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Author
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Topic: can some aspect of Darwinism be falsified?
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John A. Davison
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Member # 1425
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posted 09. May 2006 12:24
Peter
I think all changes HAVE been predetermined. That is the whole thrust of the PEH! Isn't all of ontogeny predetermined in a single cell, the fertilized egg? I have simply assumed the same for phylogeny. So apparently did Leo Berg:
"Evolution is in a great measure an unfolding of PRE-EXISTING rudiments."
Nomogenesis, page 406, my emphasis.
So did William Bateson:
"an unpacking of an original complex which contained within itself the whole range of diversity which living things represent."
ibid, page 359
EVERYTHING is determined... by forces over which we have no control."
Albert Einstein, my emphasis.
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Scott
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posted 09. May 2006 17:17
quote:
The problem with neutral genes is that they are not subject to (purifying) selection and would rapidly accumulate deleterious mutations.
Peter, you are obviously both intelligent and knowedgeable, but at times I detect glaring errors in logic which, if you intend to make a well-reasoned argument in favor of your views, need to be excised from your writings. The above is an example.
How can a gene accumulate deleterious mutations while at the same time not being subject to purifying selection? The statement is pure nonsense to me.
If a gene is not subject to selection, of whatever sort, then any mutation will be neither beneficial nor deleterious.
quote:
Bruce, I think that GUToB stands for the Grand Unified Theory of Biology, and it is a work by Peter which is still in progress.
Correction: GUToB - A General and Universal Theory of Biology.
[ 09. May 2006, 19:31: Message edited by: Scott ]
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Christopher D. Beling
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posted 09. May 2006 17:52
Peter,
I think understand your position. You are essentially saying that you observe fast mutation rates at the present - and that if these same rates were to act in the past on redundant genes - then we would expect the redundant genes to be destroyed (and hence not available for action when they are needed). From this you conclude that the redundant genes have not been around in time for very long. Right?
(i) Natural selection is not the only way of "dumping" badly mutated genetic information - and thus keeping the genome pure. What about the highly sophisticated repair mechanisms that are at work repairing damage all the time - I understand there are even repair systems for the repair system. Why do you preclude the operation of such repair systems on the redundant genes through eons of time? My understanding is that life is so thermodynamically unstable and negative mutations due to mutagens and radiation so common that without the in-built repair mechanisms the effective mutation rate would be many many orders of magnitude higher than observed, that organisms would not survive many generations.
(ii) If the mutation rates are high and you ascribe this high rate to non-random genetic elements (and I have no problem with this)- why can you not concede that the progamming (determinism) behind the non-random elements could not have been different in the past - when the genome would have been at a more "youthful" (or mid-life) stage. After all the DNA in our bodies is not programmed to express itself at the same rate throughout our lives? As John Davison says "we age fastest when we are youngest" - and this aging is non-random.
(iii) Quantitatively, what kind of mutation rates are you seeing? Could you give us some numbers? If I could quote, as a kind of benchmark, biophysicist Lee Spetner from his book Not By Chance(p92).
quote:
The rarity of copying errors is a problem for the neo-Darwinian theory. The average rate of copying errors depends on the kind of organism. In bacteria the rate per nuclotide is between 0.1 and 10 per billion transcriptions {Fersht, A.R. "DNA replication fidelity", Proc. Royal. Soc B212 (1981) pp351-379}{J.W. Drake, "spontaneous mutation" Nature , 221 ,(1991) p1132} But in all other forms of life the rate is smaller. For organisms other than bacteria, the mutation rate is between 0.01 and 1 per billion {F. Gross et al: Advances in Experimental Medicine and Biology , 179 (1984) pp 535-540}
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Spetner then goes on to show that such low mutation rates do not get anywhere near explaining the speciation seen in the horse lineage over 65 million years (50 million births!) - well I'm not quite sure how that fits in -but I thought I'd mention it anyway. It would be helpful to know how the mutation rates you are seeing compare with those mentioned by Spetner.
