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Author
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Topic: I.G.D. Strachan: An Evaluation of "Ev"
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LifeEngineer
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Member # 3446
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posted 01. February 2007 10:56
Quote: 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.
If you have a piece of information stored in DNA that is essential to the existance of the organism, then any change or rewrite of that information/DNA is likely to be harmful or fatal. There appears to be lots of direct evidence of sophisticated 'intelligent' error correction mechanisms for preventing changes or rewrites of such codes.
However, if you recognize or accept or assume that there are some forms of evolutionary/genetic change, and if you accept the hard evidence that against random mutation theories, you are left, I believe, with the option of intelligent 'write-type' mutation theories.
I suspect/predict that if look at actual genetic change data, from virus' and bacteria for example, you will find 'jumps' in genetic change that have characteristics similar to what you would see in read-write files created and modified by human intelligence.
Note that we have direct scientific evidence that the mutations that occur are more beneficial and less harmful than what would be generated by a random mutation process or theory. We also have indirect evidence, if we accept evidence for evolutionary/genetic change, of complex genetic changes that appear to have the patterns of complex human read-write data files.
If you reject random mutations because of the evidence, and if you don't advocate a read-write type mutation theories or explanations, what do you advocate?
Also note that in my view, scientific explanations have the form of 'the best available theory compatible with the data'. If, IMO, you reject one theory like random mutation theory because it is incompatible with the data, then you have an obligation to present some alternative predictive theory.
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LifeEngineer
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posted 01. February 2007 11:10
Quote: 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.
First, I appologize for responding piece meal which results in some duplication, but you are bringing up several concepts and it is useful to try to isolate them.
Second, you have to be careful when doing analysis with ev programs. It is quite easy to bury misleading and distorting assumptions into such programs. For example, Ev programs are generally based on a precise genetic determinism assumption when there is no evidence that such a mapping exist or are even possible. Also, an ev program may have no equivalent of a 'write' function that could produce or write new complex change genetic codes. You are correct, I believe, in concluding that no selection process could produce a complex new allele or new gene. Such a conclusion is not, however, the same as concluding there is no process capable of producing such a genetic change.
I will respond more tomorrow, but I believe this uses up my posting for today.
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kleinman
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posted 01. February 2007 13:22
John A Davison wrote:
quote:
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.
Not only do I believe the theory of evolution to be untrue, it is a very depressing theory. It is God who brings life out of death. That is where our hope must reside.
LifeEngineer wrote:
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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.
It is my understanding that certain areas of genes must remain invariant in order for the protein produced by the gene is able to function properly. There are other areas on the gene where substitutions may occur without altering the confirmation of the protein so that it would no longer function. Do you have data which shows that point mutations are not random?
LifeEngineer wrote:
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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.
Presently I am debating evolutionists on natural selection. I believe that natural selection can only act when there is a change in a functioning molecule (either improved or worsened function). I am arguing that natural selection can not evolve a gene de novo. The gist of the argument is as follow:
A gene is to evolve. The first base in the sequence for the gene is laid down on the genome. One base codes for nothing so there is nothing for natural selection to act upon. A second base added by random chance is laid down in the sequence. Still nothing to code for, natural selection can not act on this sequence. A third base in the sequence is laid down. You now have enough bases to form a codon for a single amino acid. A single amino acid has no functional use so there is still nothing for natural selection to act upon. So bases must be added randomly until you have a long enough sequence of bases to produce a functional polypeptide and then natural selection can act. Adding bases randomly yield probabilities so infinitesimally small that evolution is mathematically impossible.
LifeEngineer wrote:
quote:
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.
My understanding of biochemistry is that DNA is replicated with quite high fidelity. The only “write” mechanism that changes this are mutations of a variety of types.
LifeEngineer wrote:
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If you have a piece of information stored in DNA that is essential to the existance of the organism, then any change or rewrite of that information/DNA is likely to be harmful or fatal. There appears to be lots of direct evidence of sophisticated 'intelligent' error correction mechanisms for preventing changes or rewrites of such codes.
There are proteins that do error correction in the genetic code.
