molecular genetic proof against random mutation (1)

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Originally posted by peter borger:
dear SLPx,
I invite you to have a very close look at all known sequences of the GLO gene. It mutates non-randomly, implying directed mutation (while it is not even functional!). Maybe this is what you are looking for. I also invite molecular biologists to sequence the GLO gene of the (at least) two primates that still synthesize vitamin C. That would shed light on the issue.
Best wishes,
Peter

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Peter,The statistical definition of "random", as it pertains to nucleotide sequences, is specifically that each site has an equal chance of mutation. Since there are hot spots where the chance of mutation is higher, mutations are therefore non-random where hot-spots exist. However, every site does have a chance of mutation, & you cannot predict where the next mutation will occur, so it is random in that sense.You seem to be claiming that mutations are non-random in the statistical sense, then dropping the statistical definition for a more colloquial one, meaning non-random is deliberate, rather than just not-of-an-equal-chance.You cannot conflate the two definitions to suit yourself.There isn't a random chance that a car of a particular colour will be next to drive down my road, does that therefore infer that a creator is "deciding" what colour car will be next down my street?Mark------------------
Occam's razor is not for shaving with.

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[This message has been edited by mark24, 07-23-2002]

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Originally posted by peter borger:
That's not what I mean. I mean that if a non-random mechanism is operable to generate mutations in genes in response to the environemt it makes it hard not to believe in design.

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Why? Given we don't understand what causes hotspots, don't you think you are jumping the gun?Mark------------------
Occam's razor is not for shaving with.

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Originally posted by peter borger:
And I am not jumping the gun, that is what evolutionists do.

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But you ARE jumping the gun. You don't know why hot spots exist, yet they are evidence of design????? How?"Evolutionists" haven't jumped the gun because they have observed hot spots, & haven't yet enough evidence to attribute a cause.See the difference?Mark------------------
Occam's razor is not for shaving with.

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Originally posted by peter borger:
dear mark,

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You wonder:
"But you ARE jumping the gun. You don't know why hot spots exist, yet they are evidence of design????? How?"

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If mutations are (environmentally) directed than the information to do this was already present in the genome. (See also Fred's letters.)

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Question: How do evolutionist's conceive hotspots?

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Peter

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They don't conceive them, they describe them. Without further evidence, they would be jumping the gun.Mark------------------
Occam's razor is not for shaving with.

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[This message has been edited by mark24, 07-26-2002]

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Originally posted by peter borger:
Dear Mark,

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You say about hot spots:
"They don't conceive them, they describe them. Without further evidence, they would be jumping the gun."

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Mutational hot spots imply non-randomness. And non-randomness suggests (at least) the involvement of a mechanism. Either protein or RNA mediated. It is proof against NDT, since the primary tenet of NDT is random mutation.
Best wishes
Peter

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If you divided a year up into 1 minute time slots, then measured precipiation at a particular point on land, you would find that precipitation is non-random. Does that mean God makes it rain? By your logic it does.A genetic example would be the formation of chiasmata for crossing over as recombination occurs. This isn’t random either, it happens more often in GC rich parts of the genome. However, we know this, so is this evidence of design, or just something that happens naturally? How do you tell the difference? It comes back to the ID argument. How can you tell the difference between a naturally occurring object/system/mechanism, & a designed one?Without further evidence of hot spot causation, you are jumping the gun stating hot spots were designed. You don’t even know WHY there are hot spots for chrissakes.

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Originally posted by peter borger:

Either protein or RNA mediated. It is proof against NDT, since the primary tenet of NDT is random mutation.

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This is getting tedious, though I don’t know why I’m surprised. This is an anti-evolutionary staple, to change definitions in order to claim a falsification. All you have done is to introduce a definition of random that is different than intended.Here’s what D. Futuyma writes on the subject.

