The Nature of Mutations

Hi Q,
I was not trying to limit it to point mutations. I just wanted to avoid calling the results of sexual recombination mutants or mutations as that would be about as unhelpful as the Semi-Meiotic hyphothesis . The definition you dug up looks to be suitable for the purpose of this thread..what was the topic again ?The one problem with the definition is the vagueness regarding "changes in gene expression"...it covers epigenetic modification but does not account for variation induced by environment which is not really a mutation. I am thinking of variation in coat color in cloned cows or variation in paternal or maternal X chromosome inactivaition in female embryos which are driven by purely stochastic events....but I guess that is covered since the definition says heritable change.So regarding definitions...do we have a winner? crashfrog, Fedmahn, Percy, Nosyned..comments, disagreements, additions?cheers,
M

NOW THAT I S funny

I was there specifically thinking of whatever it is in the search programs for sequences that prevents easy finding of a match or alignement, i.e. point mutations, junk DNA, non-known expressible repeitions. I am not fluid in DNA base pairing lingo as of yet coming from this more from a whole organ in the ism perspective.
I am however trying to imagine if specific expressivity such as to the cell membrane is a flow in one direction from the DNA that these kinds of non-function known changes are FORCED by Newton's Third Law on the the physical chemistry say of having to get beyond any topology of a lipid/water eddy immiscibility that CHANGES when an extracellular protein for instance is expressed and expelled from the cell of "origin". Some epigensis when not "pre-programed" preformation may be involved in motions of this framed by a cell collective kind but not of the line of expression that would have to more than correlationally contiguous in terms of the chemico-physics biophysically etc etc.
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I was trying here to give you access to what Gould attempts to formalize in terms of a heirachy selectable flesh. All of my posts sum to the same thing. But once one trys to work on the actually forces involved whehter at a distance or say contiguous in Faraday's sense then some SPACE is travesered in the description in words that indeed may fail to denote the nature being attempted to be read. In this case I was trying to specify both the mutants AND the environment of them so that you, the reader, could be more able to judge if I had indeed said something of the mutation itself for which If it said nothing then the environs would be come spatially relevant and that apears tp have happened to you. This may indeed be a mutation.I was trying to describe what in DNA-RNA "compaction" may be molcular but NOT a muatation and yet the terminal place of correlation of epegenisis. What was missing as it did not pertain to this very thread was WHY i think scientifically Newton's @nd book can be re-read in mole bio terms. I may be wrong but then I would have reverted to a discussion of Helmhotlz and all sorts of nanotechology sustpect things in my opinion. I have a way of thinking about the use of Calculus and functions that Borel and Lebseque discussed that Hadamarrd deviated from that may not be "monstors" but integral to embyrogeny but that is the ADJECTIVE I used which I think Russel MISUSED as the word "ordinal" but now we make this thing being at the fringe of my acutall reading even harder for the majority of c/e users to follow lest of of best the ball.Biology is not an easy discipline to talk about if one wants to have it written that economics flows from biology and not the other standard way around. I can try to unpack this notion further but you are at my current bounds and that will only liekly lead to more frustration as I simply write what I think than what I think I can teach.

I think it's a winner but don't know what epigenetic means.

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.

Yeah, that works for me too. Unfortunately, it looks like PG lit out of here once he figured out that the beneficial mutations argument was one he couldn't win.FK

If that's so, I wish he could have posted something like "Blah blah blah I'm done wasting my time with you people" like other people who give up seem to do, that way we wouldn't be wasting our time coming up with definitions we're not going to use.Although I'm holding out for his return. He seemed pretty adamant that he was right. I don't think he's just going to give up. There's a number of things that I for one would like him to address...

Hmm, I may be trying to force too much into that definition, but I think the "chemical rearrangement ... in a chromosome" covers structural mutation while leaving normal recombination and random shuffling during fertilization as "non-mutation". Feel free to make it more clear by changing the wording. After all, the objective is to come up with a definition that covers the wide range of possible mutations while at the same time restricting things to something that the creationist can't weasel out of...

