The Nature of Mutations

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The utility (or lack of same) of ANY mutation is due to environment. Specifically, the chemical envrionment of the new protein. That includes the chemical envrionment of the cell as well as the environment of the organism.

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Negative. If this is true, please explain how such genetic diseases that are caused by mutations have to do with their environment. Such diseases as Huntington's Disease, or Tay-Sach's Disease, or how about Parkinson's Disease?

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I don't see how you can just blanketly assert that even beneficial mutations are deleterious. No mutation is inherently good or bad on it's own right. It's only as it relates to the organisms survival in it's envrionment that we can make that judgement.

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First, see above comment. Second, I don't blanketly assert anything but what the data says. The data says that all mutations that have an affect upon the organisms to which they occur, have deleterious effects, regardless of whether they also confer some degree of beneficial outcome. Again, SCA mutation, it damages the blood cells, are you going to deny this FACT? No, I didn't think so. It is a deleterious mutation. It just so happens to carry with it some degree of guard against a certain disease. Tell me, does Huntington's disease or any of the other two prevously mentioned carry with them any kind of beneficial outcome along with their deleterious nature? No, they do not. Your argument is mute.

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You call it "damage" because to you, the protein doesn't work as it's "supposed to". Inherent in your view is a kind of platonic idealism, where organisms have some kind of "perfect state" that any deviation from is, by nature, inferior.

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Nice try, but you fail. If you are going to revert to spindly kinds of argumentation instead of relying on the facts, then you might as well say the wicked witch did it. In case you can't see it, proteins and such do have SPECIFIC functions...they do have certain things that they are "supposed to" do. And when they are damaged and cannot perform their jobs, we get Huntington's disease and Parkinson's disease and a whole host of others. You are arguing from a black hole.Greetings!

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Phospholipid, are you Phospho that once was on the Origins Discussion forum? If you are, do you remember our discussion of Hemoglobin C?

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Probably, I am pretty sure that I am the only one who has ever used this screen name, and I do remember vaguely a conversation with someone on that issue, but beyond that my memory is pretty fuzzy.How are you doing? I don't remember your screen name.Greetings!

Well spoken, Paul.Keep up the good work!

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Are you saying that there are no new species?...And what are those original "kinds"? And what is the barrier between them?

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I would answer this, but I do not want to get off topic. The best answer that I can give on this subject without going off topic is this...if there is no way to gain new variation within the genome of an organism, then there is no room for speciation.Since mutation was the only possible answer for adding new variation to the genome, and beause the evidence has since failed to demonstrate that mutation is capable of providing new variation, the point is a mute one. There can be no speciation. This was at one time considered a possibility, but since the 1960's its plausibility has gone out the window according to the data.There is adaptation, but adaptation is NOT evolution, it is merely adaptational variation that is already well defined within the genome. This is one reason why the genome is referred to as a "gene pool" instead of a "gene stream," because there are definite limits to variation that cannot be by-passed by mutation or any other genetic machinery. This is what the evidence dictates, not how I, or any other person, wants it to be like. Its just the facts without all of the evolutionary assumptions.Greetings!

As a matter of fact, I will deny that they are "damaged" cells. While they may have a funny shape, and be less able to carry oxygen than the cells of another individual, they grow exactly the way their programmed to by the DNA. They just grow differently than the majority of human blood cells. You calling them "damaged" implies that they're somehow not what they're supposed to be. But biologically, that's a meaningless assertion. Your assumption of design permiates your worldview, however, so I don't imagine you can see how wrong you are to suggest that blood cells have some way they're "supposed" to be.Whether or not the genes for these unique cells is beneficial or not depends on the envrionment. In an environment where organisms have to breathe as much oxygen as possible (say, high altitudes) they're quite harmful. In an environment of blood-bourne parasites, these genes are beneficial. It's all environment. And sometimes, the organism is in an environment where their old job doesn't matter. (Ala bacteria and the nylon substrate.) If they are made to mutate and change, suddenly not being able to do their old job means they could be doing a new job. Like digesting nylon.All proteins do is fold into a shape. All possible proteins have shape. Whether or not that shape is useful (i.e. it catalyizes chemical reactions) depends on what chemicals surround the protein - its environment.I'm sorry, I think you fail, because you can't divorce yourself of a teleogically driven biology. I'm afraid your double standard for mutations just won't fly.

