|
Author
|
Topic: can some aspect of Darwinism be falsified?
|
Zachriel
Member
Member # 1793
|
posted 19. May 2006 16:59
Bruce Fast: "If, however, the redundancy, with supporting mechanism, produces an error correction system, then this error correction system should be fully immune to random mutation."
No copying system can be "fully immune" to error. That's true whether or not it includes duplicate copies, correction channels, or error-correction algorithms. That was Claude Shannon's fundamental 1948 insight.
http://cm.bell-labs.com/cm/ms/what/shannonday/paper.html
IP: Logged
|
|
John A. Davison
Member
Member # 1425
|
posted 19. May 2006 17:57
Zachriel
I agree and that be an important feature leading to inevitable extinction which seems to be the story of the fossil record. 99.999% plus of all species that ever existed ultimately became extinct. Semi-meiotic reproduction purges the genome each time it comes into play by purging the genome of lethal genes because these are automatically expressed as homozygotes in a single cytogenetic event. In-breeding accomplishes the same result but for God's sake don't quote me. I have enough enemies already!
IP: Logged
|
|
DaveScot
Member
Member # 1545
|
posted 19. May 2006 18:43
Zachriel
You are correct that nothing can be completely immune to error in copying, transmission, or storage but it can be good enough and that includes good enough for a finite amount of data on the order of a terabyte to be preserved with adequate fidelity over billions of years in a microbial genome. It's a simple mathematical exercise to use checksums long enough to insure that the chance of an error escaping detection is larger than the universal probability bound of 10^150. Errors don't have to be corrected, which is a much more resource intensive task. What you do in the case of an error is discard that copy of the data. Destroying a bad copy is what preserved the genetic code virtually unchanged since the dawn of life on this planet. Each bit of information in the genetic code, except for synonymous substitutions, is so critical and used in so many codependent protein products that virutally any error in copying it is fatal - the copy is discarded. In that way God only knows how many trillions of trillions of copy operations over billions of years resulted in only a tiny number of small variations. And AFAIK that's without using checksums. Checksums of arbitrarily length can simply be substituted for selection until you get the fidelity you need. If the arbitrarily complex checksum doesn't match the copy is discarded (dies before it is born in this case).
[ 19. May 2006, 18:44: Message edited by: DaveScot ]
IP: Logged
|
|
Bruce Fast
Member
Member # 924
|
posted 19. May 2006 19:57
Zachriel: quote:
No copying system can be "fully immune" to error.
The Hystone H4 has proven to be desparately close. I understands that it differs by only 4 aminos between the bovine and the pea.
IP: Logged
|
|
Scott
Member
Member # 1222
|
posted 19. May 2006 22:26
quote:
No copying system can be "fully immune" to error.
How immune can such a system be?
How does the error-detection and correction capabilities of cells stack up?
Given that mutations are required as the ultimate source of variation available to evolutionary mechanisms, why would a system evolve which inhibits or removes the very basis of variability?
IP: Logged
|
|
John A. Davison
Member
Member # 1425
|
posted 19. May 2006 22:31
Civilized society is rapidly aquiring lethal genes in heterozygous form due to the interventiion of medicine. We are crawling with them. Sexual reproduction does not get rid of them efficiently which is one of the reasons I believe it is a primary cause of extinction. The only thing that selection ever did was to eliminate the unfit. The moment that is relaxed degeneration sets in. It sets in anyway because the sexual mode tends to preserve defective genes because it also preserves the normal allele. Once the defective genes reach a certain threshold inbreeding will even fail which would seem to be the story of the fossil record. All large, slowly reproducing animals, have ultimately become extinct and we are no exception.
This is where the semi-meiotic hypothesis has come to the rescue. Every time it produced a new reorganized chromosome homozygote, theoretically a new species, it also at the same time purged the genome of most defective genes. That is because in semi-meiosis the sister (identical) strands always remain together in Meiosis I. That offers an explanation for the observed fact that newly emerged species typically have flourished early in their history only to ultimately succumb to genetic degeneration, what Schindewolf called "typolysis." His cycles of "typogenesis", "typostasis" and "typolysis" can all be accommodated within the constructs of the PEH and the restraints of sexual reproduction. Apparently "typogenesis," which I believe was semi-meiotic in character, is no longer in progress and accordingly neither is organic evolution. I also feel Homo sapiens was the terminal mamalian product of a "prescribed" evolution. It looks to me as though it is all down hill from here on. There is no doubt in my mind that, in agreement with Robert Broom, there was a Plan, a word he capitalized. The Plan has been executed. There is now and there never was a role for chance in either ontogeny or phylogeny.
