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Branko Kozulic Responds

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Dr. Kozulic has requested UD to post the following response to Dr. Torley’s recent retraction vis-à-vis the fixation issue:

Since my reputation is at stake, I kindly ask you to make my position public in another post at Uncommondescent under the title: ‘When I am not wrong’, with the following text:

Dr. Kozulic would like to state the following:

There is nothing wrong with the arguments and questions put forward in the post “Branko Kozulic responds to Professor Moran”
In his reply “On being “outed” as a closet Darwinist” Professor Moran has not answered any of the questions and arguments raised. Until that happens, his claim that 22,000,000 million neutral mutations can be fixed in 5,000,000 years cannot be but considered impossible, together with all the implications. Should Professor Moran answer the questions and arguments posed, I will reply to him at any public forum of his choice.

As it relates to the retraction of Dr. Torley, his change of mind is the consequence of confusion, as for example illustrated here:

“The fallacy in the logic here should now be apparent. There is no reason to suppose that one singleton has to be fixed in the population before another one can be. The paper has therefore failed to demonstrate that speciation is an event that lies beyond the reach of chance.”
The issue with singletons – in contrast to nucleotide mutations – is not fixation, but their origin.

If any issue related to this request is in need of explanation, please let me know.

Sincerely yours,

Branko Kozulic, Ph.D.

