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Topic: I.G.D. Strachan: An Evaluation of "Ev"
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kleinman
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Member # 3541
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posted 08. January 2007 22:54
Is there still any interest in discussing this topic. I have done a parametric study with ev which shows that the number of generations which are required to evolve binding sites becomes huge as you increase genome lengths in the model. Does anyone have a comment?
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LifeEngineer
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posted 09. January 2007 06:33
It would be interesting to see people actually doing simulations to test rates of evolutionary change under different sets of assumptions.
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kleinman
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posted 09. January 2007 10:44
[quote="LifeEngineer"]It would be interesting to see people actually doing simulations to test rates of evolutionary change under different sets of assumptions.[/quote]
This thread started by Dr Strachan is a discussion of such a model capable of doing such simulations. Since this thread has been quiescent for a couple years, I’ll summarize what I have been doing.
Last year I became interested in the mathematics of the theory of evolution. I did my own simple probability computations and discussed these on Panda’s Thumb a little. It became clear that the mathematics was more complicated than these simple random probability models I was working on. I searched the net and came across the web site maintained by Dr Tom Schneider of the National Cancer Institute.
Dr Schneider wrote a computer simulation which he calls ev. What ev does is models random point mutations and natural selection. Dr Strachan wrote a very good evaluation of this computer model and started this thread to discuss this model.
I contacted Dr Schneider by email and started an email discussion with him about his model. He invited me to try out the model which I took him up on. His model is available online at the following URL: http://www.ccrnp.ncifcrf.gov/~toms/paper/ev/evj/evjava/index.html
With his computer simulation, you can vary genome size, mutation rate, population, number of binding sites (the evolving sites) and a variety of other parameters. What became apparent very quickly was that as you increased genome size, the number of generations required to evolve the binding sites became huge. The number of generations is so large that it appears that his model is so profoundly slow at accumulating information by random point mutations and natural selection that you can not achieve any macroevolutionary change on a realistic length genome in the time available.
Dr Schneider has engaged in online discussions but refused to discuss this with me online. He had started a thread on the Evolutionisdead forum so I decided to initiate a discussion myself on the same forum. Dr Schneider’s programmer for the online version of ev, Paul Anagnostopoulos has been willing to discuss this issue. This thread can be found at http://www.evolutionisdead.com/forum/viewtopic.php?t=348&sid=3c264e24a96bbb03d439eeead4859b0a
There were only a few evolutionists willing to discuss this issue and of those few, only 2 or 3 were willing to put in the effort necessary to get an understanding of this computer model.
Paul Anagnostopoulos is a moderator on the James Randi forum and invited me to debate this issue on his site which I have taken him up on. This thread is located at http://forums.randi.org/showthread.php?t=67385
These are long threads and not easy to read through. However, I believe there are some important mathematical principles that are demonstrated by the ev model which show that macroevolution is mathematically impossible (at least by random point mutations and natural selection).
My motive for posting on this thread is explain my findings and hopefully recruit other creationists and intelligent designers with some mathematical and computer programming skills to show a serious flaw in the theory of evolution.
If you have interest in this topic, my first suggestion is to visit Dr Schneider’s site where the online version of ev is available and try running his model. Again, it can be accessed at http://www.ccrnp.ncifcrf.gov/~toms/paper/ev/evj/evjava/index.html . You should also read his associated publication from Nucleic Acids Research which is available from Dr Schneider’s web site. The URL is available on Dr Strachan’s first post on this thread and is called Evolution of Biological Information.
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LifeEngineer
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posted 10. January 2007 08:26
Kleinman,
When you start investigating the mathematics of evolutionary biology, there are a couple of general principles that are useful to keep in mind.
First, simulation models are primarily of value in testing competing theories of micro-evoluition. Too many people incorrectly assume that because we can observe instances of micro-evolution, we automatically have valid scientific theories of micro-evolution.
Second, the first micro-evolutionary theories most people are going to want to test are theories of the general RM&NS type. Contrary to popular misconceptions, little or no testing of these theories has been performed, or at least none of the testing has been reported in peer reviewed journals.
Third, there are lots of potential tests that can be performed to evaluate the RM theories, the NS theories, and the genetic determinism theories.
Fourth, formal testing definitely falsifies all three of components of modern evolutionary theory listed above.
Fifth, there are plenty of alternatives to MET, particularly goal directed intelligence based theories of micro-evolution that can pass the tests failed by MET.