"Neither in the one nor in the other is there room for chance."
Leo Berg, Nomogenesis, page 134
IP: Logged
|
|
David L. Hagen
Member
Member # 323
|
posted 19. May 2006 23:29
Chris
quote:
ii) That perhaps the eight varieties H1a, H1b, H1c, H1d, H1e, H1t,H1oo,H1o are all homologous and equally capable of doing the nucleosome linking job if required to do so?
By using "homologous" you are saying they evolved!
Recommend using origin neutral terms:
Spalog
"The term 'spalog' (pronounced [spailog]) denotes a 3-D structure that is spatially similar, to a specified extent, to another 3-D structure. This term is strictly about spatial similarity and implies nothing about evolutionary relatedness and functional properties of structures.
Defined by Alexander Varshavsky"
-------------
Sequelog
The term 'sequelog' denotes a nucleotide or amino acid sequence that is similar, to a specified extent, to another sequence. This term is strictly about sequential similarity and implies nothing about evolutionary relatedness and functional properties of sequences.
Defined by Alexander Varshavsky
See also: homolog, ortholog, paralog, pseudoortholog, pseudoparalog, sequelog, xenolog"
IP: Logged
|
|
Bruce Fast
Member
Member # 924
|
posted 19. May 2006 23:47
Scott: "How immune can such a system be?"
To the best of my knowledge, the Hystone H4 is the least mutated gene so far discovered. To get a sense of how resistant it is to mutation, consider just what 4 aminos separating the bovine (cow) and the pea really means. It is understood that the common ancestor between the bovine and the pea is at least 600 mya. Therefore the pea and the bovine have each offer 600my to contribute to these four mutations. That is a glorious rate of 1 mutation per 300 million years.
(If we use standard extrapolation methods and the molecular clock theory, we see that, at this rate, this gene would have had to have started its evolutionary path a few weeks before the big bang.)
Now, consider the proposed algorithm which would rescue PB's H1 puzzle from being good evidence for a young earth. (We certainly wouldn't want to do that.) The proposition is that there are between 3 and 8 identical H1 genes in each mammal. (Two genes were able to be knocked out, if we are dealing with "redundant genes" as PB suggests, well, you could knock out all but 1 of the redundant genes and get a working organism.) The proposition is that there is a mechanism which uses these 3 to 8 identical genes to implement a "voting" error correction algorithm.
The proposed algorith works this way: for each amino (or possibly nucleotide) the three genes are compared. If the three are identical, all is well. If they are not identical, if two are the same, the "odd one out" would be corrected to become like the other. (The mechanism itself could not be broken or the young earth equations would rise up again.)
Now, if such an algorithm exists for the H1 gene (of course we remember that this theoretical mechanism is being presented because the other option is a young biology) it would take quite a tuned assult to produce a mutation. Any single mutation would be corrected for in one generation. For a pair of mutations to get through a 3 H1s filter, the mutations would have to involve the same amino acids in two separate copies of the H1 gene (they would not have to be the same mutation however) and would have to happen in the same organism. To get through an 8 H1s filter would require the following: 4 identical mutations (to the same amino acid, at the same position, in four copies of aminos) or 5 mutations where three are the identical mutations, or six mutations where two are identical, or seven simultaneous mutations, all in the same organism at the same time.
To add insult to the above injury, of course, any such mutation would also have to not be deleterious. One would presume that if such a protection system exists, it is because mutations are likely to be deleterious.
The above 3 H1 model should offer mutational resistance akin to that of the H4, and the 8 gene model should be orders of magnitude more resistant.
Scott: quote:
Given that mutations are required as the ultimate source of variation available to evolutionary mechanisms, why would a system evolve which inhibits or removes the very basis of variability?
This is an intriguing paradox of genetics. The maxim genome size in an organism is limited by the precision of the copying. To produce larger genomes, improved precision is requred. (This is the case whether the organism is developed via ID or via NDE.)
Think about it, if random mutation produces 1% mutations (of nucleotides) per million years, then in an organism that has about 10 million coding nucleotides, and a 10 year generation rate, it will be experiencing, on average, 1 mutation in coding DNA per organism. If the error rate was an order of magnitude higher, that size genome would unquestionably be unsustainable.
IP: Logged
|
|
John A. Davison
Member
Member # 1425
|
posted 20. May 2006 06:54
Variability had little to do with evolution because it is expressed largely through allelic mutation which had nothing to do with evolution either. That is why all dogs are wolves and all of Darwin's precious finches one species. Sooner or later it will become clear that absolutely nothing in the Darwinian model ever had anything to do with organic evolution, not variability, not selection, not population genetics.