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Mutation as a Random Process

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Mutations occur at random. It is extremely important to understand what this statement does & does not mean. It does not mean that all conceivable mutations are equally likely to occur, because, as we have noted, the developmental foundations for some imaginable transformations do not exist. It does not mean that all loci, or regions within a locus, are equally mutable, for geneticists have described differences in mutation rates, at both the phenotypic & molecular levels, among & within loci (Woodruff et al. 1983; Wolf et al. 1989). It does not mean that environmental factors cannot influence mutation rates: ultraviolet & other radiation, as well as various chemical mutagens & poor nutrition, do indeed increase rates of mutation.

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Mutation is random in two senses. First, although we may be able to predict the probability that a certain mutation will occur, we cannot predict which of a large number of gene copies will undergo the mutation. The spontaneous process of mutation is stochastic rather than deterministic. Second, and more importantly, mutation is random in the sense that the chance that a particular mutation will occur is not influenced by whether or not the organism is in an environment in which that mutation would be advantageous

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(Evolutionary Biology 2nd Edition, Douglas Futuyma p281-2)So, you’ve really set fire to that strawman!
Mark------------------
Occam's razor is not for shaving with.

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Originally posted by peter borger:

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And:
"His argument is that if something "random" but statistically weighted is necessarily from God, as you assert, then precipitation is necessarily from God because it is statistically weighted in a very similar manner."

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This is not true. The introduction of mutations is NOT random since it seems to be introduced by some sort of mechanism that has been programmed in the DNA.

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Precipitation in my example above is non random, nor is precipitation at different sites around the world random. So when it rains & where, is designed by your logic.Your entire argument depends on the impossibility of naturally occurring non-random events, I have shown that events CAN be non-random & natural.It once again comes down to being able to tell the difference between naturally occurring systems, & non-naturally occurring ones, how do you tell them apart? If you can’t answer this, ID is dead.Mark------------------
Occam's razor is not for shaving with.

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Originally posted by peter borger:
dear Mark,

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Thanks for your summary of what Futuyma has to say on the subject:

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"Mutations occur at random." Indeed here it says: "RANDOM!!!!!"

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You are aware that there is more than one definition of random, aren’t you? & that you are gainsaying the meaning that is intended? Here, random means, quite clearly, that you cannot pre-determine the locus that the next mutation will take place etc. You are also aware that the contentious issue is the definition of random, as intended by the author. So saying Indeed here it says: "RANDOM!!!!! just makes you look childish. Because, what is patently clear to me, & everyone else, is that Futuyma isn’t using a strict statistical definition (it's the whole point of the passage), as he is going to great pains to describe to you. So when he says "random", you need to take it in the context of the authors meaning, not your own rigid, a priori meaning, OK?

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Originally posted by peter borger:

but next...:

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"It is extremely important to understand (WELL I DO NOT, SINCE THE FORTHCOMING IS CONTRADICTING THE PREVIOUS!!!)what this statement does & does not mean. It does not mean that all conceivable mutations are equally likely to occur, because, as we have noted, the developmental foundations for some imaginable transformations do not exist. It does not mean that all loci, or regions within a locus, are equally mutable, for geneticists have described differences in mutation rates, at both the phenotypic & molecular levels, among & within loci (Woodruff et al. 1983; Wolf et al. 1989)."

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...it says: "but not really RANDOM"

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No, it doesn’t. He is separating the statistical all sites have equal probability meaning, from it cannot be determined where the next mutation will occur meaning.

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Originally posted by peter borger:

So, what he says is that mutations are random but not really. Come on, I do not buy a theory that says: Something is but not really.

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You are beginning to look silly, Peter.Futuyma has clearly set out what random means in the context of RM&NS. Using THAT DEFINITION OF RANDOM, mutations at hotspots ARE random in the sense that the locus for any particular mutation cannot be deterministically predicted, OK? It’s not a difficult concept. So, no, the NDT isn’t expecting you to buy something that is random but not really. IF YOU APPLY THE GIVEN DEFINITION, AND THAT DEFINITION ONLY!!!!!!!!

