more about this part of it:

Even under creationism, there would need to be a means of creating alleles. Otherwise, how did any of us ever end up possessing alleles? The creationist means of creating alleles is whatever design process was used by the Designer.

The actual observable situation is that all species have genomes and alleles for variations of different traits. They are already in place, and a creationist has no need to explain their origin beyond their having always been there. The evidence of their actual existence and also their operating acccording to laws such as Mendel's is in favor of this claim. Science can be carried on with them and about them just fine without our knowing anything specific about their origin.

Because no such process has been demonstrated to exist, scientists are required to exclude it from our models.

Nonsense. They are there. You are required to take them for granted as there. It is only your theory that requires you to explain their origin OR exclude the creationist idea. The actual facts, the evidence itself, the empirical evidence, correspond just fine with their originating all together at a point of time called the Creation.

If you want it to be considered in scientific models, demonstrate that it exists.

The evidence is so heavy in favor of such an explanation that it has to be evolutionists who have the burden of proof against it.

In science, we can only use those means of creating alleles that have been demonstrated to exist, and, so far, mutation is all we’ve got. We are literally---literally---out of options, Faith. We don’t really have a choice but to conclude that mutations are all there is.

Yes, bluejay, and I feel your pain, but a single one-time origin at the beginning of life does just fine with the actual facts, and it is only your evolutionary theory that demands a means of creating alleles.

But truly, if mutations have been shown so far never to have produced an actual healthy normal allele but only diseases and gobbledygook -- in the thousands yet -- if mutations are all you've got, clearly you have to abandon the whole idea that you need a source of alleles beyond the assumption that they are built in. It is mystification and in fact lying to talk about alleles AS IF they were the product of mutations when there isn't one iota of evidence that they are and plenty that they aren't.

In religion, we have the luxury of tossing around indemonstrable processes, but the standards in science are such that we can only base our models on things we can demonstrate.

Well, with mutations the demonstration has failed. Science at that point has an obligation to look elsewhere in that case instead of insisting on something that CAN'T be demonstrated, has NEVER been demonstrated despite LOTS of evidence.

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Hi, Faith.

Faith writes: Why is it so hard to come up with a real example of an actual mutation you can point to that produces a genuine normal trait in the organism?

As long as you believe that there are such things as “diseased genes,” this will not help you. It would be a bit like “casting my pearls before swine.”

I’m trying to dispel your notion that disease is genotypic, and not just phenotypic. I thought the best way to do this was to appeal to something we both agreed on (i.e. neutral mutations, which are clearly not pathogenic, but are of the same kind as deleterious mutations).

But, since that's not going to work, I present you with a beneficial mutation: here and, for good measure, here.

These papers were done in 1991 and 1989, respectively. They document the genotypes and phenotypes of, collectively, 26 mutations to the gyrA and gyrB genes that confer resistance to a type of antibacterial drug called quinolone. All were confirmed as mutations, because they were induced in populations of bacteria whose genotype for the gene in question was known beforehand.

If mutation is a pathological process, common sense should tell us that it cannot possibly produce something that is useful to an organism. Yet, I just presented 26 examples of proven, documented mutations that confer a beneficial phenotype on bacteria (13 each from two different genes).

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I’m sure Wounded King or some other geneticist could provide a longer litany of these.

You should concede the point that mutations are relevant to your model, given that I have demonstrated that beneficial mutations exist, and have demonstrated the massive potential for new mutations to have been introduced into a growing population, such as the northern elephant seal.

If you do, we can then proceed to discuss the implications of this for your model of bottleneck speciation.

Edited by Bluejay, : Edited content for civility, as per Admin's request. My apologies.

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-Bluejay (a.k.a. Mantis, Thylacosmilus)

Darwin loves you.

Could we please return to more of a "Just the facts, ma'am" kind of discussion?

PS - The quote is a dragnet reference, which Faith might recognize and Bluejay might not.