Finally, you are unlikely to find individuals from any of the fields of biology who are competent to evaluate the results of formal testing performed using simulation models.
But even recognizing all the technical and political issues associated with the mathematical and scientific analysis of evolution, the analysis is interesting and worth the effort.
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Daniel Smith
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posted 13. January 2007 15:08
kleinman,
I just spent the last several days reading through the evolutionisdead and the James Randi threads. I see that now, they are trying to tweak the selection algorithm to make ev more "ToE friendly". That's the Richard Dawkins "METHINKS IT IS LIKE A WEASEL" trick: Select for potential, and you will always arive at your goal.
True natural selection is an uncompromising beast. In order for an advantage to be passed on, the organism must still make it to the reproductive stage. That stage is a long way off and frought with many dangers for most organisms.
Let's say that, through some miracle of recombination and massive mutation, a chicken is conceived that has a genetic makeup that makes it completely impervious to disease. Surely that chicken will be selected right? But what if a fox gets in the henhouse and eats the egg before the chicken is hatched? No selection! What if the "super chicken" is infertile? What if she dies crossing the road before she ever lays an egg? What if a tornado wipes out the whole chicken colony? These and many other factors work against the "perfect selection" mechanism evolutionists use in their arguments.
Keep up the good work. You've got them on the run!
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kleinman
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Member # 3541
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posted 13. January 2007 16:22
LifeEngineer said:
quote:
Kleinman,
When you start investigating the mathematics of evolutionary biology, there are a couple of general principles that are useful to keep in mind.
First, simulation models are primarily of value in testing competing theories of micro-evoluition. Too many people incorrectly assume that because we can observe instances of micro-evolution, we automatically have valid scientific theories of micro-evolution.
Second, the first micro-evolutionary theories most people are going to want to test are theories of the general RM&NS type. Contrary to popular misconceptions, little or no testing of these theories has been performed, or at least none of the testing has been reported in peer reviewed journals.
Third, there are lots of potential tests that can be performed to evaluate the RM theories, the NS theories, and the genetic determinism theories.
Fourth, formal testing definitely falsifies all three of components of modern evolutionary theory listed above.
Fifth, there are plenty of alternatives to MET, particularly goal directed intelligence based theories of micro-evolution that can pass the tests failed by MET.
Finally, you are unlikely to find individuals from any of the fields of biology who are competent to evaluate the results of formal testing performed using simulation models.
But even recognizing all the technical and political issues associated with the mathematical and scientific analysis of evolution, the analysis is interesting and worth the effort.
One thing that distinguishes soft sciences from the hard mathematical sciences is accounting.
The concept of point mutations can be observed in the laboratory and if one is going to extrapolate this process to evolution by a selection process, an accounting system should be set up to see whether you can balance the books. Dr Schneider has written a peer reviewed and published mathematical model of this process and shows that as you lengthen the genome, the number of generations becomes huge, far too large to support the theory of evolution by this process. This occurs despite Dr Schneider’s unrealistic but precise selection process. Perhaps you know of a way to correct this mathematical hurdle.
Daniel Smith said:
quote:
kleinman,
I just spent the last several days reading through the evolutionisdead and the James Randi threads. I see that now, they are trying to tweak the selection algorithm to make ev more "ToE friendly". That's the Richard Dawkins "METHINKS IT IS LIKE A WEASEL" trick: Select for potential, and you will always arive at your goal.
True natural selection is an uncompromising beast. In order for an advantage to be passed on, the organism must still make it to the reproductive stage. That stage is a long way off and frought with many dangers for most organisms.
Let's say that, through some miracle of recombination and massive mutation, a chicken is conceived that has a genetic makeup that makes it completely impervious to disease. Surely that chicken will be selected right? But what if a fox gets in the henhouse and eats the egg before the chicken is hatched? No selection! What if the "super chicken" is infertile? What if she dies crossing the road before she ever lays an egg? What if a tornado wipes out the whole chicken colony? These and many other factors work against the "perfect selection" mechanism evolutionists use in their arguments.
Keep up the good work. You've got them on the run!
What Unnamed has done on the Randi forum is design a selection process that weight the selection to the evolution of the binding sites in the binding site region of the genome. His selection process almost completely ignores mutations in the non-binding site region of the genome. This effectively uncouples the selection of mutations in the binding site region from mutations in the non-binding site region. This is why they can lengthen the genome without getting big increases in the generations for convergence. I guess they never heard of harmful mutations.