Comments
Is it relevant now to introduce once again into the discussion the term "genetic entropy"? I will admit I'm a bit confused. Is the human genome constantly accumulating more junk, a la the "genetic entropy" argument? Is "junk in the genome" evidence for genetic entropy and thus for young earth creationism, or is it the lack of junk in the genome that is evidence for young earth creationism? How much "junk" does young earth creationism predict was introduced into the human genome in 6000 years according to "Mendel's Accountant" and the "genetic entropy" argument?Mung
April 18, 2014
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Scordova I’m not expert in this area, but when you said that “”Moran’s argument: neutral evolution is true as evidenced by the genome being mostly junk”" That’s when I knew that Moran was wromg as we are finding out more and more each day that so called junk DNA isn’t really junk DNA, and it keeps getting worse every day for the JUNK DNA advocates as we keep finding more and more function in this area .
Moran said:
What Sal is saying is that practically all of the mutations being fixed in humans are either neutral or slightly deleterious. That has implications. It strongly suggests that most of our genome is junk.
If Moran changed his claim ever so slightly and said:
What Sal is saying is that IF practically all of the mutations being fixed in humans are either neutral or slightly deleterious. That has implications. It strongly suggests that most of our genome WOULD HAVE BEEN junk.
He'd would have essentially made the argument the Mendel Team was making.scordova
April 15, 2014
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Quick answer: 1000 is too many to run a direct experiment quickly, the fixation time would be 4000 generations if 1000 is the effective population. 10 flies are better. :-) One study that had a different aim, but did indirectly confirm that after a few generations, a small fruitfly population fixes. Evidence of this is the lack of heterozygosity. In breeding depression not random Again, to emphasize, the reason YECs promote some of the findings of neutral theory is for different reasons than why Moran advocates neutral theory. As I pointed out, the irony is the YECs are in partial agreement with Moran. YECs promote neutral theory because it is non-Darwinian, and part of that is the fixation argument for SMALL populations. I obviously believe the mechanism of fixation was not neutral evolution, but special creation. But it takes a differently line of reasoning than just attacking neutral fixation. Mendel's Accountant work provides that alternate line of creationist reasoning using neutral theory.scordova
April 15, 2014
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The Fate of Darwinism: Evolution After the Modern Synthesis - January 2012 Excerpt: We trace the history of the Modern Evolutionary Synthesis, and of genetic Darwinism generally, with a view to showing why, even in its current versions, it can no longer serve as a general framework for evolutionary theory. The main reason is empirical. Genetical Darwinism cannot accommodate the role of development (and of genes in development) in many evolutionary processes. http://www.springerlink.com/content/845x02v03g3t7002/ Experimental Evolution in Fruit Flies (35 years of trying to force fruit flies to evolve in the laboratory fails, spectacularly) - October 2010 Excerpt: "Despite decades of sustained selection in relatively small, sexually reproducing laboratory populations, selection did not lead to the fixation of newly arising unconditionally advantageous alleles.,,, "This research really upends the dominant paradigm about how species evolve," said ecology and evolutionary biology professor Anthony Long, the primary investigator. http://www.arn.org/blogs/index.php/literature/2010/10/07/experimental_evolution_in_fruit_flies http://eebweb.arizona.edu/nachman/Suggested%20Papers/Lab%20papers%20fall%202010/Burke_et_al_2010.pdfbornagain77
April 15, 2014
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OK- someone needs to take a population of 1000 fruit flies, sequence every genome, let the fruit flies have at it and keep checking until we see a neutral mutation become fixed. 1000 is too many? Start with 10, 5M, 5F. See how long it takes. Then keep increasing the starting population and see what happens.Joe
April 15, 2014
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wd400, I find it interesting that you think population genetics gives conclusive support for unguided evolution, when in fact it is nothing more than a futile exercise in mathematical wish fulfillment that has next to nothing to support it terms of actual empirical evidence:
The next evolutionary synthesis: from Lamarck and Darwin to genomic variation and systems biology Excerpt: If more than about three genes (nature unspecified) underpin a phenotype, the mathematics of population genetics, while qualitatively analyzable, requires too many unknown parameters to make quantitatively testable predictions [6]. The inadequacy of this approach is demonstrated by illustrations of the molecular pathways that generates traits [7]: the network underpinning something as simple as growth may have forty or fifty participating proteins whose production involves perhaps twice as many DNA sequences, if one includes enhancers, splice variants etc. Theoretical genetics simply cannot handle this level of complexity, let alone analyse the effects of mutation.. http://www.biosignaling.com/content/pdf/1478-811X-9-30.pdf Thou Shalt Not Put Evolutionary Theory to a Test - Douglas Axe - July 18, 2012 Excerpt: "For example, McBride criticizes me for not mentioning genetic drift in my discussion of human origins, apparently without realizing that the result of Durrett and Schmidt rules drift out. Each and every