Annoying creationists

[kleinman]

Annoying Creationists

Paul, I didn’t say that ev doesn’t show that population helps, what I said was that huge populations don’t markedly reduce the number of generations for convergence sufficiently to allow macroevolution to occur. In addition large populations contradict Gould’s concept of punctuated equilibrium which he said occurs in small sub-populations.

We don't know this, because we haven't modeled more than a measly million creatures. You won't let me extrapolate using that fitted curve, but if I did extrapolate to a lousy billion creatures, it would require 103 generations; to a trillion creatures, 21 generations. Of course, there is some asymptote it's approaching, although I haven't the slightest idea what that is. I think that is a sufficient reduction for macroevolution to take place. Wait, what was macroevolution, again? And how small is a small population of bacteria? Hang on, does punctuated equilibrium pertain to the evolution of an ancient mechanism such as genetic binding?

Why don’t you post the data you used for your curve fit and why don’t you use your equation to predict the generations for convergence with a population of two million and then run the case with ev and see how accurate your extrapolation is?

I really thought you had more to offer. I guess we know now.

I’m not offering anything, it is Dr Schneider’s ev program that is offering up the data. Have you run any cases yet?

Ev and the basics of information theory.

The Shannon definition for information turns out to be mathematically equivalent to the negative of the quantum mechanical definition for entropy. If one considers that entropy is the measure of randomness this relationship becomes intuitively apparent. Increasing the information in a system reduces the randomness and thus reduces the entropy. So how does this relate to genetic evolution. One of the basic problems of Information theory is to take an initial ensemble with an initial probability distribution to a final ensemble with a final probability distribution by the input of information. In other words, you take a more random higher entropy ensemble to a less random lower entropy ensemble by the input of information. When information theorist talk about 1 bit of information, they are saying that based on a single yes or no question, the answer to that question allows them to decide which ensemble has a lower entropy. The answer to the binary question allows you to reduce the entropy and therefore the randomness by 1 bit.

So you comment on the relationship between information theory and statistical mechanics. Your simply stating increased order(information) equals decreased entropy. So? Why does this matter to your kinetic arguement?

The kinetics of this model is strongly dependent on genome size and mutation rate. The smaller the genome the faster evolution by random point mutation and natural selection occur. Dr Schneider’s single published case from his model used a genome length of only 256 bases. This is 2000 times smaller than the smallest genome of any free living organism. The mutation rate also strongly affects the kinetics of this model. I have done series of cases investigating how mutation rate affects the kinetics of this model and Dr Schneider used a mutation rate of 1 mutation per 256 bases per generation which is near the optimum value for the most rapid kinetics. This mutation rate is about 4000 times higher than the average mutation rate seen in prokaryotes. He used the kinetics from his single published case to predict the evolution of a human genome in one billion years. If you simply change his mutation rate to the realistic value of 1 mutation per 1,000,000 bases per generations, his estimate for the evolution of a human genome in 1 billion years becomes 4 trillion years. If you use a larger genome than 256 bases, his estimate becomes even more preposterous. This would be equivalent to you using the rate constant for an imaginary chemical reaction that is millions of times faster than any realistic chemical reaction and applying that rate to the realistic chemical reaction. There is no scientific basis for this type of arithmetic.

Unlike many IDers who have criticized Dr Schneider’s simulation, I find his basic concept plausible. What I don’t find plausible is Dr Schneider’s use of unrealistic parameters. Dr Schneider used a genome length of only 256 bases (2000 times smaller than the smallest genome known in any free living organism) and a mutation rate of 1 mutation per 256 bases per generation (4000 times higher than the average mutation rate in prokaryotes) in his publication on ev. When more realistic parameters are used in the model, the rate of acquisition of information become profoundly slow as will unfold as the data from ev is presented. This rate of information acquisition becomes so slow that it shows that it takes hundreds of millions of generations to evolve less than 100 loci on a genome of only 100,000 bases. Point mutation and natural selection is a profoundly slow process. Far too slow to evolve a gene de novo.

That's it? Um, again, Not enough time? THere are never situations where mutation rate changes? I'm sorry, the model is interesting in it's ability to show increased information with improvements in the binding site sequence. But you ignore, not all point mutations are created equal. Some loci are not as improtant as others (consider consensus sequences). You ignore insertion/deletion errors You ignore genetic exchange You ignore the ADMITTED limitations to the code presented

Dr Schneider said the following about his code from the following URL:
http://www.ccrnp.ncifcrf.gov/~toms/paper/ev/truman/

A good simulation does not attempt to simulate everything; only the essential components are modeled. For the issue at hand, the form of the genetic code is not relevant; information measured by Shannon's method is more general than that.

I do not ignore any of the other mechanisms that you mention. My contention has been from the beginning that ev show that macroevolution by random point mutations and natural selection is mathematically impossible when realistic parameters are used in the model. If you think that frame shift mutations, recombination, genetic exchanges or any other mechanism for altering a genome are more important than random point mutations, produce the evidence and a mathematical model that shows how these mechanisms can accomplish macroevolution. Or are you going to use your anything is possible scientific explanation? The theory of evolution remains without a mathematical foundation. The best model of evolution by random point mutations and natural selections shows that macroevolution is impossible by the mechanism it models.

I'm sorry, you claim an understanding of engineering, but haven't exercised any of the critical analysis required in the disipline. As an engineer, you MUST know what a math model is and what it can and can not do. I don't want to believe that you are being delibertly missleading, but you are leaving me little room to think otherwise.