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Were you aware that all scientists and even the majority creationists accept the reality of speciation?

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Not all creationists, only those who are confused about the issue and therefore concede that it is a possibility. The facts, however, dictate otherwise.

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There's hundreds of examples of a single interbreeding population splitting into two populations who can no longer breed with each other, gaining unique characteristics in the process. That speciation has been observed to happen in the wild and in the lab is a fact that you may wish to acquaint yourself with.

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If you are referring to trueorigins.com, try again. I have gone over their entire collection of supposed speciation events, and they fail miserably when the assumption of the fact of evolution is taken out of the equation. Most of the time it is only variation being expressed, or adaptation. Nothing more. Care to provide us with an example so that I can demonstrate to you the fallacy of your argument?

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This is why scientists reject the idea of immutable "kinds".

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Not all scientists, only evolutionary scientists, and most of those do not even work in biology.

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Firstly, there's no scientific definition for the word.

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Sounds like you need to read some papers on Baraminology and Discontinuity Systematics. "Kinds" has been defined, and very well, I might add.

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Thirdy there's no observable barrier to the capacity of speciation to create new variety in taxonomic forms.

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Tell you what, crashfrog, go buy yourself some plywood, chicken wire, nails and some pigeons and begin to breed them. When you produce a purple pigeon, or even a pigeon with more than two wings, then you will have some ground to stand on. Right now your stand is bankrupt, as 10,000 years of animal breeding has aptly demonstrated.

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You may wish to learn about population genetics.

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It wouldn't do him any good. Population genetic has absolutely nothing to do with TOE in fact-hood. Population genetics only counts changes in expressed gene frequencies, and nothing more. Changing gene frequencies gives about as much scientific explanation of TOE as my big toe-nail falling off does. Zilch! Try again.

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you need to think of species not as individuals but as populations.

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I hear this so many times...and it is so laughable. What is a population made up of? Individuals. Individuals inherit and reproduce, populations do not. This is another one of those argumentative word-games utilized so many times in trying to throw our attention off of the real situation. And what is that? It is the fact that there has never been, nor will there ever be, a case of speciation recorded or observed. If there had been, population genetics would be looked upon for what it is today, only a mechanism for tracking variation within a population to assertain why some populations die out and others within the same species do not.

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Not really a dilemma. Can a cell reproduce a cell? yes it can. Do unicellular organisms even have a mature state? No, they're always "mature". A bacillus can divide as soon as it has been "born" (by division of it's parent).

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This has no real bearing in the discussion. If you are going to address Paul's statement, do so on the grounds that he began, within sexual reproducing organisms.

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No one argues that reproduction "evolved", anyway. Reproduction and replication are the foundation of life. The first living molecule must have been one that could self-replicate. In the beginning, asexual reproduction was the order of the day. The path to sexual reproduction follows a large number of transitional states, some of which persist in species today.

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This also has no bearing on this topic, but I will say that you have now confused things. Reproduction is not the foundation of life, life is. Secondly, there is no such thing as a living molecule, if you have found one, please let us know, I will put your name in for a Pulitzer. And finally, you have entered into the world of origins, and you have absolutely no standing here, neither.Good day!

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The basis of your thinking from this and other posts appears to be that you think that organisms have some kind of "perfect", normal state that any mutation represents a deviation from. Since any deviation from perfection must be worse, you label all mutations that have effect as "destructive".

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Negative. It is not what I think, it is what mainstream data sictates. Try again. There are only two kinds of mutational prime affects, neutral and deleterious. All mutations that seem to confer some kind of beneficial side affect (only two that I am aware of), are deleterious as their prime phenotypic affect. Try doing some research and quit arguing for arguments' sake.

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Basically what you're saying is that all mutations that have effect are deleterious because they make the organism different than it's "supposed" to be. And what we're saying is that organisms have no ideal state, and the difference between a "better" and "worse" change is based only on environment.

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Your repeated references to Platonic states is in greave error. First, if you have even ever read Plato, you grossely misunderstood what he was saying. Either that or you read some one else's gibberish who misunderstood him. Probably Mayr.The Platonic point of view is that each "kind" was created as perfect, not that they remain in that perfect state. Yes, I do acknowledge that the original kinds were created in a perfect design, but mutation has seen to change that on a grand scale. So all of your arguments on imperfection are mute and go no where, try again.