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--	Percy
	EvC Forum Director

Trying to find some information to include in my answer.

Bluejay, I'm sorry but I can't concede that. As I said, the best I can do is proceed AS IF mutations are the source of alleles, for the sake of the discussion here. But concede, no way. You haven't proved a thing. I asked a long time ago that bacteria not be used in this discussion for one thing, but for another I doubt that example is of a mutation that produced an allele, but probably just knocked out another allele. There is no clue that that is the case though I couldn't find a reference to make the point for sure.

Well, let me go through the post at least:

Faith: Why is it so hard to come up with a real example of an actual mutation you can point to that produces a genuine normal trait in an organism? As long as you believe that there are such things as “diseased genes,” this will not help you. It would be a bit like “casting my pearls before swine.”

I see, I have to ignore the evidence. Got it.

Seems to me that mutations that reorganize the coding of normal alleles and produce either disease or nothing can be fairly called "sick genes." It’s only evolutionist assumptions – or hypotheses – that claim otherwise.

I’m trying to dispel your notion that disease is genotypic, and not just phenotypic.

Sorry, the evidence is against you.

I thought the best way to do this was to appeal to something we both agreed on (i.e. neutral mutations, which are clearly not pathogenic, but are of the same kind as deleterious mutations).

Perhaps you misspoke? “Deleterious” does mean pathogenic.

http://www.merriam-webster.com/dictionary/deleterious:

harmful often in a subtle or unexpected way -- deleterious effects -- deleterious to health

In any case, neutral mutations is a strange concept. Does that mean you don’t KNOW what they do or you know they don’t do anything? They just displace a REAL allele which probably WAS doing something, right? Destruction.

But, since that's not going to work, I present you with a beneficial mutation: here and, for good measure, here. These papers were done in 1991 and 1989, respectively. They document the genotypes and phenotypes of, collectively, 26 mutations to the gyrA and gyrB genes that confer resistance to a type of antibacterial drug called quinolone. All were confirmed as mutations, because they were induced in populations of bacteria whose genotype for the gene in question was known beforehand. If mutation is a pathological process, common sense should tell us that it cannot possibly produce something that is useful to an organism.

Depends on HOW it's useful. If it's useful by playing off one disease process against another, as is known to happen, or by simply knocking out an allele that was sensitive to the antibiotic, that's not useful in the sense a normal allele is useful and for all I know that's the kind of usefulness your bacterial mutations have, i.e. a pathological process in its essence.

Yet, I just presented 26 examples of proven, documented mutations that confer a beneficial phenotype on bacteria (13 each from two different genes).

Thirteen mutations to a SINGLE gene? Two genes with 26? What kind of "mutation" could that possibly be? What sort of random process changes the same gene thirteen times all toward the same result and another at the same rate yet? Something very weird about this idea. Sorry, this gets curiouser and curiouser. It may superficially look like a mutation but anything that behaves with such consistency has to be built into the organism somehow or other. No way I can concede anything with such a strange example.

But apart from that, whatever happens in bacteria is a pretty sorry example for answering the glaring fact that there are thousands of known disease-causing mutations in human beings, which has been my example here. There is NO reason you can’t produce a normal allele from a mutation in human beings unless they don’t do what you think they do. Sorry, that’s what you need, not bacteria.

The DNA sequencing study on the family of four that you linked would be a great source of material if such an event has ever happened. Something like 70 mutations were identified. Why can't their function also be identified?

I’m sure Wounded King or some other geneticist could provide a longer litany of these.

Perhaps you should invite him to give the info on the other thread. If we aren't just trying to win points here but get to the bottom of our topic instead, it could only be a good thing to be as complete as possible.

