Annoying creationists

[Paul C. Anagnostopoulos]

I don’t understand what you are asking. The ratio of the non-binding site region size to the binding site region size will always affect the rate of convergence with Dr Schneider’s selection process.

If you'll look at the experiments I ran, you'll see that some produce a perfect creature and some do not, even with the same size genome. You are claiming that it is the increasing size of the genome that eventually stops evolution, but I have shown a counterexample.

Perhaps I don't understand what you're actually claiming, in which case you could present your claim in greater detail.

So what? When you weight the errors in the binding site region differently than those in the non-binding site region you will affect the rate of convergence of ev. If you give no weight to the errors in the non-binding site region, you will uncouple the convergence of ev from the genome length and your Rcapacity problem will disappear.

I agree, but this has nothing to do with what Unnamed did.

Nice use of fonts. It’s also an interesting coincidence that 2*bindingsitewidth gives a value that matches the point where ev no longer converges with Dr Schneider’s selection process, but it is the errors in the non-binding site region which is preventing convergence.

No, it's not. In each of those experiments I outlined above, the mistake count drops to 8, which is the number of binding sites, and then never budges. It is precisely the errors at the binding sites that prevent improvement.

So your equation gives an interesting estimate of where ev fails to converge with Dr Schneider’s selection process but your equation does not explain why ev does not converge. That explanation is the non-binding site errors dominate the calculation and prevent binding sites from evolving.

No, see above.

The point here is that it is the competition of the two selection processes (spurious binding in the non-binding site region and unlocated binding sites in the binding site region) that causes the failure of convergence when the first selection condition dominates.

No.

Your problem of large genomes making evolution of binding sites more difficult is a valid issue, it's just not the Rcapacity problem. Nor would it cause evolution to stop dead.

~~ Paul

 

[kleinman]

Annoying Creationists

I’ll go around on this topic as many times as you want. You already understand that if you rewrote ev such that you tried to evolve two independent sets of binding sites with two different sets of selection processes on each genome that you would slow down the evolutionary process. Selection processes by their very nature are competitive phenomena. A good mutation and a bad mutation occurring on the same genome would have countering effects. Unless you insure that you have two different good mutations on the same genome at the same time, selection processes will be working against each other. The more selection processes in action on a population at a given time, the more likely they evolutionary process will be stymied.

Evolution is not nearly that simple. If two mutations arrise in a genome, their value to the organism is independantly calculated, and the sum of that calculation is used to determine the overall fitness of the organism. For example, if 10 mutations arrise, 9 on which are deletarious, but the last mutation adds a large evolutionary benefit, then the overall fitness of the organism will be higher then the wild type.

Not quite Taffer, you can have hundreds of beneficial mutations arising on a genome but one fatal mutation will cancel out the effects of those hundreds of beneficial mutations. You can not apply the principle of superposition to a non-linear system.

I don’t understand what you are asking. The ratio of the non-binding site region size to the binding site region size will always affect the rate of convergence with Dr Schneider’s selection process.

If you'll look at the experiments I ran, you'll see that some produce a perfect creature and some do not, even with the same size genome. You are claiming that it is the increasing size of the genome that eventually stops evolution, but I have shown a counterexample.

What you are seeing with your data is that smaller binding sites (and the smaller weight matrix) are more likely to identify spurious binding sites. As you increase the size of the weight matrix, the less likely you are to identify spurious binding sites and the larger the non-binding site region on the genome can be used and convergence still attained.

Perhaps I don't understand what you're actually claiming, in which case you could present your claim in greater detail.

What I am claiming and what the data from ev is showing is that convergence is slowed when you have competing selection conditions. The selection in ev is based on two possible errors, identification of spurious binding sites and the failure to identify binding sites. When the identification of spurious binding sites is driving the selection process in ev, binding sites will not evolve.

So what? When you weight the errors in the binding site region differently than those in the non-binding site region you will affect the rate of convergence of ev. If you give no weight to the errors in the non-binding site region, you will uncouple the convergence of ev from the genome length and your Rcapacity problem will disappear.

I agree, but this has nothing to do with what Unnamed did.