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Basically all you're offering is your own value judgement that no effacious mutation could be beneficial because it makes the organism different from it's ideal state. And what we're saying is that no ideal state has ever existed. Just because something is different doesn't make it worse.

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This is not what I am stating. But, still, nice try, but you need to do it better.Greetings.

PG: The data says that all mutations that have an affect upon the organisms to which they occur, have deleterious effects, regardless of whether they also confer some degree of beneficial outcome.Pardon my intrusion. I don't have time to reread this entire thread, but it seems that you are denying that any purely benefical mutations are known. Is that your position? If so, I can provide examples. If that is not what you are saying, then pardon my interruption.FK

OK, I have read through a few more of your posts and see that you do believe there are no purely beneficial mutations. Answers in Genesis would certainly disagree with you, as they acknowledge that they do exist (they just declare that they are all decreases in information).Here is a list that was posted earlier today at NAIG: http://www.science.doe.gov/...
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http://www.cs.colorado.edu/...ay/creation/dup_favorable.html
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Are Mutations Harmful?There are a number of purely beneficial mutations listed.FK[This message has been edited by Adminnemooseus, 04-21-2003]

crashfrog: Here's an example that comes up a lot: bacteria that, on a nylon substrate, mutated to become able to digest mylon. (Well, only a few of them did. The rest died because there was nothing else to eat. Eventually the population consisted mainly of nylon-eating bacteria.) In doing so, they lost the ability to digest carbohydrates. (I don't have the link on hand, maybe somebody could post it?)http://www.nmsr.org/nylon.htm

For what reason do you assume that the bad effect is the main effect, and the good effect is the (presumably lesser in your view) side effect? See, it's just that kind of subjective language - which permeates your arguments - that makes it hard to believe you're not making subjective value judgements. I could just as easily say that a beneficial mutation has a positive main effect but a negative side effect. I think you mean "moot", by the way.Your argument stands on yet another untestable assumption (and is probably therefore circular). Who is to say that these perfect, ideal "kinds" ever existed? Certainly there's no such evidence in the fossil record. yet you assume they existed, assume any deviation from their original genotype is a destructive degeneration, and try to characterize all variation from these ideal originals as inferior, when the fossil record shows the exact opposite.Let's examine a very beneficial mutation, as provided from a link by Fedmahn Kassad:

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"A mosquito species called Culex pipiens can now survive massive doses of organophosphate insecticides. The mosquitoes actually digest the poison, using a suite of enzymes known as esterases. The genes that make these esterases are known as alleles B1 and B2. Many strains of Culex pipiens now carry as many as 250 copies of the B1 allele and 60 copies of B2."

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The Beak of the Finch p.254
The mosquitoes acquired B1 and B2 by two mutations. They then acquired the huge number of copies by duplication mutations. They benefit because the extra copies cause their bodies to produce extra esterase. Whenever a huge amount of insecticide is sprayed, mosquitoes that have lots of resistance are the most likely to live and reproduce.

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Until 1984, California mosquitoes had neither B1 nor B2. They acquired all those copies in a single decade.

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(Thanks for the links, Fedmahn Kassad.)Now, explain to me how the main effect of this mutation is destructive?------------------
Epimenedes Signature: This is not a signature.

Can I just ask - what does that even mean? Life is the foundation of life? You are aware of the fallacy known as the "circular reasoning", right? I think this pretty much fits the bill.Honestly, how do you hope to convince anyone with this level of dicourse? So let me ask you, then, what is the foundation of life? Life didn't begin with sexually reproducing organisms. Life began with clonally reproducing organisms. Sexual reproduction evolved later, through a number of transitional forms preserved in the fossil record (and even in some hermaphriditic organisms alive today.) Here's one example, chosen at near-random from that page...

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5.3.1 Drosophila paulistorum Dobzhansky and Pavlovsky (1971) reported a speciation event that occurred in a laboratory culture of Drosophila paulistorum sometime between 1958 and 1963. The culture was descended from a single inseminated female that was captured in the Llanos of Colombia. In 1958 this strain produced fertile hybrids when crossed with conspecifics of different strains from Orinocan. From 1963 onward crosses with Orinocan strains produced only sterile males. Initially no assortative mating or behavioral isolation was seen between the Llanos strain and the Orinocan strains. Later on Dobzhansky produced assortative mating (Dobzhansky 1972).

