The Nature of Mutations

The nature of mutations have been discovered to be changes in amino acid sequences during the replication of DNA. This includes additions, deletions and substitutions of those amino acids which may have an effect upon the protein that is being synthesized.Mutations fall into two main catagories depending upon their phenotypic effects, they are neutral and deleterious. There is no such catagory for "beneficial" mutations in reality, for a very good reason. The term "beneficial mutation" can only be defined according to the organism and the environment to which it is applied, it has absolutely nothing to do with the mutation itself.Mutations that confer "beneficial" effects upon the affected organism are still deleterious mutations. The fact that they may in some small way give an organism some degree of solice in its environment does not change the fact of the nature of the mutation.Evolutionary theorists favorite mutation to quibble about is the sickle cell anemia mutation...this is a deleterious mutation by catagory. It damages the cells to the point that they cannot function as they were intedned to function, they have been damaged. True, that in certain areas this gives the seeming benefit of conferring "resistance" to those affected with the mutation, but this does not erase the damage that the person sustains due to that mutation.Second, it has not been proven anywhere at any time to my knowledge that variation arises from mutations. This is part of the grand assumption that evolution is a fact and, therefore, the naturalistic paradigm demands endless variational changes, so theorists assume it into the equation. This is why it is called a "gene pool" and not a "gene stream" because there is NOT an endless supply of variation streaming into the genome of species.Without endless variation, you have no evolutionary change. Adaptational changes in organisms are due to changes in gene expression by environmental ques, and are not due to mutations.All of your examples of bacterial adaptation that I have come across to date are just that, changes in gene expression, from inactivated to activated sites. Nothing more. I also find it hilarious that after touting that evolutionary change takes hundreds of thousands of years to take hold, now suddenly we can take a bacteria and bring about evolutionary changes in months. This is not evolutionary change, this is adaptation.And adaptation is not evolution, it is not speciation. It is change, but if you are going to go to that silly and ridiculous length to try to prove evolutioanry theory, then we better start calling every single kind of change in the all of all as evolution.Gotta go, looking forward to your comments.Have a nice weekend!

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So if there was a specific example of a mutation that was not there to be activated but occured by chance and that mutation confered benefit then you'd be wrong in your assertions?

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A mutation is nothing that can be activated, it is only an accidental copying error made during DNA translation. And again, if the mutation happened to give any degree of "beneficial" effect, which I never said did not happen, then we must remember that this mutation is still deleterious in its direct effect upon the organism.

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Just to clarify: You're saying that all beneficial mutations are a result of a gene activation?

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No, that is not what I said. I said that there is no such thing as a catagory of pure "beneficial" mutations, any such mutation that confers a benefit does not fall into the catagory of neutral mutation, so it must fall under the catagory of deleterious mutations. Genetic changes that are activiated via environmental ques are NOT mutations. They did not become expressed by mutations.

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But you will agree that there are "real" mutations (that is genetic changes which were not there at all before)?

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Definitely.

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What stops the "real" mutations from ever being beneficial?
What causes the gene to be activated when needed?

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A mutation may confer some degree, however slight, of beneficial outcome, but there is no evidence at all that there has ever been a mutation that was not neutral, or deleterious, but only beneficial. Adaptational genes are activiated by an environmental que, whatever they may be. I do not ever remember reading any papers on discussions of what those ques were.Greetings!

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Are you saying in the above that if there was any mutation that didn't have the deleterious side effect that the sickle cell mutation does that it would still not be "beneficial"? How could you say that?

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Or do you mean that you don't think there can be any such mutation that while beneficial don't also have some deleterious effect?

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First, let me clarify that mutations aren't "side effects". Mutations that are neutral have no effect, and deleterious mutations have destructive effects upon the organism in which they occur. The "side effect" would be such as the SCA mutation, where the side effect is the protection against the disease. It is not that I don't "think" that there is such a thing as a purely beneficial mutation, it is that this is what genetics has observed and recorded.Greetings!

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The mutation has some effects which are beneficial, and other effects which are detrimental. How, then, can you label it as deleterious? There are some environments in which it is a benefit.

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(There is a subtle point here also, in that the major deleterious effect is in homozygotes for the mutated allele.)

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What this demonstrates is that beneficial and deleterious are both defined with respect to an environment.

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First, thanks for clearing up my verbology!
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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This is merely berwildering. What do you think variation means? Of course mutations lead the variation. How could they not?

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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.How then can you come up with variation from deleterious mutations? For that is all that one has to work with. No, evolutionary theorists assume purely beneficial mutations and they assume that variation originates from mutations because there is no other place form them to come from in a naturalistic paradigm. But, who ever said that the naturalistic paradigm is the correct one?

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The mutations change the DNA sequence, which changes the protein sequence, which has an effect, which is sometimes advantageous and hence tends to spread through the bacterial culture as generation pass.