(iv) quote:
quote:
Nuclear physics shows anomalies we cannot explain using long ages (Polonium halo's, for instance).
I think one must be very careful in pinning too much on Parentless Polonium. This idea has been pushed by young earther Robert Gentry (who deserves much credit for all his hard work on halos) - but Gentry did not take his samples from primordial granite - but much more recent outcrops of granite {J.R. Wakefield "The Geology of Gentry's Tiny Mystery" J. Geological Education 36 (1988) 161}. Some suggestions have also been made that the 218Po halos are from other sources { Science 246 (1989) 107} . There are some other highly plausible mechanisms for producing 214Po and 218Po that at present I am not at liberty to mention.
Hope I have not come over as too critical. I appreciate and learn much from your posts. Chris
[ 09. May 2006, 23:34: Message edited by: Christopher D. Beling ]
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peter borger
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posted 10. May 2006 03:23
quote:
Peter, you are obviously both intelligent and knowedgeable, but at times I detect glaring errors in logic which, if you intend to make a well-reasoned argument in favor of your views, need to be excised from your writings. The above is an example. How can a gene accumulate deleterious mutations while at the same time not being subject to purifying selection? The statement is pure nonsense to me.
If a gene is not subject to selection, of whatever sort, then any mutation will be neither beneficial nor deleterious.
This is the paradox you get using Darwinian logic (paradoxes falsify theories, you know).
It is without doubt that redundant genes have functions in biochemical networks. For instance, it is well known to oncologists that cancers do not just form after the inactivation of only one proto-oncogene but several of them need to be mutated or inactivated before malignant cells arise. There is a high level of redundacy in the regulatory networks that control cell proliferation. The problem is how can such redundancies stably reside in the genome?
It should be noted that selection is on the level of reproductive succes of the organism. Selection is acting on essential genes (essential to the reproducitve succes of the organism), and damage to essential genes poses the organism immediately to a selective disadvantage. We can therefore understand the stability of essential genes from selection hypothesis. For neutral genes this does not hold, and because selection does not act on neutral genes (as you can knock them out any time you like) they cannot be old. How do you explain neutral genes? You could propose recent duplication event, but there is NO association between genetic redundancy and duplication. Besides then they would no longer qualifiy as redundant genes but rather as high abundance genes, such as the histon genes or tRNA genes (which are identical genes and also poses devastating problems for Darwinism and long aged evolutionary theories)
peebee
[ 10. May 2006, 09:21: Message edited by: peter borger ]
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peter borger
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posted 10. May 2006 03:45
Chris ,
Spetner's figures refer to point mutations, which are irrelevant for evolution anyway. The measured point mutations in bacterial cells generally lower than one in a million, indeed. However, they shuffle their genomes almost every generation. They are in a constant state of flux: they loose genes, duplicate genes and translocate genes. That is muations as well.
For human mtDNA, the usual tool for genetic studies changes so immensely fast that if we look at the mutations in the HV region (which is assumed neutral) we observed that humans, chimps, bonobos and neandertalers all have a common ancestor around 150 thousand years ago. Variability inducing mutations (by jumping genetic elements and repetitive sequences) can also be assumed neutral and occur with high incidences, too. The RFLP techniques in use by forensic investigaors are based on this phenomeneon and are able to discriminate between father and son.
peebee
[ 10. May 2006, 08:05: Message edited by: peter borger ]
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John A. Davison
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posted 10. May 2006 06:10
I agree with Peter that point mutations (allelic changes) never had anything to do with evolution. As nearly as I can tell nothing ever had anything to do with evolution. That is the whole thrust of the PEH. After all, nothing has anything to do with ontogeny. The egg requires only to be activated. From that moment on everything that happens results form internally controlled events right up to the moment of death. The error that has been made by both the Darwinians and the Lamarckians was to assume that there was an identifiable exogenous "cause" that could be tested and verified. Such a "cause" has never been identified for the simple reason that it never existed. Is there an identifiable "cause" for mathematics? Of course not. It was always there just waiting to be discovered. The mind of man had absolutely nothing to so with it.