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So, yes, given that the new population experienced total reproductive isolation from the parent population and was unable to be fertile with it, how is this not speciation? By the most widely agreed definition of species, this represents a new one. If you disagree then be prepared not only to state why, but under what definition of species you're using (and be prepared to defend it as well). And that definition is...? (Honestly, you just begged that question. Seriously, why didn't you enlighten me with it in the next sentence? That seems like a logical thing to do. As it stands I have only your word and opinion.)Better yet, take that definition over to Buddika's Creationist's Cannot Define "Kind" thread, as I think he's in desparate need of such a clarification.I'll freely admit not to having done any real research. Most of the time, one doesn't have to do any to refute the shallow and fallacious claims of creationists. But the sheer volume of links to real, scientific research that appear in these discussions (and for which I am thankful to those that post them, like Fedmahn Kassad) indicate to me that the weight of the data is on my side, not yours. Perhaps you could post some counter-data? I haven't seen too many links from you, just empty assertion.

I'm posting this is response to Crash, because trying to respond to specific posts by PhospholipidGen and Paul would be redundant and a little late. So here's my contribution to the thread, so far.Crash:I think you may be in a no-win argument here. Both Phospho and Paul have stated plainly that what they require for the ToE to be true is instantaneous (one generation) transmutation (Paul's term) before they will accept the possibility of evolution. Since outside of relatively rare cases in plants this is impossible, nothing that you present is going to be effective. In essence, they have erected an impregnable barrier based on a strawman argument which allows them to ignore all contrary evidence - no matter how many journal articles are presented. As I see Phospho's and Paul's stance, it boils down to (and hopefully they will correct me if I've mistated something):1. Evolution can only occur in individuals, because only individuals reproduce. This of course eliminates in one go all of evolutionary ecology, ecological genetics, population genetics, etc. The stance allows them to ignore population and metapopulation dynamics and the ecological basis of speciation. For example, they are free to ignore hybrid zones between divergent geographic populations, ring species such as Ensatina, the genetic basis for polinator preference observed in Mimulus, the observed genetics of bird speciation, etc etc. Any speciation you present based on the observations that have accumulated over the last 150 years can be safely ignored, because as Phospho has asserted: Obviously, pop gen scientists would disagree - but you'll never get such an admission from either of your two interlocutors. However, if you have access to a decent library, you personally might find the following articles interesting:Orr, A 1995, "The Population Genetics of Speciation: The Evolution
of Hybrid Incompatibilities", Genetics 139:1805-1813Via, S 2002, "The Ecological Genetics of Speciation", American Naturalist (supplement) 159:S1-S7Jiggens, CD and Mallet, J 2000, "Bimodal Hybrid Zones and Speciation", Tree 15:250-255And last but not least, the seminal paper on a 30-year study of speciation by Grant, PR and Grant, BR 1997, "Genetics and the origin of bird species", PNAS 94:7768-7775Of course, since there's no such thing as populations, feel free to ignore them. You might also take a look at the on-line articles I posted earlier for Salty which discuss incipient speciation and Mammuthus's cichlid references. Just remember, it's all variation within a kind. 300,000 species of Coleoptera are all still beetles. On the one hand, we have an extraordinarily broad definition of what constitues "species", and on the other we have an immutable barrier where a significant morphological change is "required" on the order of a chicken-from-a-lizard's egg. As Paul puts it, the demand is:2. Mutation doesn't cause variation within the non-existent populations. Mutation is always negative or neutral. There can be no beneficial mutations (and hence no speciation) without a corresponding and confounding deleterious mutation. Of course, this begs the question of what happens when there ARE positive mutations, such as outlined in numerous articles like:Zhang, J and Rosenberg, HF 2002, "Complementary advantageous substitutions in the evolution of an antiviral RNase of higher primates", PNAS 99:5486—5491