Their idea of a graduated selection process for the evolution of a gene de novo is pure fantasy. Nothing of the kind has ever been observed. This concept is as ridiculous as abiogenesis. There are no physical laws or mathematics that would support either theory.
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LifeEngineer
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posted 14. January 2007 10:58
Quote: Perhaps you know of a way to correct this mathematical hurdle.
The fact that point mutations occur is not sufficient to support the conclusion that point mutations are the source or cause of observed mutations. If you look at the available evidence, you are quickly led to reject the theory or hypothesis that mutations are generated by any type of random change process.
The best evidence available is that meaningful genetic changes are produced by intelligent agency or intelligent goal directed causation. There is lots of evidence readily available that complex systems with read-write capabilities produce patterns of changes in stored data that are compatible with observed changes in genetic data.
If we assume or hypothesize that DNA is a data storage mechanism, then it is reasonable to theorize that there exist both read and write mechanism associated with this data storage process. Such theories would be logical consistent with the observed patterns of genetic data and changes in genetic data.
The concept or theory that genetic data changes as a result of random variation and natural selection is totally unsupported by the evidence. This does not mean that the observed pattern of data and data change can not be explained scientifically.
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Daniel Smith
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posted 14. January 2007 20:07
Life Engineer,
I agree with your assessment of the various ways to interpret the data. Perhaps the ID movement will focus it's efforts on such research in the future.
Kleinman,
It would seem to me that any realistic model of natural selection would have to include a factor to represent the forces of nature that regularly eliminate organisms before they reach reproductive age (see my previous post).
I'm not sure how you would model this (I'm no mathematician), but a suggestion would be to randomly eliminate a percentage of the surviving population after selecting for good mutations. I think it would have to be random since no mutation can guarantee survival against everything - especially in the young vulnerable stages of life.
This seems more realistic to me and would also eliminate some of the unrealistic positive effects of large populations on the ev model - since you're using a percentage and not a fixed number.
Of course the percentage would have to be a realistic number (no idea how you'd arrive at this since it probably differs wildly among organisms).
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LifeEngineer
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posted 15. January 2007 11:48
Quote: I agree with your assessment of the various ways to interpret the data. Perhaps the ID movement will focus it's efforts on such research in the future.
I believe there are already people who have already done the type of analysis suggested. The problems appear to be that 1) the people doing the analysis tend to be sloppy in defining the assumptions actually used and 2) there is a strange refusal to apply the conclusions of the analysis to evolution.
If DNA is viewed as a data file, then we have lots of evidence regarding complex systems that are capable of changing data in data files. We can readily demonstrate that the observed changes in DNA are compatible with changes in data files and not compatible with random change/selection processes.
Again, the issue is not getting ID supporters to perform a certain type of analysis, but getting all scientists to recognize the rather obvious significance/implications of analysis that has already been performed.
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Daniel Smith
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posted 15. January 2007 14:41
Life Engineer,
Could you please keep us informed of this type of research by posting a link whenever something new comes out?
Thanks.
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LifeEngineer
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posted 16. January 2007 08:41
Quote: Could you please keep us informed of this type of research by posting a link whenever something new comes out?
You are asking the wrong question. The question that should be asked are "When data is published showing patterns of genetic data, 'Did the authors perform tests to determine if the data could be fit to a random mutation/natural selection model or is there a better fit to intelligent goal directed data generation and storage models?' and 'Is the volume of stored genetic data analyzed sufficient to explain the phenotype phenomenon associated with the data?""
Although no knowledgable scientist is likely to actually support such theories, 'random variation and natural selection' is still the dominant genetic change theory and genetic determinism is still the dominant genetic coding theory. If data currently being gathered and published is in contradiction to the dominant theories, and if the data being gathered and published is supportive of hard science design by intelligence theories, then those publishing such materials would seem to have a reponsibility and obligation to report conclusions that contradict dominant theories.
It is a reasonably simple matter to create models to simulate the allele patterns and gene change patterns generated by true random variation and natural selection processes. It is also very easy to contruct patterns of alleles and allele changes that would be generated by intelligent goal directed gene change processes. There is lots of data available of allele/gene patterns, and there is no doubt that the data is far more compatible with intelligent change processes than with random change processes.
There is also by this time no real question that the data stored in genes has no where near the complexity or content necessary to control the processes associated with the genetic data.
The issue is not looking for articles published on this topic because we all know you won't find any. The issue is to look for articles published on gene/allele distributions and ask the question why weren't the implication of the data for the existing dominant theories evaluated?