LifeEngineer wrote:
quote:
However, if you recognize or accept or assume that there are some forms of evolutionary/genetic change, and if you accept the hard evidence that against random mutation theories, you are left, I believe, with the option of intelligent 'write-type' mutation theories.
What I think evolutionist have done is extrapolated the rapid changes that are seen with recombination and natural selection to mutation and natural selection. I think both Darwin and Gould made this extrapolation error. In examining Dr Schneider’s ev program, it becomes apparent that the accumulation of information is profoundly slow by random point mutations and natural selection when realistic genome lengths and mutation rates are used in the model. I don’t understand how intelligent ‘write type’ mutations would work.
LifeEngineer wrote:
quote:
I suspect/predict that if look at actual genetic change data, from virus' and bacteria for example, you will find 'jumps' in genetic change that have characteristics similar to what you would see in read-write files created and modified by human intelligence.
There are phase shift mutations and translocations of genetic material but these are usually harmful to the creature.
LifeEngineer wrote:
quote:
Note that we have direct scientific evidence that the mutations that occur are more beneficial and less harmful than what would be generated by a random mutation process or theory. We also have indirect evidence, if we accept evidence for evolutionary/genetic change, of complex genetic changes that appear to have the patterns of complex human read-write data files.
How are you getting this evidence?
LifeEngineer wrote:
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If you reject random mutations because of the evidence, and if you don't advocate a read-write type mutation theories or explanations, what do you advocate?
Also note that in my view, scientific explanations have the form of 'the best available theory compatible with the data'. If, IMO, you reject one theory like random mutation theory because it is incompatible with the data, then you have an obligation to present some alternative predictive theory.
I don’t reject that random mutations exist. What I reject is that random point mutations and natural selection is a viable mechanism to explain macroevolution. Dr Schneider’s program shows this process is far to slow.
I happen to be a creationist. I think special creation fits observation far better than any alternative.
LifeEngineer wrote:
quote:
Second, you have to be careful when doing analysis with ev programs. It is quite easy to bury misleading and distorting assumptions into such programs. For example, Ev programs are generally based on a precise genetic determinism assumption when there is no evidence that such a mapping exist or are even possible. Also, an ev program may have no equivalent of a 'write' function that could produce or write new complex change genetic codes. You are correct, I believe, in concluding that no selection process could produce a complex new allele or new gene. Such a conclusion is not, however, the same as concluding there is no process capable of producing such a genetic change.
The advantage of working with a mathematical model is that assumptions are much better delineated than with a verbal discussion. You can selectively change parameters in the model and look at the behavior. I realize that ev only considers random point mutations and neglects other forms of mutations. What Dr Schneider has done though is formulated mathematically a selection process. In doing this, you can ask the question is this realistic and does it properly describe a physical phenomena. I don’t believe it does and there is no realistic substitute.
I will be busy for the next few days and won’t be able to respond on a daily basis but I will try to respond next week.
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LifeEngineer
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posted 02. February 2007 12:05
It is interesting that while computerized simulation models are a very powerful tool for use in the scientific analysis of complex processes, these models seem to be far more often misused than used properly. Evolutionary biologists and AI practitioners routinely make misleading claims that if an extremely simplified version of a phenomenon can be simulated under clearly artificial and misleading conditions, then scientists are justified in making broad general claims that the same phenomenon explains extremely complex forms of the phenomenon produced under diverse and complex conditions. I get the impression that you are attempting to support the equally dubious claim that “If evolutionary/genetic change can not occur via simple RM&NS then there is no logical alternative theory”.
If computer simulations models are used properly, I suggest, there is hard evidence that:
1. Neither random mutation nor natural selection play a significant role in either evolutionary change or in genetic change and
2. There are alternative goal directed intelligence based testable predictive theories of evolution/genetic change that can explain/fit the available evidence.
At issue here, I believe, is the question of the proper use of simulation models in evaluating scientific theories. An appropriate topic for discussing this issue is to look at the hard evidence rejecting ‘random mutation theories’ and ‘supporting designed by goal directed intelligence’ mutation theories.