Unnamed did two things with his selection process. He allowed for a graded identification of binding sites and he weighted the selection towards failed identification of binding sites. This is why your Rcapacity equation does not give a good estimate for when ev will fail to converge with Unnamed’s selection process. Unnamed’s selection process can evolve binding sites on much larger genomes than Dr Schneider’s selection process. This is due to the fact that Unnamed’s selection process almost completely ignores spurious binding errors. The only problem with Unnamed’s selection process is that it has nothing to do with reality.

Nice use of fonts. It’s also an interesting coincidence that 2*bindingsitewidth gives a value that matches the point where ev no longer converges with Dr Schneider’s selection process, but it is the errors in the non-binding site region which is preventing convergence.

No, it's not. In each of those experiments I outlined above, the mistake count drops to 8, which is the number of binding sites, and then never budges. It is precisely the errors at the binding sites that prevent improvement.

The total mistake count may remain at 8 but track each of the individual mistakes counts, that is, errors due to spurious binding and errors due to missed binding sites. When you do, you will find that spurious binding errors are driving the selection, not the missed binding site errors.

So your equation gives an interesting estimate of where ev fails to converge with Dr Schneider’s selection process but your equation does not explain why ev does not converge. That explanation is the non-binding site errors dominate the calculation and prevent binding sites from evolving.

No, see above.

Paul, it is not the failure of the weight matrix to be able to identify binding sites. What difference does genome length make to the weight matrix? All that you do with the weight matrix is walk it along the genome and if value computed exceeds the threshold, you have a match for a binding site. The only thing that changes with the lengthening of the genome is the number of potential sites for spurious binding increases. As you increase the number of potential sites for spurious binding, you increase the effect of this selection condition. When this spurious binding condition selection process becomes the dominant selection condition, the failed identification of binding site condition no longer can select for the evolution of the binding sites. Ev will only evolve binding sites when the failed identification of binding site condition drives the selection of creatures.

The point here is that it is the competition of the two selection processes (spurious binding in the non-binding site region and unlocated binding sites in the binding site region) that causes the failure of convergence when the first selection condition dominates.

No.

Your problem of large genomes making evolution of binding sites more difficult is a valid issue, it's just not the Rcapacity problem. Nor would it cause evolution to stop dead.

Paul, evolution stops dead when the wrong selection condition is driving the evolution. In the case of the ev model, when you lengthen the genome, spurious binding errors become the dominant selection condition. When that happens, you no longer see the evolution of binding sites. Competing selection conditions slow and as ev shows ultimately can stop evolution. This effect is seen in reality and is another reason why the theory of evolution is mathematically impossible.

 

[cyborg]

Seriously people, put him on ignore. It really is a waste of time trying to argue with him. As far as he's concerned he's lashing evolution to a cross using ev as nails. He will hear nothing else.

 

[delphi_ote]

You can not apply the principle of superposition to a non-linear system.

Right! Just like you you can't apply mathematical terms in an irrelevant context and expect people to think you know what you're talking about!

 

[Paul C. Anagnostopoulos]

You're right Cyborg, I'm tired. And what purpose is my fatigue serving? None.

~~ Paul

 

[Taffer]

Not quite Taffer, you can have hundreds of beneficial mutations arising on a genome but one fatal mutation will cancel out the effects of those hundreds of beneficial mutations. You can not apply the principle of superposition to a non-linear system.

Not all deletarious mutations are fatal, kleinman.

 

[kjkent1]

Not quite Taffer, you can have hundreds of beneficial mutations arising on a genome but one fatal mutation will cancel out the effects of those hundreds of beneficial mutations. You can not apply the principle of superposition to a non-linear system.

Disagree. Very few mutations are immediately fatal, so as to prevent future reproduction. Life evolves when an organism reproduces, so even if there is a "fatal" mutation, this doesn't necessarily prevent beneficial mutations from being inherited by successors. Nor, is it necessarily true that a "fatal" mutation in one generation may not be overcome or replaced by later neutral or beneficial mutations.

The raw odds overwhelmingly favor reproduction of all mutations -- beneficial, neutral, or harmful. And, as long as an organism can survive to reproduce, natural selection will eliminate the weakest members in favor of the stronger, until the harmful mutations are minimized.

What I am claiming and what the data from ev is showing is that convergence is slowed when you have competing selection conditions. The selection in ev is based on two possible errors, identification of spurious binding sites and the failure to identify binding sites. When the identification of spurious binding sites is driving the selection process in ev, binding sites will not evolve.