And your idea of critical analysis is not to run any cases with ev and examine the behavior of the model and still jump to conclusions anyway. You don’t need much room to think when you don’t do any.

How do you get the original gene to cross-over or invert? You must still have some mechanism to create the original gene.

Yes, and point mutation is one mechanism, but there are others (insertions, deletions, translocations, inversions, duplications...) in addition to genes from other organisms (intra- and inter-species).

If you think that frame shift mutations are the main mechanism for producing new genes, produce the evidence, make a mathematical model and show how it happens. Again, inversions, duplications and recombination require existing genes. Ev shows the rate acquisition of information is so profoundly slow for random point mutations and natural selection that creating a gene de novo by this mechanism is mathematically impossible. Intra and inter species transfers still require an existing gene. How do you make the original gene? At least Dr Schneider put his ideas into mathematical terms. Your arguments may convince naïve grade school students and devout evolutionarians but they don’t constitute a hard mathematical scientific proof.

But new genes are not created solely by random point mutations. I mention other mechanisms above. And yes, recombination does usually refer to resorting alleles, but recombination with errors can effectively create new genes. And this is in addition to horizontal transmission of genetic material.

Would you like to give some examples of errors in recombination that have created new genes? Then apply this mechanism in a mathematical model and show how macroevolution occurs by recombination errors. Of course this mechanism would not be very useful to prokaryotes.

What you appear to be doing is using a computer simulation, of part of the real world, that is only valid within it's design parameters of single point mutations, to show that life could not have evolved this way, thereby showing that the theory of evolution is not correct. Since you are extrapolating the results outside the design parameters (ie. there are more factors than just point mutation), any results you get are completely meaningless since they are not valid in the real world.

The following quotes were taken from Dr Schneider’s blog web page: http://www.lecb.ncifcrf.gov/~toms/paper/ev/blog-ev.html

The following are Dr Schneider’s responses to a critique of his paper Evolution of biological information by Dr Stephen E Jones.

"Schneider's paper is misleadingly titled: "Evolution of biological information". But it is just a *computer* simulation. No actual *biological* materials (e.g. genomes of nucleic acids, proteins, etc) were used, nor does Schneider propose that his simulation be tested with *real* genomes or proteins

Actual biological materials were used to determine the original hypothesis. Read the literature: Schneider1986

It only becomes *real* biological information and random mutation and natural selection, when the simulation is tested in the *real* world, using *real* DNA, proteins, with *real* mutations and a *real* environment does the selecting. It is significant that Schneider does not propose this, presumably because he knows it wouldn't work.

You are very bad at reading my mind, I have considered doing this experiment. Given the right conditions, it WILL WORK. Do you have th gumption to do the experiment yourself? That's the way real science works! FURTHERMORE, if you read the literature, you will recognize that related experiments have been repeatedly done for 20 years. Look up SELEX.

In the rest of the paper he uses the single word "selection". I take this as a tacit admission that his model is not a simulation of *real* biological natural selection.

No. A rose is a rose by any other name. Selection is selection whether it be natural (generally meaning the environment of earth), breeding (by humans usually, though perhaps some ants select their fungi), SELEX or in a computer simulation. Of COURSE it is a simulation of natural selection! The paper would not be relevant to biology and would not have been published in a major scientific journal if it were not!

Schneider lets slip that there is another unrealistic element in his (and indeed all) computer simulations in that it (they) "does not correlate with time":

So? Run the program slower if you want. Make one generation per 20 minutes to match rapid bacterial growth. THIS WILL NOT CHANGE THE FINIAL RESULT!

Well, when Schneider's simulation is actually tested with *real* "life" (e.g. a bacterium), and under *real* mutation and natural selection it gains information, then, and only then, would "creationists" be favourably impressed. But if they are like me, they would already be impressed (but unfavourably) that Schneider does not mention in his paper that his simulation should now be so tested in the *real* "biological" world.

1. The simulation was of phenomena in the "real" world.
2. Dr. Jones is invited yet again to do an experiment.

The following is a response Dr Schneider made to a statement made by David Berlinski.

Where attempts to replicate Darwinian evolution on the computer have been successful, they have not used classical Darwinian principles, and where they have used such principles, they have not been successful.

The ev program disproves this statement since it uses classical Darwinian principles and was successful.

The previous statements are clear that Dr Schneider believes that ev simulates the real world. If the simulation is appropriate for small genomes then it is appropriate for large genomes. Macroevolution by mutation and natural selection is mathematically impossible.

Ev and the basics of information theory. The Shannon definition for information turns out to be mathematically equivalent to the negative of the quantum mechanical definition for entropy.

Well in case anyone cares, this is untrue.

Blame that quote on Frank Andrews. I got it out of his text Equilibrium Statistical Mechanics. He has a chapter in that text where he derives Shannon’s definition for information and then relates this to the quantum mechanical definition of entropy.

There is a big difference when we consider both A and another system B, and the (possibly correlated) states - call them "QR" - between A and B (i.e. correlated probability distributions in the classical case). The Shannon entropy on Q is always less than or equal to that on QR, for the simple reason that in classical information theory you cannot be more uncertain about Q than you are about the joint variable QR. But in the quantum case, in certain cases the opposite is true - the von-Neumann entropy of the joint system can be 0 while that of the individual subsystems is >0!