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Originally posted by peter borger:

Open up your eyes, Mark, don't you see that he set up a theory that cannot be falsified (And still the 1G5 gene falsifies the theory).

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Then, according to you, he didn’t set up a theory that cannot be falsified. Jeez you wan’t it HOW many ways?You’re beginning to lose credibility, mate.

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Originally posted by peter borger:

"Mutation is random in two senses. First, although we may be able to predict the probability that a certain mutation will occur, we cannot predict which of a large number of gene copies will undergo the mutation. The spontaneous process of mutation is stochastic rather than deterministic. Second, and more importantly, mutation is random in the sense that the chance that a particular mutation will occur is not influenced by whether or not the organism is in an environment in which that mutation would be advantageous"

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These are axiomata of NDT. It does not have to be true.

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Doesn’t have to be true? What doesn’t?The meaning that Futuyma gave to random is as valid as any, what’s not true about it?You have attempted to apply a meaning to random that was never intended by the authors, and in showing that your definition actually contravenes observed incidences of mutation, you have created a strawman.You have destroyed a meaning of random mutation that never pertained to evolution. Well done.Mark------------------
Occam's razor is not for shaving with.[This message has been edited by mark24, 08-09-2002]

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Originally posted by peter borger:
dear Mark,

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You say:
"Futuyma has clearly set out what random means in the context of RM&NS. Using THAT DEFINITION OF RANDOM, mutations at hotspots ARE random in the sense that the locus for any particular mutation cannot be deterministically predicted, OK? It’s not a difficult concept. So, no, the NDT isn’t expecting you to buy something that is random but not really. IF YOU APPLY THE GIVEN DEFINITION, AND THAT DEFINITION ONLY!!!!!!!!"

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For the last time:
Since the mechanism is unknown --and the mechanism is currently not known-- but there are more and more genes that do not change at random, but rather subject to the environment (directed evolution). This falsifies NDT, since the first tenet is randomness independent from the environment.

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Cites please for directed evolution.Now the first tenet is randomness independent from the environment, I do wish you’d make up your mind!Directed evolution hasn’t been accepted by the scientific community.Regardless, under Futuymas meaning of random, even alleged directed evolution is random, because individual mutations cannot be deterministically predicted. You still haven’t falsified random mutation, but attempted a goalpost move to directed evolution. [QUOTE]Originally posted by peter borger:
[B]
As soon as the mechanism is elucidated we will be able to predict where mutations are introduced. For clarity's sake, imagine the time before the discovery of the genetic code. How was DNA related to protein? Nobody knew, since the mechanism was unknown. Now we know the relationship between DNA and protein since we know the mechanisms involved (including the code, transcription and translation) [/quote][/b]We know the mechanism that causes evaporation & rainfall, yet we still cannot predict when & where it will rain. We know that chiasmata prefer high GC concentrations, yet still cannot deterministically predict where the next chiasmata will occur.I’m very sorry, Peter, but you will NEVER be able to deterministically predict where a given mutation will occur. Take any sequence you like, there are both (statistically) random & non-random loci. Assume you understand everything that is possible to know about mutations.Q/ At what loci will the next substitution occur?You have no idea, mate. The best you can do is make a prediction based on stochastically derived probability, this is not the same as a deterministic prediction.It is random.Think about it, every loci in a sequence has a probability of mutation. Therefore, regardless of your degree of knowledge on the subject, you cannot make a deterministic prediction about the next mutation. [QUOTE]Originally posted by peter borger:
[B]
For the rest you keep repeating yourself that mutations are random since they cannot be predicted. I simply state that as soon as we know the underlying mechanism, i.e. if we know how the specific proteins integrate/replace nucleotides in the 1G5 gene (and other genes) we will be able to know where they occur and maybe we will also know when these proteins are induced. [/quote][/b]See above, re. Random mutation & your hope that you will be able to predict mutations.