Try changing the three mistake weights in the java program, but, don't set any to zero. As long as all three mistake weights are non-zero, binding sites will evolve. And, contrary to your claim that failing to give substantial weight to non-binding site region spurious bindings will speed up evolution, the fastest convergence appears to occur when mistakes in the non-binding site region are overweighted.

Unnamed did two things with his selection process. He allowed for a graded identification of binding sites and he weighted the selection toward failed identification of binding sites. This is why your Rcapacity equation does not give a good estimate for when ev will fail to converge with Unnamed’s selection process. Unnamed’s selection process can evolve binding sites on much larger genomes than Dr Schneider’s selection process. This is due to the fact that Unnamed’s selection process almost completely ignores spurious binding errors. The only problem with Unnamed’s selection process is that it has nothing to do with reality.

Totally false. You don't know how the algorithm works -- otherwise, you would not draw this conclusion. The algorithm overweights both mistakes and successful bindings, regardless of where they occur in the genome. So, the real reason why the algorithm speeds up evolution is because a mistake in the non-binding site region is treated as more harmful to the creature -- and because there is so much more non-binding site space in the genome, more mistakes will occur therein, and be overly harmful, which leads to the destruction of that creature.

This, is not realistic, in my opinion, but also isn't what you are claiming, i.e., that Unnamed's selection process ignores spurious binding errors. It's exactly the reverse: Unnamed's selection process gives greater selective power to any mistake, but it also gives greater selective power to correct bindings. The algorithm doesn't count the mistakes and compare them to the correct bindings -- it adds the weights of the mistakes and compares them to the weights of the correct bindings and then sorts on that comparison. This makes selection much more powerful. Whether this is actually more realistic, I have no idea.

I would like to see a graph of the values of the sorted creatures immediately prior to ev's killing by copying function, for both the original selection method and for Unnamed's. This would show how dramatically different the selective power is between the two methods. However, it doesn't tell us much about reality.

The issue always comes back to the question of what sort of selective power (benefit v. harm) is most realistic. Until this can be quantified, ev's ability to evolve at any particular generational rate is pure speculation.

 

[Mr. Scott]

Annoying Mice

Seriously people, put him on ignore. It really is a waste of time trying to argue with him. As far as he's concerned he's lashing evolution to a cross using ev as nails. He will hear nothing else.

Good suggestion, but I don't find Dr. Kleinman annoying. I find him amusing, as a cat finds a mouse amusing. I play until he bores me, then come back later to play again when I think of another way swat at him so I can watch him jump.

What these fanatical biblarians do, is when they come across a scientific development they think contradicts their bronze age manuscript, they attempt to undermine the science. They never consider questioning their manuscipt, written thousands of years ago by demonstrably ignorant authors. Where are microbes in the bible? Genes? Where is micro-evolution??? The bible reports nothing but what ordinary people knew when it was written. Nothing only observable with telescopes or microscopes was reported in the bible.

When science contradicts the bible, it's the bible we should dismatle, not the science. The developments of science work and bring us the bounties of modern life. The dead hand of religon wants to trap us in the bronze age. The harping of creationists is, except when it helps evolutionarians improve their science and their arguments, a pathetic waste.

 

[kleinman]

Annoying Creationists

You can not apply the principle of superposition to a non-linear system.

Right! Just like you you can't apply mathematical terms in an irrelevant context and expect people to think you know what you're talking about!

Oh really Delphi? Are you going to claim that the mathematics of mutation and selection is linear? Are you going to claim that selection processes can be superimposed and you obtain the same evolutionary events when the selection processes are applied independently? Perhaps you could explain to us when triple anti-HIV medications are used, it is much less likely to evolve drug resistant strains of HIV than when using the same drugs used in sequence, one at a time.

I’m pretty sure I have more experience and training in solving non-linear mathematical problems than you.

Stick with your gene duplication argument for your theory of evolution, even though you can’t explain how the original gene evolved. You have no selection process for this. And lay off the sterno.

You're right Cyborg, I'm tired. And what purpose is my fatigue serving? None.