Biology Direct, by the way, seems to provide an opportunity for analysts to raise these questions.
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LifeEngineer
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posted 20. January 2007 10:04
It is kind of interesting to note the differences between 1)running simulation programs and 2) performing formal scientific or mathematical analysis using simulation programs. It is fairly easy to teach people how to push 'run' buttons. It is apparently, extremely difficult to teach people how to analyze and interpret the results.
The entire ID/Darwin debate could be resolved in favor of ID given a dozen people qualified scientists willing to analyze and interpret the results of so called genetic algorithm type search programs. Scientists with the ability to perform such analysis exist, but almost none of them apparently have the courage to engage in analysis that will challenge the beliefs of the academic power structure. Interesting.
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kleinman
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posted 31. January 2007 18:52
Sorry I’m a little slow in responding to posts here but I’ll try to catch up.
LifeEngineer wrote:
quote:
The fact that point mutations occur is not sufficient to support the conclusion that point mutations are the source or cause of observed mutations. If you look at the available evidence, you are quickly led to reject the theory or hypothesis that mutations are generated by any type of random change process.
My analysis of the ev computer model simply shows the impossibility of the mechanism of random point mutations and natural selection as the driving force for the theory of evolution. Perhaps you can explain why you don’t believe base substitution errors that occur when DNA is replicated are not random.
LifeEngineer wrote:
quote:
The best evidence available is that meaningful genetic changes are produced by intelligent agency or intelligent goal directed causation. There is lots of evidence readily available that complex systems with read-write capabilities produce patterns of changes in stored data that are compatible with observed changes in genetic data.
Is this some sort of intelligent goal directed evolution?
LifeEngineer wrote:
quote:
If we assume or hypothesize that DNA is a data storage mechanism, then it is reasonable to theorize that there exist both read and write mechanism associated with this data storage process. Such theories would be logical consistent with the observed patterns of genetic data and changes in genetic data.
If you are going to make this analogy, I would say that DNA is primarily read only memory. Writing on preexisting DNA would seem particularly harmful to that creature.
LifeEngineer wrote:
quote:
The concept or theory that genetic data changes as a result of random variation and natural selection is totally unsupported by the evidence. This does not mean that the observed pattern of data and data change can not be explained scientifically.
I agree with you almost completely and I think this is shown in Dr Schneider’s ev program when realistic genome lengths and mutation rates are used. Clearly, recombination and selection can and does occur. This is shown with breeding of dogs, cattle, plants, etc. Occasionally there seems to be mutations that have some beneficial affect for living things such as antibiotic resistance and sickle cell hemoglobin in malarial endemic areas, however, there is no selection process known that would evolve a gene de novo.
Daniel Smith wrote:
quote:
It would seem to me that any realistic model of natural selection would have to include a factor to represent the forces of nature that regularly eliminate organisms before they reach reproductive age (see my previous post).
I'm not sure how you would model this (I'm no mathematician), but a suggestion would be to randomly eliminate a percentage of the surviving population after selecting for good mutations. I think it would have to be random since no mutation can guarantee survival against everything - especially in the young vulnerable stages of life.
If you have been following the “Annoying Creationists” thread on the James Randi Forum you will see that I have been holding evolutionists feet to the fire by challenging them to explain a selection mechanism that would evolve a gene de novo. I don’t believe there is any sort of a selection process. What natural selection can do is determine whether particular properties that a creature has give it a survival benefit for that creature. I think natural selection is a restatement of the first law of thermodynamics. Any characteristics that a creature has that allow that creature to put more of its available energy to reproduction will survive. I don’t believe that natural selection has the capability to select for bases and generate genes from scratch (de novo).
Daniel Smith wrote:
quote:
This seems more realistic to me and would also eliminate some of the unrealistic positive effects of large populations on the ev model - since you're using a percentage and not a fixed number.
Of course the percentage would have to be a realistic number (no idea how you'd arrive at this since it probably differs wildly among organisms).
It turns out that population does not have as large an affect as you might think initially. All the population series cases I ran with ev appear to quickly approach an asymptote that is far to large to rescue the theory of evolution. The reason I believe this happens is that population has less than an additive effect on the chance that an appropriate mutation will occur at the appropriate loci. This issue was discussed in some depth on the Evolutionisdead forum and the probability calculation was done by Myriad. It shows the importance of doing the calculations debating the theory of evolution.