Even the restructuring of chromosomes seems to have been through "preferred" loci. There is no role for chance in a determined universe. I am sure everyone is tired by now of Einstein's dictum but I think it bears frequent repitition until perhaps some day it will be accepted as the mandatory starting point for a further understanding of both ontogeny and phylogeny
"Everything is determined... by forces over which we have no control."
I would only replace is with was and add "millions of years ago" after determined.
He went to his grave a convinced determinist and so will I.
Leo Berg knew this as well. Referring to ontogeny and phylogeny:
"Neither in the one nor in the other is there room for chance."
Nomogenesis, page 134
If not chance then what? I say the Prescribed Evolutionary Hypothesis.
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Scott
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posted 11. May 2006 10:31
quote:
For neutral genes this does not hold, and because selection does not act on neutral genes (as you can knock them out any time you like) they cannot be old. How do you explain neutral genes? You could propose recent duplication event, but there is NO association between genetic redundancy and duplication.
Peter, this is exactly my point. Selection would (by definition) not act on neutral genes. Therefore they cannot accumulate deleterious mutations. Do you agree or disagree?
They may accumulate mutations, but all such mutations will be neutral. No mutation will be either beneficial or harmful until the gene begins to undergo selection, whatever it may be that would bring that about. But then the gene will not be a neutral gene.
How do I explain neutral genes? Frankly I can hardly conceive of such a thing. What is a neutral gene, in actual practice?
It seems to be that if there is no gene product or the gene does not perform some function or is not used in some manner, then it is not a gene. It's just a stretch of unused DNA.
If the gene does have a product, perform some function, or has some use in the organism, then I would think that by the Darwinian definition of the all-powerful, all-seeing, "natural selection" that the gene could not be "neutral."
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peter borger
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posted 12. May 2006 07:09
quote:
For neutral genes this does not hold, and because selection does not act on neutral genes (as you can knock them out any time you like) they cannot be old. How do you explain neutral genes? You could propose recent duplication event, but there is NO association between genetic redundancy and duplication.
quote:
They may accumulate mutations, but all such mutations will be neutral. No mutation will be either beneficial or harmful until the gene begins to undergo selection, whatever it may be that would bring that about. But then the gene will not be a neutral gene
Indeed, selection would (by definition) not act on neutral genes. Now you say, that therefore they cannot accumulate deleterious mutations. But this is a non sequitur, so I do not agree.
What you are saying is that when I design a car with 2x4 tires (2 by 2 as some trucks have), while 1x4 would be sufficient, the tires cannot be damaged. But this logic is false. If one of the tires was pierced by a nail, it would of course, be damaged, but the driver would not notice as the driving-system still functions as a whole. That is the whole crux, this is the redundancy I am talking about. That is why I believe that redundant systems cannot be old.
There is another falacy in your reasoning. Genes are not selected, rather organisms -- the carriers of the genes are. I know, this has been a hot debate topic (Gould-Dawkins), but the reproducing unit (=organism=a bag full of genes) is what is subject to selection. This is because selection is another way of saying differential reproduction.
If you cannot hardly conceive of an explanation for neutral genes you can join the darwinian club. A neutral gene in actual practice is a back up system to provide organismal robustness (as the 2x4 wheels provide the car's robustness=decreased sensitivity to damage).
Biological networks provide the genetic redundancy and are a bit like the internet, or a spider's web. They are all remarkably resistent to damage due to manyfold backup systems.
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If the gene does have a product, perform some function, or has some use in the organism, then I would think that by the Darwinian definition of the all-powerful, all-seeing, "natural selection" that the gene could not be "neutral."
Redundancies are not subject to selection. That is why we find them inactivated in many biological systems. The no-phenotype knockout caused a lot of commotion in the Darwinian community, but ebbed away a bit, although the problem has not been solved. Genetic redundancy advocates a recent origin of biology.
peebee
[ 12. May 2006, 07:54: Message edited by: peter borger ]
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Bruce Fast
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posted 12. May 2006 11:56
PB, let me suggest that the spare tire is a better metaphore for the neutral gene. With this metaphore, I think the issue is more clear. One has no trouble driving on a car without a spare tire. One can take a knife and stab the spare periodically (random mutation). It is conceivable that one's random stabbing could in fact produce a tire that offers better traction. However, more likely the stabbing will at some point make the tire go flat.