specific genetic change needed to produce humans from apes would have to have conferred a significant selective advantage in order for humans to have appeared in the available time (i.e. the mutations cannot be 'neutral'). Any aspect of the transition that requires two or more mutations to act in combination in order to increase fitness would take way too long (>100 million years). My challenge to McBride, and everyone else who believes the evolutionary story of human origins, is not to provide the list of mutations that did the trick, but rather a list of mutations that can do it. Otherwise they're in the position of insisting that something is a scientific fact without having the faintest idea how it even could be." Doug Axe PhD. http://www.evolutionnews.org/2012/07/thou_shalt_not062351.html Majestic Ascent: Berlinski on Darwin on Trial - David Berlinski - November 2011 Excerpt: The publication in 1983 of Motoo Kimura's The Neutral Theory of Molecular Evolution consolidated ideas that Kimura had introduced in the late 1960s. On the molecular level, evolution is entirely stochastic, and if it proceeds at all, it proceeds by drift along a leaves-and-current model. Kimura's theories left the emergence of complex biological structures an enigma, but they played an important role in the local economy of belief. They allowed biologists to affirm that they welcomed responsible criticism. "A critique of neo-Darwinism," the Dutch biologist Gert Korthof boasted, "can be incorporated into neo-Darwinism if there is evidence and a good theory, which contributes to the progress of science." By this standard, if the Archangel Gabriel were to accept personal responsibility for the Cambrian explosion, his views would be widely described as neo-Darwinian. http://www.evolutionnews.org/2011/11/berlinski_on_darwin_on_trial053171.html Here is a Completely Different Way of Doing Science - Cornelius Hunter PhD. - April 2012 Excerpt: But how then could evolution proceed if mutations were just neutral? The idea was that neutral mutations would accrue until finally an earthquake, comet, volcano or some such would cause a major environmental shift which suddenly could make use of all those neutral mutations. Suddenly, those old mutations went from goat-to-hero, providing just the designs that were needed to cope with the new environmental challenge. It was another example of the incredible serendipity that evolutionists call upon. Too good to be true? Not for evolutionists. The neutral theory became quite popular in the literature. The idea that mutations were not brimming with cool innovations but were mostly bad or at best neutral, for some, went from an anathema to orthodoxy. And the idea that those neutral mutations would later magically provide the needed innovations became another evolutionary just-so story, told with conviction as though it was a scientific finding. Another problem with the theory of neutral molecular evolution is that it made even more obvious the awkward question of where these genes came from in the first place. http://darwins-god.blogspot.com/2012/04/here-is-completely-different-way-of.html Ann Gauger on genetic drift - August 2012 Excerpt: 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. https://uncommondescent.com/evolution/ann-gauger-on-genetic-drift/ Oxford University Admits Darwinism's Shaky Math Foundation - May 2011 Excerpt: However, mathematical population geneticists mainly deny that natural selection leads to optimization of any useful kind. This fifty-year old schism is intellectually damaging in itself, and has prevented improvements in our concept of what fitness is. - On a 2011 Job Description for a Mathematician, at Oxford, to 'fix' the persistent mathematical problems with neo-Darwinism. http://www.evolutionnews.org/2011/05/oxford_university_admits_darwi046351.html Using Numerical Simulation to Test the Validity of Neo-Darwinian Theory - 2008 Abstract: Evolutionary genetic theory has a series of apparent “fatal flaws” which are well known to population geneticists, but which have not been effectively communicated to other scientists or the public. These fatal flaws have been recognized by leaders in the field for many decades—based upon logic and mathematical formulations. However population geneticists have generally been very reluctant to openly acknowledge these theoretical problems, and a cloud of confusion has come to surround each issue. Numerical simulation provides a definitive tool for empirically testing the reality of these fatal flaws and can resolve the confusion. The program Mendel’s Accountant (Mendel) was developed for this purpose, and it is the first biologically-realistic forward-time population genetics numerical simulation program. This new program is a powerful research and teaching tool. When any reasonable set of biological parameters are used, Mendel provides overwhelming empirical evidence that all of the “fatal flaws” inherent in evolutionary genetic theory are real. This leaves evolutionary genetic theory effectively falsified—with a degree of certainty which should satisfy any reasonable and open-minded person. http://www.icr.org/i/pdf/technical/Using-Numerical-Simulation-to-Test-the-Validity-of-Neo-Darwinian-Theory.pdf
bornagain77
April 15, 2014
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kevnick. I think you've misunderstood what Joe Felsenstein is saying. He's making the point if you want to know why there are 35 million SNPs different between a particular chimp and a particular human then you don't have to use the fixation equuatios, you can just point out there is a single line on descent onto which mutations fall. This also deals with a slight quibble you could make about within-species variation effecting the calculations since they are based on individuals. As it happens, and as Joe points out, almost all the differences between any human and any chimp are indeed fixed differences ("are in fact most probably fixed in both populations...”) so there is no saving Kozulic for his mistakes. I find it pretty extraordinary that Kozulic want's to stake his reputation on something he obviously knows so little about, and that others seem to want to line up behind him.wd400