Dr Schneider’s model consists only of a single system A that starts out with an initial ensemble and probability frequency distribution. Information is added by random mutations and natural selection to take system A to a final ensemble and probability frequency distribution. There is no other system B in Dr Schneider’s model. Tez, have you even looked at Dr Schneider’s model or are you like joozb and jump to conclusions without examining Dr Schneider’s model? Not only do evolutionists carry the thin skinned crybaby gene, it appears they carry the jump to conclusion without examining the facts gene as well.

I wish I got a cookie every time I spotted someone invoking quantum mechanical things they do not understand in the hopes of gaining credibility for their ideas....

Tez, how did you figure out Dr Schneider’s model, telekinesis?

So far, no one posting on this thread has tried Dr Schneider’s program besides Paul and I. You know that Paul put a lot of work into this model. Shouldn’t you at least do him the courtesy of at least trying out the model. I’m sure that it would please Dr Schneider as well if more of his fellow evolutionists would come to understand what he is has done.

 

[joobz]

The kinetics of this model is strongly dependent on genome size and mutation rate. The smaller the genome the faster evolution by random point mutation and natural selection occur. Dr Schneider’s single published case from his model used a genome length of only 256 bases. This is 2000 times smaller than the smallest genome of any free living organism. The mutation rate also strongly affects the kinetics of this model. I have done series of cases investigating how mutation rate affects the kinetics of this model and Dr Schneider used a mutation rate of 1 mutation per 256 bases per generation which is near the optimum value for the most rapid kinetics. This mutation rate is about 4000 times higher than the average mutation rate seen in prokaryotes. He used the kinetics from his single published case to predict the evolution of a human genome in one billion years. If you simply change his mutation rate to the realistic value of 1 mutation per 1,000,000 bases per generations, his estimate for the evolution of a human genome in 1 billion years becomes 4 trillion years. If you use a larger genome than 256 bases, his estimate becomes even more preposterous. This would be equivalent to you using the rate constant for an imaginary chemical reaction that is millions of times faster than any realistic chemical reaction and applying that rate to the realistic chemical reaction. There is no scientific basis for this type of arithmetic.

You've repeated this, "I've changed the mutation rate..." statement several times. And I've stated several more that this point is moot. You don't know the actual mutation rate. Mutation rate can vary by the addition of any mutagenic compound. Multiple mutagenic pathways exists. And I'm sure there are more to be discovered. Also can you tell me HOW this program accounts for genetic exchange that occurs between cells?

You clearly are performing the model with blinders on. feel free to continue. Don't expect it to mean much to anyone.

Dr Schneider said the following about his code from the following URL:

http://www.ccrnp.ncifcrf.gov/~toms/paper/ev/truman/

I do not ignore any of the other mechanisms that you mention. My contention has been from the beginning that ev show that macroevolution by random point mutations and natural selection is mathematically impossible when realistic parameters are used in the model. If you think that frame shift mutations, recombination, genetic exchanges or any other mechanism for altering a genome are more important than random point mutations, produce the evidence and a mathematical model that shows how these mechanisms can accomplish macroevolution.

This may be the smartest thing you've said. I agree, that we need to verify this hypothesis. But the game that, "This model bad=evolution bad" wouldn't be acceptable for a freshman engineering course. It won't fly here. Sorry, try again.

Or are you going to use your anything is possible scientific explanation? The theory of evolution remains without a mathematical foundation. The best model of evolution by random point mutations and natural selections shows that macroevolution is impossible by the mechanism it models.

The fact that evolution can occur at all with JUST point mutations is a fairly substantial discovery. The fact that it alone doesn't explain evolution isn't unexpected. You can call it anything goes, but nothing have I said contridicts known scientific concepts. You can't state the same.

And your idea of critical analysis is not to run any cases with ev and examine the behavior of the model and still jump to conclusions anyway. You don’t need much room to think when you don’t do any.

I don't need to look at the blueprints to know that the Empire State Building can't be built with Laffy Taffy and I don't need to run the simulations because your ENTIRE PROPOSITION IS FLAWED.

 

[fls]

If you think that frame shift mutations are the main mechanism for producing new genes, produce the evidence, make a mathematical model and show how it happens. Again, inversions, duplications and recombination require existing genes. Ev shows the rate acquisition of information is so profoundly slow for random point mutations and natural selection that creating a gene de novo by this mechanism is mathematically impossible. Intra and inter species transfers still require an existing gene. How do you make the original gene? At least Dr Schneider put his ideas into mathematical terms. Your arguments may convince naïve grade school students and devout evolutionarians but they don’t constitute a hard mathematical scientific proof.

Would you like to give some examples of errors in recombination that have created new genes? Then apply this mechanism in a mathematical model and show how macroevolution occurs by recombination errors. Of course this mechanism would not be very useful to prokaryotes.

I am not attempting a hard mathematical scientific proof (although I agree that that is a valuable endeavour). You are demonstrating that Ev cannot account for reality. You are claiming that Ev accurately models the proposed mechanism by which we arrived at the current state of affairs, therefore the flaw is in the proposed mechanism (point mutation and selection). I and others are pointing out that if your model doesn't account for reality, it is also possible that there is a flaw in the model. This especially becomes a consideration when the model lacks content validity. That you dismiss these concerns by insulting me does not change this.

My point all along has been this - you have not excluded reasonable alternate explanations for your results, which makes all this effort meaningless; it cannot persuade.