They are all illusions dreamed up by mentalities unable for whatever reasons to recognize that evolution, like ontogeny, has been driven entirely from within those organisms capable of leaving offspring obviously different from themselves, creatures that, as far as I can ascertain, are no longer with us. Obviously the time is not yet ripe for this to be accepted. That is unfortunate. As the old ballad from the nineteen twenties claimed - "Don't Blame Me."
"If you tell the truth you can be certain, sooner or later, to be found out."
Oscar Wilde
"Neither in the one nor in the other is there room for chance."
Leo Berg, Nomogenesis, page 134
IP: Logged
|
|
John A. Davison
Member
Member # 1425
|
posted 20. May 2006 10:31
The only reason microbes and a very few eukaryotes have survived for millions of years is because they reproduce faster than they aquire lethal mutations. The only really large eukayote living fossil of which I am aware is the coelocanth. The reason it has been able to survive may well be simply because it lives at such depths in a very stable environment, the ocean, that it is shielded from virtually every source of damaging radiation. Besides that, there is no compelling reason to even think it is really old. The PEH can easily accommodate any number of species recreations. George Gaylord Simpson once suggested that modern horses had been indpendently produced on more than one occasion. I'll buy that possibility as it is well within the potentials offered by the PEH. So you see even monophyleticism may be a myth. Personally I think it is and so did Leo Berg.
IP: Logged
|
|
Sandor Szabados
Member
Member # 1969
|
posted 20. May 2006 11:38
Dr. Davison,
quote:
“…evolution, like ontogeny, has been driven entirely from within those organisms capable of leaving offspring obviously different from themselves, creatures that, as far as I can ascertain, are no longer with us.”
“55 million years ago the evolutionary march was marked by the 'sudden' appearance of the first 'true birds', a small pigeon-like creature which was the ancestor of all bird life… and it sprang directly from the reptilian group, not from the contemporary flying dinosaurs nor from the earlier types of toothed land birds.”
The above is on p. 691 of The Urantia Book, a 2097-page tome comprised of 196 papers written by celestial personalities in the 1920s and early ‘30s and published as a book in 1955. The statement corroborates Otto Schindewolf’s proposal that the first bird must have hatched from a reptilian’s egg.
Urantia is the name of our planet and information regarding how life originated and evolved validates your Prescribed Evolutionary Hypothesis. “The original life plasm of an evolutionary world must contain the full potential for all future developmental variations and for all subsequent evolutionary changes and modifications. The provision for such far-reaching projects of life metamorphosis may require the appearance of many apparently useless forms of animal and vegetable life. Such by-products of planetary evolution, foreseen or unforeseen, appear upon the stage of action only to disappear, but in and through all this long process there runs the thread of the wise and intelligent formulations of the original designers of the planetary life plan and species scheme.”
“Concerning the origin of life we are informed that “550 million year ago the Life Carrier corps returned to Urantia. In cooperation with spiritual powers and super-physical forces we organized and initiated the original life patterns of this world and planted them in the hospitable waters of the realm.” About saltation we are told that “…from era to era radically new species of animal life arise. They do not evolve as a result of the gradual accumulation of small variations; they appear as full-fledged and new orders of life, and they appear 'suddenly'.” And information on the first human beings includes the following: “From the year A.D. 1934 back to the birth of the first two human beings is just 993,419 years. These two remarkable creatures were true human beings. They possessed perfect human thumbs, as had many of their ancestors, while they had just as perfect feet as the present-day human races. They were walkers and runners, not climbers; the grasping function of the big toe was absent, completely absent. When danger drove them to the treetops, they climbed just like the humans of today would. They would climb up the trunk of a tree like a bear and not as would a chimpanzee or a gorilla, swinging up by the branches.”
An electronic copy of The Urantia Book be found at http://www.urantia.org
Sandor
IP: Logged
|
|
Bruce Fast
Member
Member # 924
|
posted 20. May 2006 11:56
Hey, this thread has been pursuing PBs redundant H1 gene challenge. This is the best thread I have seen on the net yet. Let's not loose this thread. Can we take discussions of Urantia into its own thread?
IP: Logged
|
|
Sandor Szabados
Member
Member # 1969
|
posted 20. May 2006 12:08
Errata corrige: The quote on page 691 should read: "...marked by the sudden appearance of the first 'of' the true birds..."
Sandor
IP: Logged
|
|
Zachriel
Member
Member # 1793
|
posted 20. May 2006 12:59
DaveScot: “You are correct that nothing can be completely immune to error in copying, transmission, or storage but it can be good enough and that includes good enough for a finite amount of data on the order of a terabyte to be preserved with adequate fidelity over billions of years in a microbial genome.”