Thanks for responding guys. Now with a definition of mutation in hand maybe we can proceed with more of what PLG posted...as several have noted, he bolted and may or may not come back. But the thread is interesting so I for one would like to continue...PLG:
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.M: This is a rather odd way of looking at things. PLG ultimately does not want to concede that mutations can confer any benefit but he ignores the meaning of beneficial in the context of natural selection. Sickle cell heterozygotes can survive and are more resistant to malarial infection than normal individuals. Thus, the detrimental effects of the slight sickle phenotype are outweighed by the benefits (RELATIVE to wild type) of malaria resistance...thus heterozygotes have a better chance of reproducing and the sickle mutation is maintained in the population. In a non-malaria environment the mutation would likely be weeded out quickly as homozygotes and heterozygotes would be at a great disadvantage. Ultimately, the heterozygous state of the sickle cell trait IS beneficial.PLG:
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.M: This makes no sense whatsoever. If I have an C at a particular position in my mitochondrial D loop and PLG has a T at that position, this is part of the genetic variation of the human mitochondrial gene pool and it directly derives from a mutation event. This is the case for all mutations. If genetic variation does not derive from mutation then why are we not all clones?PLG:
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.M: This is also completely false. One does not require endless variation for evolutionary change. In fact genetic drift which reduces variation can do as much for evolutionary change as increase in mutation accumulation in a large population.
Adapatational changes are not a mere response of genes to environmental queues unless PLG is proposing Lamarkian molecular biology. Changes in promoter sequences have more to do with changes in gene expression that are adaptive...and for more on adaptive mutations:Elena SF, Cooper VS, Lenski RE.
Punctuated evolution caused by selection of rare beneficial mutations.
Science. 1996 Jun 21;272(5269):1802-4.PLG:
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.M: First he says there are no examples of bacterial adaptation and then it is only adaptation...in any case, the above reference demonstrates that this statement is false. I have posted other references from the same and other groups that experimentally show that it is not changes in "activated or inactivated sites"...whatever that means. In any case, evolution takes thousands of years to observe in organisms with long generation times...like mammals. Bacteria do not have this constraint and thus we can observe many thousands of generations (Richard Lenski's group is up to 20,000 generations and counting) and hence evolution in action. If you try to do the same with say elephants with an 18 month gestation period you better be immortal to see the outcome of the experiment.PLG:
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.M: Another strange statement and a misunderstanding of evolution...from your basic evo textbook"In the broadest sense, evolution is merely change, and so is all-pervasive; galaxies, languages, and political systems all evolve. Biological evolution ... is change in the properties of populations of organisms that transcend the lifetime of a single individual. The ontogeny of an individual is not considered evolution; individual organisms do not evolve. The changes in populations that are considered evolutionary are those that are inheritable via the genetic material from one generation to the next. Biological evolution may be slight or substantial; it embraces everything from slight changes in the proportion of different alleles within a population (such as those determining blood types) to the successive alterations that led from the earliest protoorganism to snails, bees, giraffes, and dandelions."
- Douglas J. Futuyma in Evolutionary Biology, Sinauer Associates 1986So, PLG or any other creationist want to pick up this argument?Anyone else feel free to add to, criticize or otherwise comment.cheers,
M

Thanks for clearing that up Brad.

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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!

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If you equate design and function you commit an error. Simple as that.

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Only if we are talking about art. Simple as that.

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A tool, or protein, has no function in the absence of the elements that it acts upon.

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Come on...you have got to be kidding, right? You are honestly going to say this? This is nothing more than mindless regurgitation of nonsense. Think about what you just said. A screwdriver has a purpose whether it is in an environment where screws are present or not. You are repeating mindless evolutionary Dawkins-like trash that makes no sense whatsoever. Try again.

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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.

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You are wrong, but I won't hold that against you.Greetings!

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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.

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Actually, I'm not playing dictionary games, thats usually what evolutionists do. Anyway, I was talking this subject over with a friend and he agrees that gene duplication technically would be considered a mutation, like you stated, because it takes place during its copying. He did state, however, that this does not help evolutionary theory because it does not make anything new, just a copy of the old. It won't cause a new ear or eye to grow from somewhere, or turn your arm into a leg.It may, or may not, help an organsim. In this case, it does, but only by providing additional enzymes that were already present. It didn't mutate new enzymes. So I can meet you half way on this one, but only because it (the mutation) took place during the gene being copied.

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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.

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Are you thinking before you ask these questions? The mechanism is called a transposon, a little piece of genetic material that "jumps" around DNA and is inserted and removed from exact locations by exact enzymes designed for the job.As for your other questions, do animals in the midst of adapting to severe climate (for example) all adapt at the same time and survive? No, they don't, some die. Thats just nature.Greetings!

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Are you suggesting otherwise? My reading of this research suggests this:
1) The genetic changes that produce the nylon digesting capabilities are known. They are exactly a one unit addition witch shifts the code.
2) They are not present in the preceeding bacteria. It is an easy random mutation to get to it however.
3) In the environment of the experiment the mutation is beneficial.

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What part do you disagree with?

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I agree with all of the above except for calling the genetic segment that turned this capability "on" as a mutation. It is an insertion of genetic material at the precise spot needed to turn this capability on, and originated via specific enzymes. Bacteria have several different ways of adapting to limited or changed nutrients. Another way is that a whole enzymes is coded for within the bacteria's genome that, again, has its coding region made active via insertion piece or insertion of an entire sequence by specific enzymes that splice them into the DNA, just before the gene that is currently turned "off".These are not mutations. They are mediated by specific enzymes.Greetings!