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True, however, these insertions are not random, and they require specific enzymes in order to be inserted into the DNA sequence. So what we have here is NOT a mutation, but a specific mechanism for turning on protein sequences when they are necessary for cell survival. These not only are not mutations (only genetic changes which are not mutations), but they do not help evolutionary theory since it is adamantly reported that evolution is NOT directed, but random as far as mutations go.

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Shrug. Any biologically heritable change is evolution, by definition.

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

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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!

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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.

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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.

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My calling them damaged implies nothing, it is a straightforward observation. Your illegitimate assertion that design is a meaningless term in regards to biology is rediculous. This is an assumption on your part, and on the part of evolutionary theory that cannot be substantiated nor proven. And if we are to get off the subject (which I do not want to do) and speak of paradigms, it is not my paradigm that is lost in space. When you can provide evidence for your naturalistic paradigm, then you may have some ground on which to stand, but right now you don't.

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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.

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Are you serious? What you mean to say is that all possible polypeptides have a shape. A protein is a polypeptide that has a specific function to carry out, otherwise it is just a conglomerate of polypeptide materials. And its "usefulness" does not depend upon its environment, where do you get this stuff from, talk.origins? A proteins usefulness comes from its funtion, which is dictated by its specific conformation, which is dictated by its amino acid sequencing. It has absolutely nothing to do with its environment.

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I'm sorry, I think you fail, because you can't divorce yourself of a teleogically driven biology.

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Actually, again, you fail. And your failure is based upon the fact that you take a theory that is based entirely upon speculation and assumption as a demonstratedly proven idea, when it is not.Something for you to think about, frog, creation has never been disproven, it was abandoned by those looking to escape God. Hint, there is no escape.Greetings!

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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.

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Yes, this is what I am saying, to the best of my knowledge. All supposed "mutations" that are considered purely beneficial are in fact not mutations at all, but simply genetic changes such as recombination. But recombination is not a mutation.Greetings!

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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).

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Actually, let's go through your provided list...The Milano mutation, this is not a purely beneficial mutation. The wild type of the protein which it affects produces HDL. The mutated form, apoA-1 Milano, destroys that capability, which is why those inflicted with the mutation had low levels of HDL. Sure, it also has the beneficial effect of working as an anti-oxidant molecule, but the key issue is that the original function of the protein is destroyed. If it had not had the beneficial side affect of acting as an anti-oxidant, those afflicted with this mutation would die early deaths due to such low levels of HDL.Culex Pipiens Mosquito did not originate the insecticide digesting enzymes via mutation, they already had them. The key that enables them to survive this particular pesticide is the copies of the gene that codes for them. The more copies they have, the more enzymes they produce which takes care of the pesticide before it can cause lethal damage. The copies of the genes are not true mutations, they are copies of genes that were already within the genome. This is not a deletion, addition or substitution of nucleotides/amino acids during translation of DNA segments.RNASE1 AND RNASE1B genes in old world monkeys, these are not beneficial mutations. They are not random copying errors within the monkeys genome. The article even admitted that these changes were not random, but adaptational in nature. Such changes are incurred via genetic switches being turned on, enabling genes prevously not expressed to now be expressed. These are genetic changes, but they are not mutations. The information has always been there, just previously unexpressed.Nylon eating bacteria is always a favorite for evolutionists on debating boards. As the article pointed out, it is not so much nylon, but nylon oligomers, which are not new to the world. They are called "nylon" and people automatically think of your household nylon rope, this is not the case. Nylon occurs naturally from certain plants as waste, as the article clearly says, the only thing is that true.origins has never been up front in any of their articles about all things. Naturally occurring nylon oligomers from plants has always been around, so how do they get away with saying that they are not found in naturally occurring products? I have no idea. The fact remains that while modern science has identified bacteria that can now "digest" nylon oligomers that before (in the scientists small sampling world) could not do so, does not mean that they did not do so in the past. This is also indicated by the fact that, we are told it has taken millions of years for evolutionary changes to take place and be selected for, waiting for the right selection pressure and environment to come along inducing such pressure. Do you really think that these bacteria evolved to be able to "eat" nylon in only a few short generations?Lets get real here. The only possible explanation that fits with the facts of known science (not the unprovable assumptions of evolutionary theory) is that these bacteria have had this adaptational capability, only it was not utilized and switched off because it was not needed. Then, when the need arose, the genetic switch was thrown into the "on" position by the organsim, and here we go. The change is not mutational, and it is not random.Greetings!P.S., I cannot answer any more today, I have to go. I will answer the others as soon as I can get the time.

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do you still maintain all beneficial genetic changes are simply recombinations?

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I never stated that all beneficial changes are due to recombination.

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There's a dozen posts about non-deleterious, beneficial mutations. I'd prefer that you address them before jumping down my throat because they're much more of a threat to your arguments.

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Nice try, but that won't work.

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I don't have to provide evidence for a naturalistic paradigm.

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Yes, you do. Especially when that naturalistic paradigm is assumed, not proven. And most especially when that naturalistic paradigm is forced to make assumptions beyond the perview of what the evidence allows.You most certainly have to prove it, and to date, evolutionary theorists have failed to do so.Greetings!