In order to evaluate whether mutations are random (or random with respect to fitness) we first have define what is meant by random. We then need to define alternatives to random mutations.
In the context of a variation/selection change process, random mutation means that ‘each member of the set of possible mutations has an equal probability of being chosen for evaluation”. The more commonly used term ‘random with respect to fitness’ means that ‘the average or expected fitness of the mutation that occur will be the same as the average fitness of all the members of the set of possible mutations”. Do you agree with these definitions?
The alternatives to random are non-random or biased. With respect to mutations, this would mean that some mutations are much more likely to occur and other possible mutations are less likely to occur. The alternatives to random with respect to fitness are biased with respect to fitness. Of interest here are situations where actual mutations tjat occur have a significantly more favorable than average fitness and where mutations that don’t occur have significantly less favorable average fitness. Again, do you agree with these definitions?
I use the term “designed with goal directed intelligence” to characterize mutations that have a strong favorable bias. This type or class of mutation suggests that the life form has the appearance of knowing in advance particular groups of mutations will be harmful or beneficial and suppresses harmful mutations and encourages the generation of mutations with a more beneficial than average expected beneficial fitness. We might debate the appropriateness of labeling such mutations as designed, but the concept or definition should be clear.
The next question is “How do we test to determine if mutations are random with respect to fitness or designed?” or “Does the available hard evidence support random mutation theories or designed mutation theories?” It seems to me that the hard evidence answers to these questions are fairly obvious, but if they are not lets work through the analysis.
To determine if mutations are random or designed, we need to find examples where 1) specific subgroups of potential mutations have a significantly higher or lower than chance probabilities of occurring, and where 2) we can determine or estimate the average fitness of the suppressed or encouraged mutations. Agree?
The simplest and most direct hard evidence on this subject involves what might be labeled ‘essential genetic information’. Any type of mutation in such an area is likely to have a seriously harmful impact. If we have evidence of such mutations being suppresses or reversed by error correction mechanisms (as opposed to being eliminated by natural selection) then we have evidence of designed mutations. Since you mentioned such evidence, I assume you are aware that there is clear hard evidence for rejecting random mutation theories and supporting designed mutation theories. Agree?
More complex and sophisticated tests of random versus designed mutations can be designed, but again it should be obvious that the conclusions of such tests will be the same. Agreed?
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kleinman
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posted 26. February 2007 15:01
Forgive me for being so slow to respond.
Life Engineer wrote:
quote:
It is interesting that while computerized simulation models are a very powerful tool for use in the scientific analysis of complex processes, these models seem to be far more often misused than used properly. Evolutionary biologists and AI practitioners routinely make misleading claims that if an extremely simplified version of a phenomenon can be simulated under clearly artificial and misleading conditions, then scientists are justified in making broad general claims that the same phenomenon explains extremely complex forms of the phenomenon produced under diverse and complex conditions. I get the impression that you are attempting to support the equally dubious claim that “If evolutionary/genetic change can not occur via simple RM&NS then there is no logical alternative theory”.
This is my basic argument with the theory of evolution, which is the hypothesis is not supported by the arithmetic of mutation and selection. Computer models are very good bookkeeping tools. If the underlying application of the arithmetic to the bookkeeping rules is done appropriately, these models can be useful for prediction. Dr Schneider’s basic concept of allowing random point mutations to a sequence of bases and selecting for those mutations which are beneficial and selecting against those mutations which are harmful seems to be a plausible approach to doing such bookkeeping. This is why I spent some time studying the ev model to analyze whether the bookkeeping was being done in an appropriate manner.
Even with Dr Schneider’s contrived selection process, the rate of information gain is profoundly slow when using realistic genome lengths and mutation rates, too slow to support the theory of evolution by this mechanism.
If you think there is a logical alternative explanation to RM&NS that would explain the theory of evolution, what is it?
Life Engineer wrote:
quote:
If computer simulations models are used properly, I suggest, there is hard evidence that:
1. Neither random mutation nor natural selection play a significant role in either evolutionary change or in genetic change and
2. There are alternative goal directed intelligence based testable predictive theories of evolution/genetic change that can explain/fit the available evidence.