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An improved understanding of the evolution of gene function at the molecular level may provide significant insights into the origin of biological novelty and adaptation. With the approach of ancestral protein reconstruction, we here address the question of how a dramatically enhanced ribonucleolytic activity and the related antiviral activity evolved in a recently duplicated ribonuclease (eosinophil-derived neurotoxin) gene of higher primates. We show that the mother gene of the duplicated genes had already possessed a weak antiviral activity before duplication. After duplication, substitutions at two interacting sites (Arg-643Ser and Thr-1323Arg) resulted in a 13-fold enhancement of the ribonucleolytic activity of eosinophil-derived neurotoxin. These substitutions are also necessary for the potent antiviral activity, with contributions from additional amino acid changes at interacting sites. Our observation that a change in eosinophil-derived neurotoxin function occurs only when both interacting sites are altered indicates the importance of complementary substitutions in protein evolution. Thus, neutral substitutions are not simply ‘‘noises’’ in protein evolution, as many have thought. They may play constructive roles by setting the intramolecular microenvironment for further complementary advantageous substitutions, which can lead to improved or altered function. Overall, our study illustrates the power of the ‘‘paleomolecular biochemistry’’ approach in delineating the complex interplays of amino acid substitutions in evolution and in identifying the molecular basis of biological innovation.

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The article is not only interesting from the standpoint of a non-existent beneficial mutation, but also shows that so-called "neutral mutations" may have a beneficial effect depending on the environment.All mutations are deleterious to the organism. As Phospho notes: "If this is true, please explain how such genetic diseases that are caused by mutations have to do with their environment. Such diseases as Huntington's Disease, or Tay-Sach's Disease, or how about Parkinson's Disease?" {"This" in the above refers to your "The utility (or lack of same) of ANY mutation is due to environment."} Phospho apparently wants to preclude the existence of any beneficial mutation by pointing out that some genetic diseases caused by mutation are deleterious - and by extension ALL mutations are deleterious. Of course, no one has ever said all mutations are beneficial, either. These are certainly deleterious, and it's highly likely that the diseases noted were only able to be fixed in the population (there's that word again) because the environment has changed to make them LESS deleterious by providing medical support, etc. Of course, they have to be homozygous at multiple loci for the full blown disease to show up - and in the case of Parkinsons' most of the really bad things happen well into late maturity (so post-reproductive in most cases anyway).I will agree with Phospho that SCA does have both a negative and positive effect. The action of stabilizing selection is what has allowed the trait to persist. Only heterozygotes get the benefit without the real negatives caused by the mutation, although even here there is some anemia - outweighed by the higher selective effect of not having it at all. Homozygotes with the full-blown anemia tend not to live to reproductive age, and homozygotes without the trait tend to produce less offspring in malaria-endemic areas. So in this case, there is a strong environmental effect that keeps the obviously negative allele in the population. It is a beneficial effect in the presence of Plasmodium, it is negative (either mildly or fatally) in the absence of the parasite.Closing with an extraordinarily revealing quote from Phospho:The funny thing is - artificial selection by humans HAS produced "purple pigeons" - or at least their equivalent. Contrast the amazing differences in pigeon breeds like fantail, owl, trumpeter, jacobin, etc. Basically, pidgeon breeders have created some of the most amazing and bizarre forms you can imagine - something on the order of 2000 recognized breeds. And since artificial selection is being used to develop specific forms pleasing or required by humans, it is directed evolution, not natural selection whose only requirement is that the organism be "well-enough" adapted to its environment to survive long enough to reproduce. As for the "two sets of wings" routine, I'm not sure that is possible. It would require a huge skeletal, muscular, etc re-design. Oh, wait, I forgot, that's precisely what Paul and Phospho demand that evolution produce. Since it doesn't (and quite likely can't), it must be false. My mistake.

Are you religious?You do seem to be implying that mutations prevent organisms from doing/being/functioning as they are 'supposed to'. But to make such a weird authority claim, you imply that [by some mysterious authority] there are such things as 'perfect' kinds.How on earth did you come to this conclusion? Where is your evidence that 'perfect kinds' ever existed? Do you happen to have discovered or chanced upon a fossil of a perfect kind? By what yardstick do you measure perfection?I draw this conclusion from the fact that you state that all mutations are 'deleterious', i.e. evolution is a process of degradation from a supposed 'higher form', supposedly, therefore, going backwards in time, each 'kind' becomes more 'perfect', and we eventually arrive at some kind of utopia [unless you deny that any mutations occur].Also, even if your 'theory' is correct, how does the supposed damaging nature of mutations prevent the creation of new species? degradation might be faster in some sectors of a population, hence producing a lower and less 'perfect' [but different nonetheless] species.