Linda

 

[kleinman]

Annoying Creationists

The kinetics of this model is strongly dependent on genome size and mutation rate. The smaller the genome the faster evolution by random point mutation and natural selection occur. Dr Schneider’s single published case from his model used a genome length of only 256 bases. This is 2000 times smaller than the smallest genome of any free living organism. The mutation rate also strongly affects the kinetics of this model. I have done series of cases investigating how mutation rate affects the kinetics of this model and Dr Schneider used a mutation rate of 1 mutation per 256 bases per generation which is near the optimum value for the most rapid kinetics. This mutation rate is about 4000 times higher than the average mutation rate seen in prokaryotes. He used the kinetics from his single published case to predict the evolution of a human genome in one billion years. If you simply change his mutation rate to the realistic value of 1 mutation per 1,000,000 bases per generations, his estimate for the evolution of a human genome in 1 billion years becomes 4 trillion years. If you use a larger genome than 256 bases, his estimate becomes even more preposterous. This would be equivalent to you using the rate constant for an imaginary chemical reaction that is millions of times faster than any realistic chemical reaction and applying that rate to the realistic chemical reaction. There is no scientific basis for this type of arithmetic.

You've repeated this, "I've changed the mutation rate..." statement several times. And I've stated several more that this point is moot. You don't know the actual mutation rate. Mutation rate can vary by the addition of any mutagenic compound. Multiple mutagenic pathways exists. And I'm sure there are more to be discovered. Also can you tell me HOW this program accounts for genetic exchange that occurs between cells? You clearly are performing the model with blinders on. feel free to continue. Don't expect it to mean much to anyone.

I have run hundreds of cases with ev and you tell me I, the one with blinders on. You are correct that there are a wide variety of mutation rates. That is why I included mutation rates in the parametric studies I have done to see how mutation rate affects the rate of evolution. I understand that data doesn’t mean much to evolutionists especially when it contradicts their belief system.

I do not ignore any of the other mechanisms that you mention. My contention has been from the beginning that ev show that macroevolution by random point mutations and natural selection is mathematically impossible when realistic parameters are used in the model. If you think that frame shift mutations, recombination, genetic exchanges or any other mechanism for altering a genome are more important than random point mutations, produce the evidence and a mathematical model that shows how these mechanisms can accomplish macroevolution.

This may be the smartest thing you've said. I agree, that we need to verify this hypothesis. But the game that, "This model bad=evolution bad" wouldn't be acceptable for a freshman engineering course. It won't fly here. Sorry, try again.

See my discussion below on problems with mechanisms for evolution other than random point mutations and natural selection. I understand evolutionists are slow to get this but I will be patient with you until you are able to get off the ground.

And your idea of critical analysis is not to run any cases with ev and examine the behavior of the model and still jump to conclusions anyway. You don’t need much room to think when you don’t do any.

I don't need to look at the blueprints to know that the Empire State Building can't be built with Laffy Taffy and I don't need to run the simulations because your ENTIRE PROPOSITION IS FLAWED.

Isn’t what you have just done what evolutionists like to call a strawman? The theory of evolution can’t be built on Laffy Taffy and it can’t be built on random point mutations and natural selection either.

If you think that frame shift mutations are the main mechanism for producing new genes, produce the evidence, make a mathematical model and show how it happens. Again, inversions, duplications and recombination require existing genes. Ev shows the rate acquisition of information is so profoundly slow for random point mutations and natural selection that creating a gene de novo by this mechanism is mathematically impossible. Intra and inter species transfers still require an existing gene. How do you make the original gene? At least Dr Schneider put his ideas into mathematical terms. Your arguments may convince naïve grade school students and devout evolutionarians but they don’t constitute a hard mathematical scientific proof. Would you like to give some examples of errors in recombination that have created new genes? Then apply this mechanism in a mathematical model and show how macroevolution occurs by recombination errors. Of course this mechanism would not be very useful to prokaryotes.

I am not attempting a hard mathematical scientific proof (although I agree that that is a valuable endeavour). You are demonstrating that Ev cannot account for reality. You are claiming that Ev accurately models the proposed mechanism by which we arrived at the current state of affairs, therefore the flaw is in the proposed mechanism (point mutation and selection). I and others are pointing out that if your model doesn't account for reality, it is also possible that there is a flaw in the model. This especially becomes a consideration when the model lacks content validity. That you dismiss these concerns by insulting me does not change this. My point all along has been this - you have not excluded reasonable alternate explanations for your results, which makes all this effort meaningless; it cannot persuade.

I am not the only one who says that ev accurately models reality, Dr Schneider says this, Paul said this until he realized what ev showed when realistic parameters are used in the model. Paul is now doing the evolutionist twist to try and explain away his broad claims that he has made. See my paragraphs below on the problems for mechanisms other than random point mutations and natural selection. I think the more you consider the position you are taking, the less tenable it becomes. Point mutations and natural selection is the cornerstone for your theory, no other mechanism can replace it.

Problems with mechanisms of genetic evolution other than random point mutations and natural selection.
There is something you evolutionophiles are not taking into account when you suggest other mechanisms for the evolutionary process than random point mutations and natural selection. Frame shift mutations such as insertions and deletions, inversions, and errors in recombination cause large numbers of bases changes suddenly. You do not have the benefit of gradualism. Not one of these base changes can be fatal to the organism. Every base change in the large number of changes that occur in a single generation must either be beneficial or neutral for that organism to survive. Natural selection must operate on all these changes at once. Even if all of the sudden changes are neutral, how would natural selection select for these changes?