Now, organism, like cars, can withstand a flat in the primary tire system, by using the spare. If so, the spare must be undamaged even though it hasn't been tested. If all of these undamaged spares are floating around in the genome, seeing as they have not been "regularly checked" by natural selection, then they can't have been around for all that long.
PB, as it is painfully obvious that natural selection works on the organism (the bag of genes) rather than on the gene, which of Dawkins & Gould presents that natural selection works on genes?
PB and others,
I have been toying around with an hypothesis that is definitely incomplete. It is defined here better than it has been defined before.
I have looked at the fact that natural selection works on the organism level. I have hypothesized that each gene in the bag is from an allele that is not necessarily optimal for the environment that the organism is in. The lack of "optimum" in the set of alleles that defines a particular organism could be described as "noise". (We see that within a group of organism which have no particular mutation, some will be more and others less fit for the environment they are in.) Now, if a mutation happens in an organism that is comprised of a rather "average" set of alleles, that mutation may make the organism fractionally fitter. However, it is not likely to make the organism significantly fitter compared to the neighboring organism with a more optimized allele mix. When natural selection does its work, it is still going to choose the organism with the optimized allele mix over the organism with the average allele mix and a slight mutational improvement on one of the 30,000 implementing genes.
This, I refer to with an electrical engineering term of signal to noise. Where the signal, again, is the improvement that an organism experiences due to a particular beneficial mutation. The noise is the amount of improvement that the neighboring organism has simply because of an improved allele mix.
Does this make any sense?
I believe that this loops around, actually, to Gould's punctuated equilibrium situation. In extremely small populations, the signal to noise ratio is improved because there is less chance that there is a neighboring organism with a significantly improved allele set. However, I have never quite figured out how inbreading was going to rescue NDE.
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peter borger
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posted 12. May 2006 12:35
No, Bruce, your metaphore of the spare tire is not better. Your spare tire is the gene without regulatory sequences required to bring it to expression. Your trunk tire does not contribute to redundancy and as it is not expressed it will erode in the trunk. Your trunk tire is like an inactivated HERV or the GULO gene. It will whither away (oxidize, erode, whatever)
[ 12. May 2006, 13:38: Message edited by: peter borger ]
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John A. Davison
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posted 12. May 2006 13:36
One of these centuries it will dawn on evolutionists that allelic mutations never played any role in evolution. Neither then did natural selection nor did sexual reproduction which is the vehicle for the transmission of such allelic mutations. There is NOTHING in the Darwinian scheme that ever had anything to do with evolution except the production of intraspecific varieties. Many life forms cannot even manage that. How wrong can an hypothesis be?
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Scott
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posted 12. May 2006 19:16
Bruce,
I think that Peter is conflating the argument over neutral genes (by which he probably means pseudogenes) with the argument over redundant genes. See if you don't agree with me.
Why should a neutral gene require any regulatory sequences? Why should it need to be expressed at all?
In fact, Peter starts out disagreeing with you, then turns right around and agrees with you! He just uses a different analogy for deterioriation.
The problem with his response is he is still assigning "fitness" to the tire, while at the same time asserting that the tire is not undergoing selection. You just cannot have it both ways.
Peter is just plain wrong. My argument is not a non-sequitur, it is in fact true by definition. But look at his response to me. He goes on and on about redundant genes. I never once mentioned redundant genes.
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peter borger
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posted 13. May 2006 05:52
Scott,
You are so stuck in your own paradigms that you cannot understand there can be genes without selection.
As a life scientists I know my literature, so you do not have to question or distort what I say. Genetic redundancies are certainly NOT pseudogenes. But they can easily become pseudogenes as there is no selection acting on them. That is what we see in real life biology. I have all literature present to proof this point scientifically and this is what I do in GUToB.
