In “On Retrospective Analysis and Coalescent Theory” (Biologic Institute Perspectives August 5, 2012), Ann Gauger notes,
The theory is that in small populations (smaller than a trillion, say) drift can overwhelm the power of selection. In such a case, organisms do not have sufficient numbers for beneficial mutations to arise and be fixed with any frequency. Most mutations are lost to drift before becoming established, even when they are beneficial. The significance of natural selection is thus greatly reduced in shaping evolutionary history.
The idea that evolution is driven by drift has led to a way of retrospectively estimating past genetic lineages. Called coalescent theory, it is based on one very simple assumption — that the vast majority of mutations are neutral and have no effect on an organism’s survival. (For a review go here.) According to this theory, actual genetic history is presumed not to matter. Our genomes are full of randomly accumulating neutral changes. When generating a genealogy for those changes, their order of appearance doesn’t matter. Trees can be drawn and mutations assigned to them without regard to an evolutionary sequence of genotypes, since genotypes don’t matter.
For Dr Gauger:
Rapid proliferation of historecognition alleles in populations of a colonial ascidian
Nooo! It used to assume that some loci are neutral, but there are several models for the effects of selection on coalescent processes.
The applications of coalescent theory usually assume that the markers being studied are neutral, but that’s not the same thing as assuming that all markers are neutral.
Rubbish. Coalescent theory models actual genetic history.
A Gene you make a bold claim that:
And your observational evidence that it is actual genetic history is what exactly? Dr Gauger herself has been extensively involved in work that has brought into severe question the unfounded assumption in neo-Darwinan thought of the virtually unlimited plasticity of genetic/protein sequences?
notes:
Indeed this observational evidence has led Dr Axe to comment:
Interesting use of Markov models. I’ve no objection to the general idea, but a sample size of 6 is absurd. It’ll be entertaining to see what use they get out of it going forward.
A Gene:
That is the unverifiable propaganda, anyway.
further notes on the severe limits found for the ability of protein to ‘randomly’ evolve to new functions:
Which begs the question, “If this complex of 8 proteins which is found throughout life, is severely intolerant to any mutations happening to it now, how in the world did it come to be in the first photosynthetic life in the first place?
In fact the Ribosome, which makes the myriad of different, yet specific, types of proteins found in life, is found to be severely intolerant to any random mutations occurring to proteins.
And exactly how is the evolution of new forms of life suppose to ‘randomly’ occur if it is prevented from ‘randomly’ occurring at the base level of proteins in the first place?
Or related note, the ‘protein factory’ of the ribosome, which is, as far as I know, the only known machine in the universe capable of making proteins of any significant length, is far more complicated than first thought:
As well, The Ribosome of the cell is found to be very similar to a CPU in a electronic computer:
On top of the lack of proteins to evolve into new shapes and functions What does the recent hard evidence say about novel protein-protein binding site generation. i.e. about the ability of protein with novel functions to combine with other proteins in a meaningful way to do something useful for the cell?
Dr. Behe’s, and others, empirical research agrees with the difficulty that is found for scientists trying to ‘purposely design’ a protein-protein binding site:
Moreover, there is, ‘surprisingly’, found to be ‘rather low’ conservation of Domain-Domain Interactions occurring in Protein-Protein interactions across various species:
There is even found to be severe difficulty in recombing different protein domains into novel protein structure
As if all of the preceding was not bad enough for the unfounded assumption in Darwinian thought for the virtual unlimited plasticity of Protein/DNA sequences, it is now found that there is a fairly substantial percentage of completely novel ORFan sequences in each new genome sequenced:
As alluded to above, completely contrary to evolutionary thought, these ‘new’ ORFan genes are found to be just as essential as ‘old’ genes for maintaining life:
Thus, despite whatever Darwinists may think of their hypothetical population genetics models which assume unlimited plasticity for protein/DNA sequences, the empirical fact is that there are now found to be severe limits for every parameter examined for protein evolvability as well as a large percentage of completely novel ORFan proteins which seemingly pop into existence out of nowhere 🙂
Corrected link:
Honors to Researchers Who Probed Atomic Structure of Ribosomes – Robert F. Service
Excerpt: “The ribosome’s dance, however, is more like a grand ballet, with dozens of ribosomal proteins and subunits pirouetting with every step while other key biomolecules leap in, carrying other dancers needed to complete the act.”
http://creationsafaris.com/cre.....#20091010a
And a few more notes:
Book Review: Creating Life in the Lab: How New discoveries in Synthetic Biology Make a Case for the Creator – Rich Deem – January 2011
Excerpt: Despite all this “intelligent design,” the artificial enzymes were 10,000 to 1,000,000,000 times less efficient than their biological counterparts. Dr. Rana asks the question, “is it reasonable to think that undirected evolutionary processes routinely accomplished this task?”
http://www.godandscience.org/e.....e_lab.html
Research group develops more efficient artificial enzyme – November 2011
Excerpt: Though the artificial enzyme is still many orders of magnitude less efficient than nature’s way of doing things, it is far more efficient than any other artificial process to date, a milestone that gives researchers hope that they will one day equal nature’s abilities.
http://www.physorg.com/news/20.....nzyme.html
The Challenge to Darwinism from a Single Remarkably Complex Enzyme – Ann Gauger – May 1, 2012
Excerpt: Meet carbamoyl phosphate synthetase (CPS), a remarkably complex enzyme. This enzyme uses bicarbonate, glutamine, ATP, and water to make carbamoyl phosphate via a multi-step reaction at three separate active sites, involving several unstable intermediates. See here for details.