Duplications of genes or entire chromosomes as with polyploidy does give working material from which to evolve new genes but the only mechanism you have is random point mutations and natural selection in order for this material to be evolved gradually. The other mechanisms you suggest do not work gradually. If these other mechanisms of large scale mutation that you suggest do contribute significantly to macroevolution, it should be easy to set up an experiment to evolve an entire gene quickly. Find an agent that causes these types of large scale mutations and make bacteria produce an entirely new gene de novo.

 

[Tez]

Blame that quote on Frank Andrews. I got it out of his text Equilibrium Statistical Mechanics.

You were the one that made the statement (unattributed to Andrews, whom I suspect you have misunderstood) - a statement which you followed by the equally trite "If one considers that entropy is the measure of randomness this relationship becomes intuitively apparent." I discussed the "two-systems" case because it shows this is nonsense - it is not intuitively apparent, because it is wrong! FWIW, I am hardly even following the particular discussion at hand (I have not the time nor patience of St. Paul A.), I was just pointing out that your statement clearly displayed ignorance of what the relationship between the Shannon and von-Neumann entropies is, and for that I need not know anything about the context in which you are trying to invoke the relationship. Of course that may or may not have a bearing on whether you know anything about the rest of what you're talking about - I'm not about to pass judgment because I haven't read the rest of it.

He has a chapter in that text where he derives Shannon’s definition for information and then relates this to the quantum mechanical definition of
entropy.

There is only one special circumstance (even for a single system) in which the relationship is one of equality. If you understood that circumstance, you could then make an argument about why it is the one relevant for this discussion (which, I repeat, I am hardly following). But you don't, so you can't.

Dr Schneider’s model consists only of a single system A that starts out with an initial ensemble and probability frequency distribution. Information is added by random mutations and natural selection to take system A to a final ensemble and probability frequency distribution. There is no other system B in Dr Schneider’s model. Tez, have you even looked at Dr Schneider’s model or are you like joozb and jump to conclusions without examining Dr Schneider’s model?

I wasn't criticizing the model. I was criticizing you. I was pointing out that you don't understand von-Neumann entropy and are invoking quantum mechanics, presumably to try and sound more educated than you evidently are. Since I doubt there is any need for you to even think quantum-mechanically in the context of this argument, my friendly advice is to only talk about that which you do understand well. We can't all know everything.

 

[delphi_ote]

Increasing the information in a system reduces the randomness and thus reduces the entropy.

If people don't stop misrepresenting Claude Shannon's work, I swear my head is going to do this:

Shannon information is a measure of randomness. It is a measure of uncertainty before you know the outcome of an event. It is a measure of how evenly distributed a discrete random variable is. Maximum Shannon entropy is achieved when the probability of each of n things happening equals 1/n. The minimum is when one thing occurs with 100% probability.

You gain Shannon information when you know something about a distribution with high Shannon entropy.

 

[Paul C. Anagnostopoulos]

I am not the only one who says that ev accurately models reality, Dr Schneider says this, Paul said this until he realized what ev showed when realistic parameters are used in the model.

You really can't stop lying, can you?

~~ Paul

 

[kleinman]

Annoying Creationists

Blame that quote on Frank Andrews. I got it out of his text Equilibrium Statistical Mechanics.

You were the one that made the statement (unattributed to Andrews, whom I suspect you have misunderstood) - a statement which you followed by the equally trite "If one considers that entropy is the measure of randomness this relationship becomes intuitively apparent." I discussed the "two-systems" case because it shows this is nonsense - it is not intuitively apparent, because it is wrong! FWIW, I am hardly even following the particular discussion at hand (I have not the time nor patience of St. Paul A.), I was just pointing out that your statement clearly displayed ignorance of what the relationship between the Shannon and von-Neumann entropies is, and for that I need not know anything about the context in which you are trying to invoke the relationship. Of course that may or may not have a bearing on whether you know anything about the rest of what you're talking about - I'm not about to pass judgment because I haven't read the rest of it.

Sorry I didn’t put a reference section in that post, I have identified the source of the statement that Shannon information is mathematically equivalent to the negative of quantum mechanical definition for entropy on other threads. If you like believing increasing the information in a system increases the randomness in the system, spread your wisdom far and wide. I can tell you are an impatient type, you don’t even have the patience to spell Paul’s last name. I have the patience to do it, it is Anagnostopoulos. Sirens and red lights used to go off in my spell checker when I entered his name into a document but something has happened, my spell checker no longer responds to his name. The amount of information in my spell checker must have increased and therefore the randomness has increased.

He has a chapter in that text where he derives Shannon’s definition for information and then relates this to the quantum mechanical definition of

entropy.

There is only one special circumstance (even for a single system) in which the relationship is one of equality. If you understood that circumstance, you could then make an argument about why it is the one relevant for this discussion (which, I repeat, I am hardly following). But you don't, so you can't.

Andrew’s derivation is for the general definition for Shannon’s information not a special case. The mathematical relationship that Andrew’s describes between Shannon’s information and the quantum mechanical definition of entropy is general as well, not for a specific case. Interestingly, Andrews does one numerical example in that chapter and it directly relates to Dr Schneider’s model. So, Tez if you want to believe that increasing the information in a system also increases the entropy, have at it.