April 15, 2014
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Funny to think of Professor Moran effectively calling Einstein, not to speak of the other great giants in the history of science, an 'IDiot'... The front-page headlines of any newspaper on the day of his demise will surely live longer in the memory of man, than his own name, with its infelicitous overtones in the context. Perhaps his name embarrasses the life out of him, and he has to overcompensate. Ironical, though, that a poster to the liberal and often loopy site, Democratic Underground, used to have an ikon of a protestor holding a large sign, with the misspelt word, 'moran', on it.Axel
April 15, 2014
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The fact that a few people fell victim to Morans little games doesn't mean most if us here fell to them. I'm glad we have some very passionate posters like Mung, BA77 and many others that didn't fall for his little BS. As for me I have seen the way evolutionists try to ridicule, and dodge any good critiques to evolution . Since I was on the other side of the coin myself as a believer in evolution for 41 years it's not too hard to see through the veil of their dishonesty. Thank. God for the knowledgeable ID posters here who didn't give in to his little childish mind games .wallstreeter43
April 14, 2014
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I’ve been trying to teach this to the IDiots for over twenty years. Yet they still insist on referring to evolution as “Darwinism” and they continue to ignore random genetic drift in their attacks on evolution.
I'd like to point out to Dr. Moran that Darwinism is different from other theories of evolution. But if he hasn't figured that out "for over twenty years," I suppose there's not much hope for him. ;-) -QQuerius
April 14, 2014
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No worries there. Professor Moran admitted that he is not an expert on the subject, which had not prevented him from lecturing Dr. Kosulic, who is. Now, Moran is finally trying to get educated on the subject first by Joe Felsenstein who gave him not only straightforward answers, but also proof: Joe: "...the differences between the reference sequences are in fact most probably fixed in both populations..." Who can ask for better proof than this? On the frustration of trying to educate IDiots No need to go to a comedy club to have a good laugh. Sandawalk has it all.kevnick
April 14, 2014
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Professor Moran is playing “god” and most of you here have fallen victims to his twisted and perverted desires. He is a very disturbed individual, who draws an unnatural pleasure from calling people names, such as “IDiots”, from attempts to destroy one’s reputation, insisting on “his way or the highway” at any cost and the list goes on. Moran’s arrogant pride is driven by his unrestrained narcissistic pursuit of gratification that has nothing to do with evidence based science. As Dr. Kozulic and others have pointed out, Moran doesn’t care where the “truth” is or whether he has evidence to back up his claims…. To him, forum debates are just a game that he loves to play due to his above mentioned issues and as most of you know, most games can be very addictive, especially if they provided instant and continued gratification. Moran’s claim that 22,000,000 million neutral mutations can be fixed in 5,000,000 years is a perfect example of his mind game that he enjoys to play…. He has not provided any evidence for his claims but he believes that the burden of proof is on others, like Dr. Kozulic, to prove him wrong and the list goes on. All one has to do is read just a few of Moran’s recent posts, such as: Jonathan Wells proves that life must have been created by gods and Junk & Jonathan: Part 4—Chapter 1 which help one to realize that Moran is not interested in true scientific discussions. But rather, his goal is to uphold his own views that have little or no scientific support. Just look at Moran’s correction regarding Coyne’s view of speciation that I linked above: “As Jerry Coyne points out, reproductive isolation is mostly due to accident (random genetic drift) and not natural selection [The Cause of Speciation]. That's in line with modern evolutionary theory and Coyne should know because he's one of the world's leading experts on speciation. [UPDATE: Coyne and some commenters have corrected me. Coyne actually does think that most speciation is due to natural selection. I'll stick with Futuyma as my authority. He's much more open to the idea of speciation by random genetic drift (Evolution 2nd ed. p. 447)]” However, it is also very unfortunate, that reputable scientists, such as Dr. Kozulic, Dr. Wells, and many others have fallen victims to Moran’s mind game. I believe that it is even more unfortunate that some, like Dr. Kozulic, have fallen victim of some non-specialist on the theme trying to do science, who were easily persuaded by Moran’s clever cunning and deception. Why? I just hope that it was not to gain a bit of applause from Moran and his camp of so-called scientists.kevnick
April 14, 2014
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Scordova I'm not expert in this area, but when you said that ""Moran’s argument: neutral evolution is true as evidenced by the genome being mostly junk"" That's when I knew that Moran was wromg as we are finding out more and more each day that so called junk DNA isn't really junk DNA, and it keeps getting worse every day for the JUNK DNA advocates as we keep finding more and more function in this area .wallstreeter43
