The Nature of Mutations

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.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.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. This is incorrect. For all you've said about biologists assuming things, it's your asusmtions I would take a closer look at if I were you. Just because a sickle-cell heterzygotes cells are "different" doesn't mean they're "broken". In fact, they work just fine. Heterozygotes for this condition lead full lives. And the upshot is the resistance to malaria. The only way you could think this was bad was if you identified "different" as "bad".Is your entire argument going to center around using terms like "beneficial", "science", and "variation" in ways totally at odds with the english language?------------------
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I agree that some deleterious (perhaps most) mutations are harmful for reasons that have nothing to do with the organism's environment; but my point was that since the cellular metabolism of the organism is itself the chemical "environment" for proteins, and that protein is beneficial or deleterious based on its interactions with other chemicals and proteins in that environment, one could consider all mutations as being defined in utility by "environment". I realize it's not generally what "environment" refers to, my point was show that the envrionment simply can't be discounted when considering the utility of mutations.Does that make any sense?------------------
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Very astute. That's what I've been getting at. I like the way you put it, though.

Were you aware that all scientists and even the majority creationists accept the reality of speciation? 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.This is why scientists reject the idea of immutable "kinds". Firstly, there's no scientific definition for the word. Secondly, new species arising from old ones is observed reality. Thirdy there's no observable barrier to the capacity of speciation to create new variety in taxonomic forms.You may wish to learn about population genetics. If your idea of speciation is an individual changing species (and finding no mates, as it is the first of it's kind) then you need to think of species not as individuals but as populations. When gene pools no longer mix (reproductive isolation) speciation occurs. 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).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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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".This platonic idea is false. It's pretty easy to prove that no organism exists that is perfectly adapted to its environment. (You may be interested to know that the aerobic metabolic pathways in animal cells are only about 20 percent as efficient at using glucose as they could be.) There's always room for improvement. Plus your blanket assertation that effacious mutations always shorten the lifespan of an organism is also false and unsupported, as evidence of life-extending mutations have been found.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.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?)It's your position (I assume) that this is a deleterious mutation because they can't eat carbohydrates anymore, thus they're worse off than before. It's the evolutionist position that it doesn't matter what they could do before because that environment (carbohydrate) is no longer avaliable to them. All they have is nylon. If they can eat it as a result of mutation they are better off than they were before because they'll outlive others in their environment. They're life expectancy has been considerably lengthened by the mutation, and their progeny are much more succesful than those without the mutation. Thus, it's a beneficial mutation.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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To the quicker - this isn't what ToE says. ToE says that any inheritable biological change that confers a survival advantage on an organism will tend to persist in the population. This IS evolution in progress because it's the combination of random, inheritable change with natural selection, which has been proven to be a sufficiently creative force. And the sooner you understand this, the sooner your protests will evaporate.

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.

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?------------------
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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.

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. I don't have to provide evidence for a naturalistic paradigm. It's the simplest assumption of them all because it doesn't require the existence of any entities that can't be tested. It's essentially a negative paradigm: "Nothing supernatural exists." If you seek to replace it with a supernatural paradigm, your model assumes far more than mine. Thus it is incumbent on you to show the evidence for your paradigm. Not so. As GP programs show, it is possible to arrive at function without design. If you equate design and function you commit an error. Simple as that. Let me pose the question this way. If you lived in a country where there was no metal, no machines, and I handed you a Phillips screwdriver, could you tell me the function of that tool? Probably not. (The best you could do would be some kind of weapon.) A tool, or protein, has no function in the absence of the elements that it acts upon. "Protein" is just a name we give to polypeptide chains that, by lucky accident, have a shape that allows them to do something we deem useful to the cell. That's part of the reason protein research is so hard - it's impossible to determine the function of a protein in the absense of its chemical context. Another assumption: Christian-style creation wins by default if evolution loses. Consider that my "World hatched from a Big Dingus Egg in 10,000 BC" theory, which I just made up, has never been "disproven" either. Now, granted, there's no evidence for it, but neither is there for specific creation.

Sure. The apparent function of the screwdriver depends on its environment. Its use as weapon depends on the presence of bodies to stab it into. Its use as a screwdriver depends on the presence of screws.

Sure it's an addition of nucleotides. The copies had to be made out of something, right? Duplications that weren't there before are still additions. As they arose through copying errors and weren't present in the genes of the parents, they're mutations. You're just playing dictionary games. Since all that it took was one point mutation in a gene normally used for carbohydrate digestion, sure. Why couldn't one mutation happen in the space of a few generations? In fact, lots of mutations happen in every generation. And what form to these "switches" take, if not genes? You're the one needlessly mutliplying assumptions. And what mechanism prompts the bacterium to switch on the ability to eat nylon? And why don't they all do it? Most of the population died on the nylon substrate. It's obviously not an effective mechanism.

Nucleotide sequences in an organism that were not inherited from its parents. This includes differences that are the result of copy errors during meiosis of gametes in the parents.Does that sound about right to the biologists? I'm trying to get a kind of semantics-proof definition, here. Comments welcome.

That's good. I like it. I'll accept that definition.Any disagreements?

Works for me. If we've made clear the difference between "normal" chromosomal re-arrangement as a result of sexual reproduction and genetic alteration as a result of damage, free radicals, base-pair copy errors, etc. then I think we're good. PLG should have a hard time trying to weasel mutations through our definition, I hope.But I guess we won't know until he comes back? Unlike me I guess he has a job or a life or something.