CPS is made of two protein chains with a combined length of over 1,400 amino acid residues. We now know from extensive biochemical data that a fully coupled CPS requires the hydrolysis of one glutamine and two molecules of MgATP for every molecule of carbamoyl phosphate formed. The three active sites of the enzyme maintain the overall stoichiometry of the reaction, without wasteful hydrolysis of glutamine and/or MgATP. In order to couple the reactions efficiently, the enzyme uses internal molecular tunnels for sequestering and rapid transfer of reactants between active sites, and allosteric conformational changes to synchronize their activity. This is remarkable, given that the first and last active sites are separated by nearly 100 Å. But even more remarkable is the fact that this enzyme carries out a series of reactions involving unstable intermediates with a half-life of seconds to milliseconds.
How does a neo-Darwinian process evolve an enzyme like this? Even if enzymes that carried out the various partial reactions could have evolved separately, the coordination and combining of those domains into one huge enzyme is a feat of engineering beyond anything we can do.
http://www.evolutionnews.org/2.....59191.html
ba77 –
That’s being modelled? I read the papers. I look at them. I see that they are modelling actual genetic histories.
Joe –
A Gene: I don’t think actual genetic histories in the context you are using it means exactly what you think it means. I think it would be far more truthful if perhaps you stated they are modeling hypothetical genetic histories at least, or until, it is actually demonstrated such step by step transitions in protein and/or DNA sequences and/or functionality into drastically new kinds of species is even feasible. Until then would not you agree that the word actual as you are using it is overstating the strength of what is actually being done in these mathematical models?
Somewhat related note:
Please note that Dr. Behe, even though the numbers from their model still supported his overall conclusion for the rarity of spontaneous binding site formation, was indignant with the weight they were giving their model over what the evidence actually said!
i.e. observational evidence trumps theory all the time in science why should now be any different?
A Gene here is an example of ‘actual’ genetic history coming into conflict with ‘hypothetical’ genetic history:
Fauna on mountaintops isolated for tens of millions of years found to defy evolutionary expectations (In evolutionary theory, a dog-like cow can become a whale in less time than 10 million years):
If you read the details of the article you will find that they go to some fairly amusing lengths trying to ‘explain away’ the observational evidence.
ba77 – just to be clear. The models are models of actual genetic histories. This doesn’t necessarily mean that any of the histories the model produces is the actual history, but they should be close enough that they’re informative.
But alas A Gene that ‘should be close enough that they’re informative’ assumption of yours is the very thing under question. ergo the reason why I object to your use of the word ‘actual’ as opposed to the more proper word hypothetical.
Of related note as to trying to see whether these ‘hypothetical genetic trees’ drawn up by Darwinists with the models are even feasible as far as reality itself is concerned, this following video shows why Darwinists are grossly oversimplifying the complexity of what they are trying to explain the origination of:
A Gene here are a few more examples of reality and Darwinian hypothesis colliding:
here are incongruities from genetics
Are you suggesting that there isn’t an actual genetic history?
A Gene you ask:
No, I’m claiming that the hypothetical Darwinian models of genetic history, from population genetics, which force fit the genetic evidence into their preconceived universal tree of common descent are a gross departure from what the actual genetic evidence is telling us, not to mention a gross oversimplification of the level of complexity being dealt with. A more accurate reflection of actual genetic history, from population genetics, that stays truest to what the observational evidence is actually telling us, is found in Dr. Sanford’s computer program ‘Mendel’s Accountant’:
Here is a short sweet overview of Mendel’s Accountant:
In fact, when one looks at a bit of the history of Darwinism’s attempt to square, mathematically, with population genetics, one finds that it started off absurd and and has ended up going down hill until what it has finally reached a point that many top researchers consider neo-Darwinism completely defunct as a viable hypothesis.
At the 2:45 minute mark of the following video the mathematical roots of the junk DNA argument, that is still used by Darwinists (though some Darwinists now try to deny that Darwinists ever predicted junk DNA), is traced through Haldane, Kimura, and Ohno’s work, in the 1950’s, 60’s and 70’s, in population genetics:
A graph featuring ‘Kimura’s Distribution’ being ‘properly used’ is shown in the following video:
Further note:
and even today, after many revisions to basic Darwinian theory (reminiscent of the many added on epicycles in geocentric theory), we find that Darwinism is still far short of giving a adequate explanation for the evidence:
further notes:
Right. So you’re saying that the modelled histories aren’t very good. But aren’t they still trying to model the histories?