You should concede the point that mutations are relevant to your model,

Such a request is ridiculous. Best I can do is TREAT THEM AS IF they’re relevant because I’ve seen only too clearly that in actual fact according to actual evidence the claims for mutations are all a delusion.

given that I have demonstrated that beneficial mutations exist,

Sorry, bluejay, you haven't demonstrated such a thing. Not any more than I already knew about and took into account here. A questionable adaptation in bacteria can't answer the fact of thousands of genetic diseases in human beings. The puzzle is that the obvious implications of this are denied by evolutionists while you try to make a single effect in bacteria prove what is so amply denied by the evidence.

and have demonstrated the massive potential for new mutations to have been introduced into a growing population, such as the northern elephant seal.

Now this I've already answered many times over. You have certainly demonstrated no such thing, The vast majority of known mutations do not produce viable alleles as I have clearly recognized and shown, and simply assuming that mutations have occurred in the seals is far from evidence that they are anything other than undesirable. No evidence, just assumption – or hypothesis. No evidence.

If you do, we can then proceed to discuss the implications of this for your model of bottleneck speciation.

As I said, I cannot concede what you ask, It’s been soundly disproved, but I can proceed AS IF what you say is true. Sorry, best I can do. If you can’t accept this then we’re at a stalemate.

But if you will, then in my accepting for the sake of argument that mutations produce alleles, how about if you now give me some numbers to work with: Just how many new “alleles” should I have to take into account and at what point(s) in the life cycle? Not math, just numbers.

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Hi, Faith.

Faith writes: I asked a long time ago that bacteria not be used in this discussion...

What reason could you possibly have for making that request?

If bacteria prove my point, I'm going to use them. I see no reason to agree to such arbitrary conditions.

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Faith writes: I doubt that example is of a mutation that produced an allele, but probably just knocked out another allele.

How can you say this? The papers I cited even identify the sequences of the new alleles!

By definition, a new allele replaces an old one when a mutation occurs: this is because all mutations are alterations to old alleles. So, in "knocking out" an allele, these mutations produced a new allele.

You cannot deny that this created a new allele, and you cannot deny that it had a beneficial effect for the organism. Both of these are documented, observed facts. And, in this case, I used the word "fact" intentionally, because these are things that have been witnessed directly.

You are now officially denying facts.

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Faith writes: Bluejay writes: I thought the best way to do this was to appeal to something we both agreed on (i.e. neutral mutations, which are clearly not pathogenic, but are of the same kind as deleterious mutations). Perhaps you misspoke? “Deleterious” does mean pathogenic.

No, you misunderstood it.

"Deleterious" is not a kind of mutation: it is a kind of phenotype.

Kinds of mutation are, for example, substitution, insertion, deletion, etc.

Substitution-type mutations (such as those in the papers I cited) can produce deleterious, neutral and beneficial phenotypes.

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Faith writes: But if you will, then in my accepting for the sake of argument that mutations produce alleles, how about if you now give me some numbers to work with: Just how many new “alleles” should I have to take into account and at what point(s) in the life cycle? Not math, just numbers.

I already provided the numbers: 0.6 new alleles per individual, at the moment the individual is born.

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-Bluejay (a.k.a. Mantis, Thylacosmilus)

Darwin loves you.

Post moved to End of Evolution by means of Natural Selection thread.

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Just because you see a series of codons in the place where an allele should be does NOT mean it's a functioning allele. It may simply be gobbledygook, and it MAY simply have knocked out a functioning allele that was sensitive to the antibiotic, thus providing the resistance. This is NOT proof of mutations making viable alleles!

And I'm denying nothing!

YOU are missing the point, and possibly not playing with a full deck yourself.

"Deleterious" is not a kind of mutation: it is a kind of phenotype.

"Deleterious" used to desribe the phenotype is new to me, but whether it can be used that way or not, the word is CERTAINLY used to describe mutations:

http://en.wikipedia.org/wiki/Mutation Therefore, the optimal mutation rate for a species is a trade-off between costs of a high mutation rate, such as deleterious mutations, and the metabolic costs of maintaining systems to reduce the mutation rate, such as DNA repair enzymes.[5]

One new allele per individual at birth? Or half an allele? I can't work with .6