Dr Schneider’s model consists only of a single system A that starts out with an initial ensemble and probability frequency distribution. Information is added by random mutations and natural selection to take system A to a final ensemble and probability frequency distribution. There is no other system B in Dr Schneider’s model. Tez, have you even looked at Dr Schneider’s model or are you like joozb and jump to conclusions without examining Dr Schneider’s model?

I wasn't criticizing the model. I was criticizing you. I was pointing out that you don't understand von-Neumann entropy and are invoking quantum mechanics, presumably to try and sound more educated than you evidently are. Since I doubt there is any need for you to even think quantum-mechanically in the context of this argument, my friendly advice is to only talk about that which you do understand well. We can't all know everything.

Both you and Dr Schneider believe that increasing the information of a system increases the randomness in the system. Why you don’t have an intuitive problem with this makes me wonder. Get Andrew’s book, you can get it at Amazon. Andrew’s does a straightforward coherent derivation.

I know what you are, you’re a Tez dispenser, somebody pushes down on your head and something pops out of your mouth.

Increasing the information in a system reduces the randomness and thus reduces the entropy.

Shannon information is a measure of randomness.

So is entropy. You need to get the Andrew’s text as well. Don’t let your head blow up, the theory of evolution is the only thing that is blowing up.

I am not the only one who says that ev accurately models reality, Dr Schneider says this, Paul said this until he realized what ev showed when realistic parameters are used in the model.

You really can't stop lying, can you?

Be careful Paul, google is watching you.

Are you ever going to post the data for your latest curve fit and then produce the next data point in that series to see how accurate your curve fit extrapolates the next point?

Any other evolutionophiles start looking at Dr Schneider’s program? Just look at this experience as a trip to the doctor’s office. The sooner you evolutionarians take your medicine the sooner you will feel better.

 

[Paul C. Anagnostopoulos]

Be careful Paul, google is watching you.

Fine and dandy.

Are you ever going to post the data for your latest curve fit and then produce the next data point in that series to see how accurate your curve fit extrapolates the next point?

Well, let's see. I ran this experiment:

genome size 1024
binding sites 16
1 mutation / genome

For populations 1024 through 92,680, the curve is [latex]$8998p^{-.20}$[/latex]. When I add your three points for populations 262K, 524K, and 1048K, the curve is [latex]$12138p^{-.23}$[/latex]. Looks good to me.

If you want to email me a Pascal Ev that runs on a PC along with the inputs, I can try to run a population of 2 million.

~~ Paul

 

[fls]

Alright. I'm ready to call it. I was willing to give you the benefit of the doubt and listen to what you had to say. But first I wanted to know why you had erected a strawman and were wasting your time disproving that. Your response so far has been, "you are too ignorant to realize that it is not a strawman". And I have given this possibility serious consideration because I realize that sometimes a statement can appear to be incorrect, but further explanation provides clarification and agreement. But in the end I cannot find that the evidence supports this supposition, despite a sincere effort (on my part) to try and make the evidence fit.

Linda

 

[joobz]

If people don't stop misrepresenting Claude Shannon's work, I swear my head is going to do this:
http://i71.photobucket.com/albums/i133/delphi_ote/HeadExplode.gif
Shannon information is a measure of randomness. It is a measure of uncertainty before you know the outcome of an event. It is a measure of how evenly distributed a discrete random variable is. Maximum Shannon entropy is achieved when the probability of each of n things happening equals 1/n. The minimum is when one thing occurs with 100% probability.

You gain Shannon information when you know something about a distribution with high Shannon entropy.

Delphi_Ote and Tez, kleinman's use of entropy is entirely off topic and has no bearing on his critique of the model. Unless there is a critical flaw in its use in the model (which he admits there isn't), there is no theoretical reason why he brings it up.

His repeated use of insults and jabs instead of substance highlights the fact that there is nothing to what he says.
At best, he's found an interesting limitation in the ev model. At worst, he's an intentionally manipulative and deceiving individual who cares not for truth and discovery only that his faith is reaffirmed.

 

[Apathia]

I've been following this thread with much interest but not posting, because back in college I dropped out of the Sciences and entered the Humanities when Calculus class gave me the final death blow. So. I'm not up to following Klinmann's math. But there is a simple issue of logic here, that even a Science numbskull like myself can see.

When I let go of Creationism, I didn't do so because of Darwin's Theory of Evolution, but because of the overwhelming evidence that macro-evolution has taken place and is still in the process of taking place. I've never thought that Darwin's model was the last word on how the process proceeds.

If Klinemann is correct in saying that the computer modeling of Darwin's Natural Selection is a faithful and accurate representation, and if this fully functional model doesn't deliver, I'd buy that the Theory of Evolution as we know it is incomplete. But I can't buy that the fact of evolution is made to vanish.

OK, I'm a doofus. Stating the obvious everyone knows already. Does everyone know?

 

[kleinman]

Annoying Creationists

Are you ever going to post the data for your latest curve fit and then produce the next data point in that series to see how accurate your curve fit extrapolates the next point?

Well, let's see. I ran this experiment: genome size 1024, binding sites 16, 1 mutation / genome

Not just the input parameters, the population/generations for convergence data used to obtain your curve fit as well.

If you want to email me a Pascal Ev that runs on a PC along with the inputs, I can try to run a population of 2 million.