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Originally posted by peter borger:

Maybe in respons to DNA damage, particular environmental factors for which they have receptors, or whatever. I don't know. All I say is that the gene does not change at random with respect to nucleotide substitions.

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Yes they do!!!!!!!!!! Good grief, man. What have I been labouring this past week?Nucleotide substitutions are random in the intended evolutionary meaning of random. See Futuyma’s meaning in my previous post.That you don’t like Futuymas definition is tough.It’s like having a conversation about transport, where I define transport as anything that moves people about. You then say that you have falsified my contention that slaves were transported across the Atlantic, because YOUR definition of transport is the motor car. And they don’t float.

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Originally posted by peter borger:

You seem to be to stuck to Futuyma's definitions.

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Because Futuyma is taking the time to describe the meaning of random as it pertains to evolution. That is the intended meaning, & I will stick to it.I’m sure you will stick to the statistical defintion of random, despite it NOT being the intended meaning.

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Originally posted by peter borger:

In addition, he does not give me a plausible explanation for mutational hotspots.

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Neither have you provided me with one.Nor would you expect him to in a passage where he describes the word random. It is enough that he points out that a mutation is random if it cannot be deterministically predicted, only probabilistically predicted.In summary (again), you have tried to falsify the NDT by claiming a definition of random that was never intended to pertain to evolution. In doing so you have created a strawman.Even if you could show that Futuymas definition is wrong, it would merely force a redefinition. If all loci are subject to the probability of mutation, & such changes are heritable, & therefore subject to genetic drift & natural selection, what really changes?Adaptive evolution is caused by random mutation culled by natural selection.Becomes..Adaptive evolution is caused by all loci being subject to the probability of mutation, that mutation being culled by natural selection.So what? It’s hardly falsified, is it?Mark------------------
Occam's razor is not for shaving with.

wj,Since you alerted me to the GLO/scurvy genes-should-get-turned-back-on argument over on Cre v Evo, I wondered if my asthma was going to get better anytime soon.......Mark------------------
Occam's razor is not for shaving with.

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Originally posted by peter borger:
Dear mark,

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You ask:
Since you alerted me to the GLO/scurvy genes-should-get-turned-back-on argument over on Cre v Evo, I wondered if my asthma was going to get better anytime soon.......

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My comments:
Maybe in the next generation? Or the next? It will at least not take millions of years, since asthma recently occurred as a Western society disease and dramatically increased from around 1% in the 1970s to almost 10% in the 1990s. Therefore, it probably involves inheritable (?) (epi)genetic modifications. (And non-random mutations in response to a Western life style?).
Best wishes,
Peter

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But why should the non-random mutations be restricted to my sperm?Why can't I have systemic somatic mutations that cure me? Similarly, what good is GLO pseudogene that allows you to get scurvy & doesn't get switched back on?Mark------------------
Occam's razor is not for shaving with.

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Sometimes, actually in a considerable amount of cases, people 'overgrow' their asthma for no obvious reasons. I do not say that this is due to somatic mutations, but it could be considered as a mechanism. Or maybe it involves compensatory mutations and/or epigenic modifications. At present, nobody knows. Time to scrutinise.

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I not unaware of such occurrences, especially in children. But what's the point of such somatic mutations if it doesn't affect everyone?Perhaps you have a basis of that testable hypothesis, now?Make a prediction, feel lucky, punk? Mark------------------
Occam's razor is not for shaving with.[This message has been edited by mark24, 10-09-2002]

Fred,

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Assuming a constant population is fine, ye ole dimbulb. What isn't fine is assuming a constant population size of ONE through the generations! Adam begot Adam Jr, begot Adam III, begot Adam IV Somewhere along the line a female mutated from the male.

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Something to do with a rib, surely?Mark------------------
Occam's razor is not for shaving with.