The reason why you are fatigued is you now understand what your model shows and rather than face up to this reality, you are quitting. Your computer model doesn’t show how evolution works; it shows why evolution doesn’t work.

Not quite Taffer, you can have hundreds of beneficial mutations arising on a genome but one fatal mutation will cancel out the effects of those hundreds of beneficial mutations. You can not apply the principle of superposition to a non-linear system.

Not all deletarious mutations are fatal, kleinman.

They don’t have to be fatal, they just have to interfere with the other selection processes and slow down evolution. That is what happens with ev with its simple two selection conditions as the genome length is increased until the spurious selection condition dominates and stops evolution of the binding sites.

Not quite Taffer, you can have hundreds of beneficial mutations arising on a genome but one fatal mutation will cancel out the effects of those hundreds of beneficial mutations. You can not apply the principle of superposition to a non-linear system.

Disagree. Very few mutations are immediately fatal, so as to prevent future reproduction. Life evolves when an organism reproduces, so even if there is a "fatal" mutation, this doesn't necessarily prevent beneficial mutations from being inherited by successors. Nor, is it necessarily true that a "fatal" mutation in one generation may not be overcome or replaced by later neutral or beneficial mutations.

None of ev’s mutations are fatal on their own. It is the sum of mistakes which determines selection. Yet evolution is slowed and ultimately stopped as you increase the genome length and potential spurious binding mistakes.

The raw odds overwhelmingly favor reproduction of all mutations -- beneficial, neutral, or harmful. And, as long as an organism can survive to reproduce, natural selection will eliminate the weakest members in favor of the stronger, until the harmful mutations are minimized.

The difference between what you are saying and what Dr Schneider did is he applied rigorous mathematics to his argument and you have not. Dr Schneider’s model shows that with competing selection processes, evolution can be brought to a standstill.

What I am claiming and what the data from ev is showing is that convergence is slowed when you have competing selection conditions. The selection in ev is based on two possible errors, identification of spurious binding sites and the failure to identify binding sites. When the identification of spurious binding sites is driving the selection process in ev, binding sites will not evolve.

Try changing the three mistake weights in the java program, but, don't set any to zero. As long as all three mistake weights are non-zero, binding sites will evolve. And, contrary to your claim that failing to give substantial weight to non-binding site region spurious bindings will speed up evolution, the fastest convergence appears to occur when mistakes in the non-binding site region are overweighted.

I haven’t run the java version of ev for a while. Has Paul posted the version that allow weighting of different errors?

Unnamed did two things with his selection process. He allowed for a graded identification of binding sites and he weighted the selection toward failed identification of binding sites. This is why your Rcapacity equation does not give a good estimate for when ev will fail to converge with Unnamed’s selection process. Unnamed’s selection process can evolve binding sites on much larger genomes than Dr Schneider’s selection process. This is due to the fact that Unnamed’s selection process almost completely ignores spurious binding errors. The only problem with Unnamed’s selection process is that it has nothing to do with reality.

Totally false. You don't know how the algorithm works -- otherwise, you would not draw this conclusion. The algorithm overweights both mistakes and successful bindings, regardless of where they occur in the genome. So, the real reason why the algorithm speeds up evolution is because a mistake in the non-binding site region is treated as more harmful to the creature -- and because there is so much more non-binding site space in the genome, more mistakes will occur therein, and be overly harmful, which leads to the destruction of that creature.

Do you want to explain to us how increasing the weights of both spurious binding and successful binding equally will alter selection?

This, is not realistic, in my opinion, but also isn't what you are claiming, i.e., that Unnamed's selection process ignores spurious binding errors. It's exactly the reverse: Unnamed's selection process gives greater selective power to any mistake, but it also gives greater selective power to correct bindings. The algorithm doesn't count the mistakes and compare them to the correct bindings -- it adds the weights of the mistakes and compares them to the weights of the correct bindings and then sorts on that comparison. This makes selection much more powerful. Whether this is actually more realistic, I have no idea.

The way to address this issue is to put counters in the program and keep track of which of the two errors (spurious binding sites and missed binding sites) are driving the selection process. Selection based on spurious binding site errors will not help evolve binding sites, this selection condition is only required to evolve a perfect creature.

I would like to see a graph of the values of the sorted creatures immediately prior to ev's killing by copying function, for both the original selection method and for Unnamed's. This would show how dramatically different the selective power is between the two methods. However, it doesn't tell us much about reality.