Dr Schneider’s posted version of ev pascal will run on a pc under the GNU version of the pascal compiler. You can download a version of that pascal compiler for your platform at:
http://www.gnu-pascal.de/binary/
The only thing I have had to change in Dr Schneider’s code to run larger cases are his variables maxgenomesize and maxbugs to get the larger cases to run. Be forewarned that the case with G=1000 and population of 1 meg took 300Mbytes of RAM. The population = 2 meg will take about 600Mbytes so if you don’t have 1 Gig of RAM on your computer, be prepared for a disk page file that will run so slow that RM&NS will seem speedy. This program also sucks up clock cycles so that any other applications running at the same time will go very slowly. The one advantage with the pascal version of ev is that you can break up the calculation into a series of small runs which you can do overnight while you aren’t using your computer.

You have the author of the program to consult with if you should have problems setting up the pascal version for your platform. If he won’t help, I’ll do what I can.

Alright. I'm ready to call it. I was willing to give you the benefit of the doubt and listen to what you had to say. But first I wanted to know why you had erected a strawman and were wasting your time disproving that. Your response so far has been, "you are too ignorant to realize that it is not a strawman". And I have given this possibility serious consideration because I realize that sometimes a statement can appear to be incorrect, but further explanation provides clarification and agreement. But in the end I cannot find that the evidence supports this supposition, despite a sincere effort (on my part) to try and make the evidence fit.

I have not said that quote you attribute to me.

What is the strawman you are talking about? I am agreeing with Dr Schneider that his ev model properly does the mathematics of RM&NS and that when you use realistic parameters in the model, this mechanism does not explain how macroevolution occurs. You have a few of choices here. You can question the validity of the assumptions that Dr Schneider used in formulating his model, you can say that the model neglects other mechanisms of evolution (as you are doing) or you can say that his model is invalid. How am I setting up a strawman?

Don’t give up so soon, I was just going to ask you how interspecies gene transfers gets these new genes to the gametes in organisms that use sexual recombination to reproduce.

 

[kleinman]

His repeated use of insults and jabs instead of substance highlights the fact that there is nothing to what he says. At best, he's found an interesting limitation in the ev model. At worst, he's an intentionally manipulative and deceiving individual who cares not for truth and discovery only that his faith is reaffirmed.

My best jabs are the mathematical data and your weak response to this is that I am manipulative and deceptive. Have you run any cases with ev yet or are you sticking with your anything is possible argument for the theory of evolution?

I've been following this thread with much interest but not posting, because back in college I dropped out of the Sciences and entered the Humanities when Calculus class gave me the final death blow.

Another evolutionist from the math is hard school of science. The theory of evolution must be true, it feels so good.

 

[Apathia]

Another evolutionist from the math is hard school of science. The theory of evolution must be true, it feels so good.

I continue to read this thread still giving you that you may be showing in concrete a substantial weakness in the Darwinian Theory of Evolution.
I admit being a doofus when it comes to math, and being a doofus in the way I worded my post, but that is irrelevant. How do you get from a flawed theory of how evolution occured to how it didn't occur at all?

 

[Beleth]

The theory of evolution must be true, it feels so good.

But that's the ironic thing, isn't it? Evolution doesn't feel good.

Evolution makes humans nothing more than mutant amoebas. And that feels bad, so we feel that it isn't true. We feel that we're so much better, so infinitely more splendid, than any other form of life on the planet, that there must be some other explanation.

And yet, when we look, all we see is evolution. There was a time when there weren't any dinosaurs, then there were dinosaurs, then they all died out again. And that's just one example. Everywhere we look in the real world of biology, we can see evolution going on. It went on in the past, and it's still going on. Everywhere.

You will have to forgive us for not ignoring the real world just because a simulation, with who-knows-how-many "reasonable sounding" assumptions, produces evidence that one or more of its assumptions is definitely wrong...

 

[joobz]

My best jabs are the mathematical data and your weak response to this is that I am manipulative and deceptive. Have you run any cases with ev yet or are you sticking with your anything is possible argument for the theory of evolution?

Why do I think you are being manipulative and deceptive? because your entire strategy has been a smoke screen.

For instance, Why bring in thermodynamics to your arguement? how does that affect the actual claim you make? I've asked this question several times. You haven't answered it.
the best you've said is:

Kinetics is a subset of thermodynamic, kinetics simply means motion.

thermodynamics is a study of equilibirium. it can be tied to kinetics when free energy is known and when activation energies are known. But to say that kinetics is a subset of thermodynamics or that kinetics is motion is not true.

Kinetics is the study of dynamics, of rates of change. Whether it is change in heat, mass transfer, chemical reactions, rate of phase change, rate of affinity binding interactions. All of these are kinetics. the study of motion is the field of mechanics. As a mechanical engineer, I'd expect you to know this.

Thermodynamics will tell you what the final result should be, but it WON'T tell you when it'll get there. UNLESS YOU KNOW THE ACTIVATION ENERGY.

I've asked for this info, but you fail to provide it. In fact, The model requries you to ENTER a rate. As such, you are simply using a kinetic analysis, not a thermodynamic one. The model shows that the system will tend to form a binding site thermodynamically. And you still claim that your arguements are based on mathematical principles, when you can't demonstrate a clear understanding of what those principles are.

Do you really claim that running simulations is equivalent to "doing math".