Let me once more summarise:
The new biology shows the major part of genes can be knocked out without inducing a phenotype. This was a big surprise and you could have read about it in Nature a few years ago that the Darwinians do not believe it, as it so obviously falsifies their non-sense (Pearson H. Surviving a knockout blow. Nature 2002, volume 415: pages 8-9).
Genetic redundancies qualify as neutral genes and are thus not subject to selection (or do you want to propose neutral selection, which has been proposed by Svente Pääbo's group recently. I wrote him two letters for a little inquiry as I didn't understand what he meant, but, unfortunately he never responded).
Neutral genes can be inactivated any time you like. The no-phenotype is the scientific evidence of neutral genes and they are the rule rather then the exception in real life biology.
These new biology data scream out:
1) biological systems are designed.
2) biological systems are not old.
Maybe you did not get it yet, but I am introducing a completely new paradigm of biology devoid of the Darwinian claptrap. In order to do that I have to falsify and completely overturn the old one. That is how the scientific method works: I am a scientist, you know. GUToB is the new theory that explains all biological phenomena.
I rest my case,
peebee
[ 13. May 2006, 05:57: Message edited by: peter borger ]
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John A. Davison
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posted 13. May 2006 07:24
The title of the thread really tickles me. The title should have been:
"Can any aspect of Darwinism be verified?"
The answer of course is yes. What can be verified is that selection, natural or artificial is capable of one thing only. It can produce intra-specific varieties and in in some instances subspecies. That is all it can do today and that is all that it ever did.
All creative evolution (phylogeny) stemmed from internal sources and proceeded independently of any environmental forces exactly as the development of the individual (ontogeny) continues to do today. The only conceivable role for the environment was to act as a stimulus for the release of latent endogenous potential. That incidentally, in ontogeny, is one of the primary roles for the spermatozoan and it can be substituted for by a needle!
Such internal sources are apparently no longer being expressed which allows us to conclude that phylogeny is finished and has been at the genus level for at least two million years. At the species level there is no compelling evidence for either true speciation or the formation of any of the higher categories in recorded history or, in other words, in the past 5000 years.
Furthermore, I have repeatedly requested evidence for any two species, fossil or extant for which it can be demonstrated that one is ancestral to the other. What we observe are the products of a long past evolution, not evolution in action as the Darwinians continue blindly to insist.
I have also asked for evidence of a younger mammal than Homo sapiens. Neither of my challenges have been either met or even acknowledged to have been offered.
I have concluded, naturally enough, that phylogeny has been a goal-directed phenomenon which reached that goal with the production of ourselves. Since there is absolutely no evidence for intervention in this process I have further concluded that it was predetermined an unknown number of times, by an unknown number of sources, at unknown times in the geological temporal record, at an unknown number of places. This hypothesis, which I regard as in complete accord with everything we really know from both the experimental laboratory and the fossil record, has been published as the Prescribed Evolutionary Hypothesis (PEH). It is available right here at "brainstorms" in case anyone would choose to respond to it.
But to continue to kick the dead Darwinian horse is an exercise in futility. It never had anything whatsoever to do with creative evolution, absolutely nothing. It is merely the invention of a mind set that demands that phylogeny had an extrinsic, identifiable and testable cause. Such a cause never existed, any more than does such an external cause exist for ontogeny, which is why it cannot be revealed.
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Scott
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posted 13. May 2006 09:46
quote:
All creative evolution (phylogeny) stemmed from internal sources and proceeded independently of any environmental forces exactly as the development of the individual (ontogeny) continues to do today. The only conceivable role for the environment was to act as a stimulus for the release of latent endogenous potential.
As I read this, by your own admission, ontogeny is not independent of environmental forces. So by your same reasoning, phylogeny did not proceed independently of environmental forces.
You have just stated that something does not happen, and then went on to say, except when it does happen.
If the environment acts as a stimulus, then how can you assert that either ontogeny or phylogeny "proceeded independently of any environmental forces?"
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