I think there is evidence that random mutations play a role in evolution. How do you explain antibiotic resistance? I also think there is a phenomenon of natural selection as well but this phenomenon is more effective in selecting out defects due to mutations rather than selecting in beneficial mutation. In addition, recombination coupled with natural selection can alter structure and anatomy of creatures.
Perhaps you can describe in a step by step manner your alternative theory.
Life Engineer wrote:
quote:
At issue here, I believe, is the question of the proper use of simulation models in evaluating scientific theories. An appropriate topic for discussing this issue is to look at the hard evidence rejecting ‘random mutation theories’ and ‘supporting designed by goal directed intelligence’ mutation theories.
How do you determine if a mutation is random vs goal directed?
Life Engineer wrote:
quote:
In order to evaluate whether mutations are random (or random with respect to fitness) we first have define what is meant by random. We then need to define alternatives to random mutations.
In the context of a variation/selection change process, random mutation means that ‘each member of the set of possible mutations has an equal probability of being chosen for evaluation”. The more commonly used term ‘random with respect to fitness’ means that ‘the average or expected fitness of the mutation that occur will be the same as the average fitness of all the members of the set of possible mutations”. Do you agree with these definitions?
I don’t understand your definition; perhaps you could give me a simple example.
Life Engineer wrote:
quote:
The alternatives to random are non-random or biased. With respect to mutations, this would mean that some mutations are much more likely to occur and other possible mutations are less likely to occur. The alternatives to random with respect to fitness are biased with respect to fitness. Of interest here are situations where actual mutations tjat occur have a significantly more favorable than average fitness and where mutations that don’t occur have significantly less favorable average fitness. Again, do you agree with these definitions?
I can see the possibility that mutations might not be completely random. For example, the binding of the enzymes for DNA replication may somehow be affected by the sequence of bases being duplicated such that certain sequences might be more prone to errors in duplication, but how would you use this to explain evolution?
Life Engineer wrote:
quote:
I use the term “designed with goal directed intelligence” to characterize mutations that have a strong favorable bias. This type or class of mutation suggests that the life form has the appearance of knowing in advance particular groups of mutations will be harmful or beneficial and suppresses harmful mutations and encourages the generation of mutations with a more beneficial than average expected beneficial fitness. We might debate the appropriateness of labeling such mutations as designed, but the concept or definition should be clear.
Bacterial drug resistance could be an example of what you are describing here. How does your concept of “designed with goal directed intelligence” differ from RM&NS?
Life Engineer wrote:
quote:
The next question is “How do we test to determine if mutations are random with respect to fitness or designed?” or “Does the available hard evidence support random mutation theories or designed mutation theories?” It seems to me that the hard evidence answers to these questions are fairly obvious, but if they are not lets work through the analysis.
What is the direction of design that you are talking about, what is the goal?
Life Engineer wrote:
quote:
To determine if mutations are random or designed, we need to find examples where 1) specific subgroups of potential mutations have a significantly higher or lower than chance probabilities of occurring, and where 2) we can determine or estimate the average fitness of the suppressed or encouraged mutations. Agree?
I think you have a similar problem that evolutionists have. Evolutionists don’t have a definition for natural selection that evolves a gene from the beginning. Your problem is to define the goal that would be directing mutations. I don’t think either exists. This is why I think creation is the best explanation for life. Evolution occurs in a very limited sense such as with recombination and natural selection and the slight variations you sometimes see with random mutations and natural selection.
Life Engineer wrote:
quote:
The simplest and most direct hard evidence on this subject involves what might be labeled ‘essential genetic information’. Any type of mutation in such an area is likely to have a seriously harmful impact. If we have evidence of such mutations being suppresses or reversed by error correction mechanisms (as opposed to being eliminated by natural selection) then we have evidence of designed mutations. Since you mentioned such evidence, I assume you are aware that there is clear hard evidence for rejecting random mutation theories and supporting designed mutation theories. Agree?