I again state your assumptions are wrong which makes the your view of the kinetic data meaningless. you can claim otherwise all you want, but you have not offered any proof.

 

[Paul C. Anagnostopoulos]

Dr Schneider’s posted version of ev pascal will run on a pc under the GNU version of the pascal compiler. You can download a version of that pascal compiler for your platform at:
http://www.gnu-pascal.de/binary/

Snore. I'm not going to bother installing stuff just to compile the Pascal version. If you have one for the PC, send it. Otherwise never mind.

What is the strawman you are talking about?

The one where evolution proceeds by single-point mutation from large random genomes and has to evolve binding sites in some ill-specified short period of time. You know, the one trick straw pony.

~~ Paul

 

[kleinman]

Annoying Creationists

Another evolutionist from the math is hard school of science. The theory of evolution must be true, it feels so good.

I admit being a doofus when it comes to math, and being a doofus in the way I worded my post, but that is irrelevant. How do you get from a flawed theory of how evolution occured to how it didn't occur at all?

If you understand the mathematics associated with balancing your checking account you will be able to get some understanding of what I am talking about in this debate.

It will become more apparent as this discussion continues to unfold that the flaws in the theory of evolution are fatal flaws. The theory of evolution is not a single simple statement like the 1st law of thermodynamics or like the statements of Newton’s laws. The theory of evolution is a complex collection of ideas and hypotheses that has to be unraveled like a ball of knotted string to disprove the theory. I am using Dr Schneider’s ev model as the starting point because of the importance of random point mutation and natural selection to the theory. Random mutation and natural selection is the slogan for the theory of evolution, the scientific response to this slogan is mathematical impossibility. The question becomes which slogan is true.

My arguments are not aimed at the devout evolutionist who will believe this theory no matter what evidence is brought against it. After all, there are still people who believe in alchemy and astrology. There is no mathematical scientific argument that you can make that would sway these people. Evolutionists like to take the mantle of scientist, so let’s see how these scientists deal with some mathematical arguments. So far, the response has been pitifully weak. They don’t even want to look at the mathematics of one of their own high placed adherents.

My best jabs are the mathematical data and your weak response to this is that I am manipulative and deceptive. Have you run any cases with ev yet or are you sticking with your anything is possible argument for the theory of evolution?

Why do I think you are being manipulative and deceptive? because your entire strategy has been a smoke screen.

Just pretend I’ve lit an incense candle.

For instance, Why bring in thermodynamics to your arguement?

Dr Schneider has used Information Theory to derive his model which is related to the 2nd law of thermodynamics. Read Dr Schneider’s paper http://www-lmmb.ncifcrf.gov/~toms/paper/ev/ev.pdf where he makes it clear that his model is derived using principles of thermodynamics.

how does that affect the actual claim you make? I've asked this question several times.

This doesn’t affect my claims, I am only agreeing that Dr Schneider has employed the principles of thermodynamics properly in the formulation of his model. I agree that is application of the underlying theory is essentially correct.

thermodynamics is a study of equilibirium.

Professor!!!! Look at the word thermodynamics. The simplest examples in the study of thermodynamics are equilibrium cases, in general, thermodynamics studies as the word says dynamic or changing situations. You must really confuse your students.

Thermodynamics will tell you what the final result should be, but it WON'T tell you when it'll get there. UNLESS YOU KNOW THE ACTIVATION ENERGY.

Dr Schneider’s model is not simulating a chemical reaction with a rate constant associated with this chemical reaction, he is simulating information gain based on random point mutations and natural selection. If you start doing some examples with his model you might begin to understand the distinction.

I've asked for this info, but you fail to provide it. In fact, The model requries you to ENTER a rate. As such, you are simply using a kinetic analysis, not a thermodynamic one. The model shows that the system will tend to form a binding site thermodynamically. And you still claim that your arguements are based on mathematical principles, when you can't demonstrate a clear understanding of what those principles are.

There are several parameters that affect the rate of convergence of this model. The obvious one is the mutation rate, however, genome length, population, number of binding sites and other parameters affect the rate of evolution as well. You have locked your mind into thinking this is the simulation of a chemical reaction based on the 1st law of thermodynamics. This is not what Dr Schneider’s model simulates. Dr Schneider is simulating how random mutations and natural selection operate under the 2nd law of thermodynamics. The only way the 1st law of thermodynamics applies to Dr Schneider’s model is implicit in natural selection. The notion of natural selection is that the organism with more efficient use of the energy available to it will be able to put more of that energy toward reproduction. This is an implicit assumption in Dr Schneider’s model.

Do you really claim that running simulations is equivalent to "doing math".

No, because that is what Dr Schneider did with his single published case. What is required to understand the behavior of this model is to do a systematic parametric study. I have done this and if you did this, you would better understand my claims.

I again state your assumptions are wrong which makes the your view of the kinetic data meaningless. you can claim otherwise all you want, but you have not offered any proof.

You have made your decision without examining the data from ev.

You will have to forgive us for not ignoring the real world just because a simulation, with who-knows-how-many "reasonable sounding" assumptions, produces evidence that one or more of its assumptions is definitely wrong...

I don’t argue with evolutionists’ observations, I argue with the interpretation of these arguments.

 

[Paul C. Anagnostopoulos]

Dr Schneider is simulating how random mutations and natural selection operate under the 2nd law of thermodynamics.

He is? ... checks Java version code ... oops! I forgot the 2LoT module!

~~ Paul