Peter,
I have decided to sum all our posts in one thread. It allows me to pull all the strings together, & re-ask questions that were looked over. It also gives others the opportunity to get a summary of what we have been arguing. I apologise now to other readers, I am repeating argument made before, that were not substantially/meaningfully responded to. It seems there’s no other way.
You have provided arguments that you think are falsifications. If you are going to falsify anything, then the tentativity in your arguments must be near zero. You cannot falsify anything whilst relying on an untested assumption.
Unless I am much mistaken, your present & previous arguments are summed below. A to E.
A/ Random mutation isn’t random, so, the tenet that says evolution is random mutation culled by natural selection falsifies the NDT.
quote:
Mutation as a Random Process
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.
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
(Evolutionary Biology 2nd Edition, Douglas Futuyma p281-2)
One of the reasons I felt I had to get everything under one roof was the opportunity to reiterate this argument. You have never substantially responded to the issue of the intended definition of random, as outlined above. It is incorrect to insist on a definition that was never intended, & as such, applying a strict statistical definition of random falsifies nothing.
YET, you still insist you have falsified the NDT because of the statistical non-randomness displayed in mutations. You do this without bringing anything new to the discussion, & I must therefore conclude you are using the time honoured tactic of, I have no argument, so I’ll repeatedly reassert my initial premise. I am giving you the opportunity to bring a new argument to the debate, rather than your reassertions.
The intended meaning of random, is that if the locus of a particular mutation cannot be predetermined, it is random (among other things, above).
This means hotspots, & even directed evolution (should such a thing exist), are random.
Let us assume that directed evolution exists, & is active in a population of 1,000 individuals. One locus is under potential directed evolution, the other 499 nucleotide sites exhibit statistically random mutational probability. After 1 generation, 250 of the organisms have had the sequence undergo directed mutation, 500 experienced no mutation at all, & 250 experienced statistically random mutation. Could you have predicted the mutation loci
deterministically in a given sequence? No, of course not. Ergo, even directed evolution is random (Futuymas definition).
You cannot gainsay evolutions intended meaning of random. Only the definer/author can do that.
Given that you can’t put words in peoples mouths, & tell them what they are
supposed to have meant by random, you cannot insert XXX meaning of random in order to falsify random mutation
being required for evolution. It ain’t allowed.
The next time you say you have falsified the NDT because of randomness, it had better come with a bloody good reason, or I claim victory. I’m tired of explaining the same thing over & over, & you just reasserting your original position without explanation.
OK?
It’s reassertions like this.
quote:
since I demonstrated that some genes change non-randomly and that falsifies NDT
..that ignore everything that has been said, & it’s beginning to piss me off.
B/ You believe you have falsified neutral rate mutation/ neutral theory. Therefore phylogenetic analysis cannot be inferred because directed evolution cannot be excluded. Put simply, you are saying that because alleged neutral sequences display non-neutral behaviour, this must be directed mutation, because it’s supposed to be neutral.
Given you accept functional constraint, or at least accept that it’s well established.
quote:
Ever heard of neutral evolution theory? What does it say for DNA sequences that are not under selective constraint? Indeed, the suppose to change more rapidly!! In fact this has been well established.
Then what do you infer from a nucleotide site that doesn’t display neutral rate substitution? It seems to me that you disregard your acceptance of functional constraint, even though it is a perfectly plausible explanation, in favour of it was designed to mutate there!.
This means that previously functionless sequences may have loci that have function, after all, since functional/selective constraint is observed. Remember, it is YOU who are claiming a falsification, & it is YOUR argument that must therefore have near zero tentativity. Therefore you must SHOW that an ENTIRE sequence is functionless. I don’t deny that the original transcribed protein has been ruined. But I do not accept that there is no function at any locus, or never has been, unless you show otherwise. But given that there are pseudogenes/transposons that HAVE been shown to have function, it is imperative that you investigate for this possibility before claiming falsifications.
If you cannot do this, then you cannot infer falsification from non-neutral rate loci in
alleged functionless sequences.
C/ You assert it is possible to locate hotspots in ancient sequences, in order to be able to infer that pseudogenes (GLO) were wrecked by hotspot mutation.
Firstly, I doubt this very much, since GLO genes are active in more mammals than not. If a hotspot destroyed our GLO function, then why not a cows? Given it has hotspots too.
Secondly, why would an ID design a functioning gene with a built in self destruct? It's like building a plane with wings that fall off, or a car where the steering wheel comes off in your hand above a certain speed.
But I digress.
I agree, you
can take an
extant sequence, mutate it a thousand times, then examine where the sequences mutate most in order to demonstrate where the hot spots are.
But, this is entirely different a proposition from being able to infer hotspots from ancestral sequences. The best you can see from an ancestral sequence is that a loci mutated
a maximum of three times, that is, from A to G, A to T, A to C, certainly not from within your paradigm. There is no way you can quantify a hotspot that has a thousand-fold higher probability of mutation than a statistically random probability. You may look at loci that appear to be random to you, but have mutated thousands of times more than adjacent loci, but because it started as A, & finished as A, you will never know.
This is probably best illustrated in the form of a question;
Q/ There is a single homologous locus in a gene in eight different related organisms.
1/The nucleotides are A,G,T,C,A,G,T, & C. Is the locus a hotspot?
2/The nucleotides are A,A,A,A,A,A,A, & A. Is the locus a hotspot?
3/The nucleotides are A,A,A,A,A,A,A, & T. Is the locus a hotspot?
So, how can you tell the location of hotspots in ancestral DNA?
D/ You claim to have falsified natural selection, specifically.
Natural selection has been demonstrated umpteen times experimentally.
I'll use a single example, the guppy, Poecilia reticulata. In waters populated by the predator Crenicichla, males have smaller less conspicuous spots that match the gravel bottom (different bottoms elicit different patterns). In effect the guppy has evolved camouflage. The alleles that express phenotypes are under SELECTIVE pressure.
Guppies that exist in waters that lack Crenicichla display a much wider range of colouration. That is to say the alleles that affect skin colour are no longer under selective pressure.
Guppy populations that are in waters that have Crenicichla populations, & are placed in waters without the predator soon display a wider variety of colouration. Again, the skin colouration alleles aren't selectively constrained, & are able to increase via genetic drift, since they are now "neutral" alleles.
If guppies from non-predatorial waters are placed in water with Crenicichla, the colourations soon begin to match the gravel bottom. That is, alleles responsible for skin colouration are under selective pressure.
(Endler 1980)
Now, given you have "falsified" natural selection, can you explain the above within your shining new paradigm?
I don't think so, there is no other explanation other than non effectively camouflaged guppies end up as lunch for Crenicichla, those that have camouflage go on to repopulate, taking their existing/newly appeared alleles with them. Namely, natural selection. If allele frequencies are being affected by natural selection, & natural selection is part of the NDT, then how can you possibly conclude that the NDT can't be seen to work at the genome level?
Falsification of natural selection? Not.
I saved the best ‘till last
E/ You assert that statistical non-randomness as evidence of design.
How can you tell a naturally occurring system/object from a designed one?
Since you are attempting to show ID, then if you can’t answer this question, then ALL your arguments come to nought.
Retrospectively, your problem is your own use of language. You drop the word "falsification" in to your argument, without realising it requires you to have all bases covered. You simply have to have a lot more information before you can get anything like a falsification of the NDT.
Mark
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Occam's razor is not for shaving with.
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