April 14, 2014
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There are complications in this discussion, not the least of which is that a highly respected segment of the ID community in some respects agrees with Dr. Moran. Moran last year responded to my assertion that fixation rate equals mutation rate, and I was merely passing on the viewpoint of a segment of the ID community: On Beating Dead Horses
I was reminded of this while reading Salvador Corova's latest post on Uncommon Descent because he refers to beating dead horses [If not Rupe and Sanford’s presentation (8/6/13), would you believe Wiki? In this case, yes]. I'm not going to make any comments. Read it and weep for the IDiots. .... Sal begins with ... Evolutionists reluctantly admit most evolution is free of selection and therefore non-Darwinian ... I've been trying to teach this to the IDiots for over twenty years. Yet they still insist on referring to evolution as "Darwinism" and they continue to ignore random genetic drift in their attacks on evolution. About 99% of all IDiots have no idea what Sal is talking about. (Sal Cordova doesn't know either.) What Sal is saying is that practically all of the mutations being fixed in humans are either neutral or slightly deleterious. That has implications. It strongly suggests that most of our genome is junk.
Moran's argument: neutral evolution is true as evidenced by the genome being mostly junk Mendel Team argument: selection is absent as a matter of principle, so then why ISN'T the genome mostly junk and why aren't we dead 100 times over? The Mendel team are creationist and they argue that with a gametic mutation rate of 100 per generation, we should be dead by now, hence the human line hasn't been around for 5,000,000 years, otherwise we'd be dead. "Why aren't we dead 100 times over?" was Kondrashov's question. Kondrashov was a researcher at Cornell, the same institution as John Sanford. The Mendel Team composed of about 10 researchers tried to highlight Kondrashov's question. Central to all this is whether DNA is really Junk. If DNA is really junk then the Mendel Team has been falsified because of neutral theory. If DNA is not junk, then Moran has been falsified by neutral theory! Neutral theory is then a two edged sword, and both the creationists and Moran are wielding the same two edged sword against each other. That is why, oddly, I was having to disagree with some claims against neutral theory since in a strange way opposing arguments put forward by the Mendel Team. In small well-stirred inbreeding populations, the fixation rate will approach the gametic mutation rate, and in fact in such small population selection becomes mostly ineffective relative to chance events for most (not all) nucleotide positions. I tried to explain why here: https://uncommondescent.com/genetics/neutral-theory-and-non-darwinian-evolution-for-newbies-part-2/ I should point out, Dr. Moran didn't criticize the content of what I, Rupe and Sanford asserted. He didn't disagree, but he just had to find a way to call us stupid. The situation is: Moran and Mendel Team agree selection is mostly absent from the genome, that fixation in small populations would happen, but they disagree as to what it means, and the answer hinges on whether DNA is mostly junk. Neutral fixation is a two edged sword and both Moran and the Mendel Team are using it against each other. Arguments against elements of neutral theory then, will oddly disarm the parties in Moran vs. Mendel Team fight. I certainly don't want the Mendel Team disarmed of one of its best weapons, and that is neutral theory! That's why this whole exchange may look a little strange because we have 2 ID parties and 1 anti-ID party in odd situations of agreement and disagreement.scordova
April 14, 2014
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Creationsgardener, I think that Dr. Moran presumes that it'll take at least 100,000 years to fix a non-directed mutation. However, I think that he proposes that there are many, say a billion such mutations in the population. This does not require 100 mutations in every organism, it requires at least 100 new mutations in every population. (Actually a lot more than that because non-directed mutation get lost at a ferocious rate until they happen to settle into the population.)Moose Dr
April 14, 2014
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Hi Mung, Dr. Kozulic is referring to my recent post, When I'm wrong. You'll find the answer to your question there.vjtorley
April 14, 2014
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I don't get how there can even be a discussion on 100 mutations of any kind fixing every generation. It's impossible. It takes many generations for a single mutation in an organism to fix in a population so how can we say that every generation 100 mutations can fix in a population. It's just insane to even say it, forget believing it. Is moran assuming that the same 100 mutations occur in every organism every generation? Because otherwise what he is saying is impossible.Creationsgardener
April 14, 2014
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Dr. Kozulic has requested UD to post the following response to Dr. Torley’s recent retraction vis-à-vis the fixation issue:
What did Dr. Torley retract and why does Dr. Kozulic disagree?Mung
April 13, 2014
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Shades of Salvador Cardoza!
Should Professor Moran answer the questions and arguments posed, I will reply to him at any public forum of his choice.
I would like to make it clear that my involvement in the public discussion ends with this post.
Mung
April 13, 2014
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