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Second, environment has nothing to do with the catagory, nor the effects of deleterious mutations. They are deleterious no matter what, and can cripple an organisms life processes or outright kill it within days or weeks. The only place where environment comes into play is with the so-called beneficial side effects of the mutation.

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You are wrong. Deleterious and beneficial are both defined with respect to evironment.The source of your confusion may be those mutations that so badly disrupt the organism that it does not survive in any environment. We can ignore these in practice, since they have a 100% negative selection; they do not persist in future generations.But this is not definitional; this is just an extreme case. What is of more interest are mutations that arise and persist and may have an effect on future generations, for good or for ill. And that is defined with respect to environment.The way deleterious and beneficial are actually defined is by measuring selection effects; and that can only be done in a particular environment.It is quite usual to have mutations which are beneficial in one environment and deleterious in another. There is a discussion of this by Joe Boxhord as a part of the Are Mutations Harmful? FAQ at talkorigins, which examines mutation studies in bacteria. There are many examples there of what I am describing. Here is one in particular, using work by Chao and other in 1977. They grew E coli. cells, and innoculated them with a bacteriophage T7 that would kill the E. Coli. In time a mutation arose in the E. coli which gave them resistance to T7. Then the T7 virus mutated to infect the mutated E. Coli, and then a new mutation arose in E. coli to give resistance to the mutated virus. The experiment had 3 strains of E coli and 2 strains of the T7 virus co-existing. But the beneficial mutations came with a cost; the E. coli tended to take up nutrient more slowly. Hence these mutations were beneficial in one environment (with T7 present) and deleterious in another (with no T7 present).Also, why do you say "so-called" beneficial "side-effects"? The existence of beneficial mutations is unambiguous, and acknowledged by groups like Answers in Genesis.

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On this part I not only disagree, but so does the observations of genetics. There is no observational evidence anywhere which states that variation has its origin within mutations. Think about that for a minute, if the only mutations that have an effect upon the genotype as well as the phenotype are deleterious (because we both know that neutral mutations have no effect) and only some very rare ones hold any kind of beneficial side effects depending upon the environment in which the organism lives, how many are left that could really lead to variation? Every deleterious mutation shortens the life span of the organism in which it occurs, as well as conferring genetic illness which is usually the reason the organism dies.

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Actually, you are wrong again. It is certainly not the case that neutral mutations have no effect. Neutral only means that the effects are neither beneficial or deterimental in the existing environment. The terms beneficial, deleterious and neutral are all defined by the selective effect of the mutation in a particular environment.If the effect makes no apprecial difference to the fitness of an organism, then it is neutral. This still gives rise to diversity. Furthermore, because these terms are most emphatically defined with respect to environment, note that neutral variations can become beneficial or deleterious when the environment changes. Again, the FAQ I cited above discusses this phenomenon with a mutation in E. coli that gives resistance to a T5 bacteriophage; but which is neutral when there is no T5 present. This was measured by tracking the levels of T5 resistance over time in a culture which had no T5 present.

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Yes, as defined by evolutionary theorists when they could not produce a viable beneficial mutation.

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You are behind the times. The existence of viable beneficial mutations is so solidly established by many different studies and direct observations that even groups like Answers in Genesis acknowledge they occur. Their new line of argument (which is just as counter factual, of course) is that mutations cannot add information. But there is no point discussing that until you catch with the basic and trivial fact that yes, there most certainly are beneficial mutations.

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To the quick - any biological change, heritable or not, is NOT evolution in progress. It is only a biological change. The sooner mainstream science understands this, evolutionary theory will disappear over the horizon. It's day is coming, and coming fast.

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It has been coming fast now for well over a hundred years.Glenn Morton may be known to some people here. Glenn is a geologist, and an evangelical Christian, and he used to be an active young earth creationist. Some of his creationist writings are still being cited by creationists now, although Glenn has long since acknowledged that they are completely incorrect. Glenn has recently produced a new document called The Imminent Demise of Evolution: The Longest Running Falsehood in Creationism. In it, he documents a trail of claims about evolution and related science being on the verge of rejection, starting way back in 1825.Glenn's title is a bit misleading, in that many of his earliest extracts refer not to evolution but to geology -- which is Glenn's own area of real expertise. However, from 1878 they start to focus upon biological evolution. The 1904 extracts are especially hilarious.