That’s not the case as observed in nature. Genomes are known to mutate on a statistically random basis. Because the mechanisms are molecular, thermodynamic entropy and cosmic radiation assures some errors. I would point out that the data-correction mechanism is also subject to mutation which makes your other calculations moot.
Scott: “How does the error-detection and correction capabilities of cells stack up?”
Accuracy in genome replication varies, but typically one in 10^9 base-pairs or one in 10^6 genes are within an order of magnitude or so in most cases. Everyone is a mutant.
Scott: “Given that mutations are required as the ultimate source of variation available to evolutionary mechanisms, why would a system evolve which inhibits or removes the very basis of variability?”
Life can be defined as imperfect replicators replicating imperfectly. But the word 'replicate' implies some fidelity to the original. Life requires an accurate copying mechanism. It provides a selective advantage by ensuring the quality of offspring and the continuation of the line. Even bacteria have such mechanisms. But mutations are inevitable, so evolution occurs.
Bruce Fast: “To get a sense of how resistant it is to mutation, consider just what 4 aminos separating the bovine (cow) and the pea really means.”
The gene sequences do not have that degree of resemblance due to synonymous substitution, so the posited perfect preservation is a phantasmagoria. Analysis of histone sequences reveals the nested hierarchy of descent (up to saturation). And there are histone pseudo-genes, as well.
--
The Theory of Evolution makes several relevant predictions. Hierarchical scale invariance implies that certain functions, once established, cannot be easily modified or removed without causing the collapse of all the other functions dependent on it. This means that some functions will be subject to strong stabilizing selection. This is the *expected* pattern. Histone is apparently one of those fundamental functions.
Gene duplication is a common mutation. It has been shown that there are new and old copies of histones. And gene duplication is not an unusual mechanism for ensuring the quality of important functions, so this clearly may be subject to selection over generations. Even if a single copy may be redundant in a single generation, it may provide an advantage over time.
Bruce Fast (snipped from earlier in the thread): “kingdom, philum, class, order, family, genus, species in that order. Every bone in my ‘let's think like a Darwin’ body says that this pattern is in conflict with NDE.”
That is precisely wrong because that is precisely the pattern, a scale-invariant hierarchy, which is *expected* by the Theory of Evolution. Once a niche has been filled, it will tend to remain filled, though populations may continue to diverge in order to fill ever smaller and smaller micro-niches within the larger environment, and to fill new niches created as the biosphere evolves. When catastrophes occur, then this may provide an opportunity for radiative adaptation from a node higher in the hierarchy.
Here are a few articles that might shed light on the subject (may require subscription or purchase):
Genetic redundancy in evolving populations of simulated robots: A number of authors have argued that redundancy in biological organisms contributes to their evolvability.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12537686&dopt=Abstract
Preservation of Duplicate Genes by Complementary, Degenerative Mutations: Focusing on the regulatory complexity of eukaryotic genes, we show how complementary degenerative mutations in different regulatory elements of duplicated genes can facilitate the preservation of both duplicates, thereby increasing long-term opportunities for the evolution of new gene functions.
http://www.genetics.org/cgi/content/abstract/151/4/1531
Purifying Selection and Birth-and-death Evolution in the Histone H4 Gene Family: Our findings suggest that the members of this gene family evolve according to the birth-and-death model of evolution under strong purifying selection.
http://mbe.oxfordjournals.org/cgi/content/abstract/19/5/689
--
Now, perhaps you could argue with this or that, but there is certainly enough scientific research into these mechanisms that a Hail Mary appeal to an unknown intelligent designer, working with an unknown mechanism (creatons or whatever), for unknown purposes, is not warranted.
[ 20. May 2006, 17:18: Message edited by: Zachriel ]
IP: Logged
|
|
John A. Davison
Member
Member # 1425
|
posted 20. May 2006 16:23
Sandor
Thank you for a source with which I was not familiar. While I am not certain that I agree with everything you have summarized, I certainly agree with the evaluation of the great work by Otto Schindewolf, undoubtedly the greatest paleontologist of all time.
Incidentally, Stephen Jay Gould, in the Foreword to Schindewolf's 1950 book, when it was finally translated in 1993, had to claim that Schindewolf's work was "spectacularly flawed."
Otto Schindewolf, Basic Questions in Paleontology, page xi
So much for Stephen Jay Gould, in my opinion the quintessential Darwinian mystic, right next to Ernst Mayr and today's Richard Dawkins.
Thank you for the interesting post.
IP: Logged
|
|
|
Printer-friendly view of this topic