LifeEngineer wrote:
quote:
If DNA is viewed as a data file, then we have lots of evidence regarding complex systems that are capable of changing data in data files. We can readily demonstrate that the observed changes in DNA are compatible with changes in data files and not compatible with random change/selection processes.
Again, the issue is not getting ID supporters to perform a certain type of analysis, but getting all scientists to recognize the rather obvious significance/implications of analysis that has already been performed.
There are several Achilles Heels to the theory of evolution. The most obvious is the selection process. Without a plausible selection process, the random assembly of genomes gives infinitesimally small probabilities.
How do you think that the mathematics of data file analysis can be applied?
LifeEngineer wrote:
quote:
It is kind of interesting to note the differences between 1)running simulation programs and 2) performing formal scientific or mathematical analysis using simulation programs. It is fairly easy to teach people how to push 'run' buttons. It is apparently, extremely difficult to teach people how to analyze and interpret the results.
The way I have approached this issue is to describe random mutations and natural selection as a bookkeeping problem. Dr Schneider’s computer simulation sets up the bookkeeping rules and you run the program with various parameters and see whether you can balance the books. I think the message is getting across to evolutionists. Explaining the issue this way also illuminates the flaw in Dr Schneider’s contrived selection method.
It is interesting to see the response of devout evolutionists who try to say that the problem is in my mathematics. I simply tell them that this computer model was written by the head of computational molecular biology at the National Cancer Institute, was peer reviewed and published in Nucleic Acids Research. The years of challenges to Dr Schneider’s model by IDers (including IGD Strachan excellent analysis) and his ardent defense of his work set the stage for my parametric study and challenge to the theory of evolution.
LifeEngineer wrote:
quote:
The entire ID/Darwin debate could be resolved in favor of ID given a dozen people qualified scientists willing to analyze and interpret the results of so called genetic algorithm type search programs. Scientists with the ability to perform such analysis exist, but almost none of them apparently have the courage to engage in analysis that will challenge the beliefs of the academic power structure. Interesting.
Anyone serious about getting involved in this debate better not have a thin skin. Academicians could lose their jobs if they challenge the theory depending on the politics of their departments. Consider how many biologists have invested their careers in the theory of evolution. Consider the number of academic and governmental institutions that are committed to this theory. There are many people in church who believe the theory of evolution is true. I think it is a mistake to underestimate the resistance you will get if you challenge the theory of evolution.
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John A. Davison
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posted 01. February 2007 02:34
Just as ontogeny ends with the death of the individual so evolution has now ended with the extinction of species. A new genus has not appeared in two million years and a new true species not in historical times. All that remains is extinction and we are not immune to that fate. No large animal has ever avoided ultimate extinction and we are definitely a relatively large animal. I know of not a single "living fossil" larger than Homo sapiens.
Just some rather depresssing thoughts.
"A past evoloution is undeniable, a present evolution undemonstrable."
John A. Davison
[ 01. February 2007, 02:34: Message edited by: John A. Davison ]
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LifeEngineer
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posted 01. February 2007 10:16
Quote: Perhaps you can explain why you don’t believe base substitution errors that occur when DNA is replicated are not random.
It is not a matter of belief, but rather a matter of evidence not compatible with random mutation theories. In order to analyze 'point mutations are random' theories, you test to determine if the observed data on alleles per gene are consistent with the pattens of alleles per gene predicted by a random mutation( and natural selection) theory.
Note that in testing such a theory, you need to make assumptions regarding the forces of natural selection (the fitness) of individual 'random point mutations'. The reasonableness or realism of these assumptions can be evaluated by looking at the relevant mortality/morbidity data.
This type of testing shows that the rates of natural selection needed to produce the observed patterns of alleles per gene would produce extinction (if the random mutation theories were valid). Since this pattern of mortality does not occur we can conclude that mutations are not random. The alternative to 'random mutation theories' are 'purposeful or designed or design by intelligence' theories of mutation.
Note that there is also lots of direct evidence for selective or intelligent error correction mechanisms that greatkt reduce or selectively eliminate harmful mutations.
My quess or speculation is that there exist some fairly complex 'write type' mechanisms for creating new alleles associated with new proteins. Geneticists, given the anti-goal directed intelligence bias that exists, probably wouldn't admit to the existence of such mechanisms.
But the main point here is that there is direct scientific evidence for rejecting random mutation theories and in support of design by intelligence theories of mutation.
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