More complex and sophisticated tests of random versus designed mutations can be designed, but again it should be obvious that the conclusions of such tests will be the same. Agreed?
Any concept that you are going to try to prove mathematically (such as what Dr Schneider attempted to do with ev) requires a sequence of cause and effect steps to model this behavior. Dr Schneider’s model reveals what I consider the fatal flaw in the theory of evolution, which is a selection process that can evolve a gene from the beginning and a selection process that can transform genes from one function to a new function. Neither of these selection processes exists. You are now proposing a design/goal based mechanism. You need to define this mechanism.
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LifeEngineer
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posted 01. March 2007 09:49
Quote: If you think there is a logical alternative explanation to RM&NS that would explain the theory of evolution, what is it?
A rather broad general question. If you start by viewing evolutionary change in terms of search processes, then the alternative to a process of random variation and natural selection is a process where the variations are 'designed by intelligence' and where most harmful or variations are selected out without harming the organisms. The alternative to theories of evolution based on a random search are theories of evolution based on intelligent or efficient goal directed searches.
It may be helpful to note that not only do I believe that the evidence supports intelligent search theories, but I also reject the idea that evolutionary change is the result of genetic searches. Evolution, by the theory I support, is the result of efficient or intelligent 'evolution' or causal relationships or information procesing algorithms or assembly and operating processes.
But to answer your basic question, the alternative to theories based on random search are theories based on intelligent or efficient goal directed search. Such theories are readily simulated on computer systems and the results of such simulations can be compared to actual evolutionary change data.
Quote: I think there is evidence that random mutations play a role in evolution. How do you explain antibiotic resistance? I also think there is a phenomenon of natural selection as well but this phenomenon is more effective in selecting out defects due to mutations rather than selecting in beneficial mutation. In addition, recombination coupled with natural selection can alter structure and anatomy of creatures.
You seem to be confusing 1) instances of mutations that could be characterized as stochastic and 2) a 'theory' of evolution random mutation. Evidence that cheese exists is not evidence that the moon is made of green cheese. The fact that one genetic change appears under special conditions to follow a predictable stochastic pattern is in direct contradiction to the observation that all the other likely point mutations do not appear to be occurring.
To test if mutations are random or random with respect to fitness, we look not at one mutation, but at the entire range of expected point mutations. When we do such analysis, we find that most 'expected mutations' are not present and have not been eliminated by natural selection.
Quote: Neither of these selection processes exists. You are now proposing a design/goal based mechanism. You need to define this mechanism.
No you don't. What is needed are testable predictive theories that fit the data. Scientific theories of evolution do not depend upon knowing the mechanisms. They depend on producing predictive theories that fit the data.
Using models to falsify RM&NS is fairly trivial operation. The real value of these models is in testing alternative intelligence based theories.
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LifeEngineer
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posted 02. March 2007 08:23
There appears to be a fundamental misunderstanding about the nature of and use of mathematical simulation models in scientific analysis. Many, probably most people believe that simulation models are attempts to express how complex processes operate in the real world. This is not accurate.
Simulation models represent sets of logically consistent theories operating in an idealized abstract universe. When we perform testing with an ev model, it is not sufficient to just see if the model does or does not produce the expected behavior. In to validate the results obtained using a simulation model, we need to go back and test every assumption/theory buried in the model.
Does, for example, if a model perports to simulte random mutations, we need to determine if 1) the random mutations simulated are actually compatible with a random mutation theory and 2) we need to determine if the random mutations used in the model are compatible with the types of mutations actually observed to occur. If the model diverges from either the existing theory or from actual data, we then need to test to determine if the variance will bias or inproperly influence the result of the test being performed.
If this type of validation is actually performed, you find that models that adhere to so called RM&NS or Darwinian theories can neither evolve nor be reconciled to actuall observed data. By contrast, models based on intelligent purposeful variations or mutations and intelligent selection can fit the available data and can simulate evolutionary change.
EV or GA models, if properly used, provide clear evidence for rejecting Darwinian theories and for supporting evolution via intelligent goal directed processes.
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