The values you need are which errors are determining selection. If the spurious errors are determining selection, it doesn’t matter how far along the evolution of the binding sites are in these creatures, they get selected out because of spurious binding errors.

The issue always comes back to the question of what sort of selective power (benefit v. harm) is most realistic. Until this can be quantified, ev's ability to evolve at any particular generational rate is pure speculation.

It is not just the defining of realistic selection process, even Dr Schneider’s contrived selection process with two selection conditions demonstrates an important mathematical principle for mutation and selection, that is two different selection conditions leads to a slowing and ultimately the stopping of the evolutionary process. This effect is seen in reality.

Seriously people, put him on ignore. It really is a waste of time trying to argue with him. As far as he's concerned he's lashing evolution to a cross using ev as nails. He will hear nothing else.

Good suggestion, but I don't find Dr. Kleinman annoying. I find him amusing, as a cat finds a mouse amusing. I play until he bores me, then come back later to play again when I think of another way swat at him so I can watch him jump.

Mr Scott, I particularly like when you play like this:

Paul, is what Alan saying here true? In a large population, when different genes in the same organism duplicate and mutate in parallel, does evolution, as simulated by Ev, slow down?

You have asked a crucial question here. Let me rephrase it a little. Do selection processes which when acting in parallel, does evolution, as simulated by ev, slow down? Paul side stepped your question by saying that ev does not model gene duplication. Ask him the same question without your gene duplication condition and let’s see how he answers, that is if he is not too fatigued.

By the way, one of my cats is sitting on my shoulder as I type this. You don’t want to be a mouse around this cat.

What these fanatical biblarians do, is when they come across a scientific development they think contradicts their bronze age manuscript, they attempt to undermine the science. They never consider questioning their manuscipt, written thousands of years ago by demonstrably ignorant authors. Where are microbes in the bible? Genes? Where is micro-evolution??? The bible reports nothing but what ordinary people knew when it was written. Nothing only observable with telescopes or microscopes was reported in the bible.

[/quote]
Well, your rust age theory doesn’t have a mathematical basis. As it becomes clearer what the mathematics of parallel selection processes leads to, you will have to get yourself a new manuscript because evolutiondidn’tdoit.

When science contradicts the bible, it's the bible we should dismatle, not the science. The developments of science work and bring us the bounties of modern life. The dead hand of religon wants to trap us in the bronze age. The harping of creationists is, except when it helps evolutionarians improve their science and their arguments, a pathetic waste.

The problem for you is your own mathematics is contradicting your theory. In fact your own mathematics is showing why your theory is impossible. You have no selection process to evolve a gene from the beginning and competing selection processes operating in parallel interfere with evolution, initially slowing down the process and ultimately stopping evolution. This is shown in ev and in reality.

 

[articulett]

Seriously people, put him on ignore. It really is a waste of time trying to argue with him. As far as he's concerned he's lashing evolution to a cross using ev as nails. He will hear nothing else.

Now, now--

You have to admire his tenacity and the way at which religion has demented him. There is entertainment value in participating in his delusion and reading the responses. This is why creationism must not be taught in schools--it makes you positively unteachable and arrogant on top of that. You can only compute that which proves the belief you've been told leads to salvation. All else is stuff from that evil tree of knowledge...

 

[kleinman]

Annoying Creationists

Seriously people, put him on ignore. It really is a waste of time trying to argue with him. As far as he's concerned he's lashing evolution to a cross using ev as nails. He will hear nothing else.

Now, now--

You have to admire his tenacity and the way at which religion has demented him. There is entertainment value in participating in his delusion and reading the responses. This is why creationism must not be taught in schools--it makes you positively unteachable and arrogant on top of that. You can only compute that which proves the belief you've been told leads to salvation. All else is stuff from that evil tree of knowledge...

What is particularly entertaining is that your own computer model shows why the theory of evolution is mathematically impossible. You evolutionary dogmatists have nothing to counter these mathematical facts so you retreat to playground tactics. Your theory of evolution by mutation and natural selection has no selection process to evolve a gene from the beginning and ev shows that selection processes acting in parallel slow and ultimately stop evolution. This effect is seen in reality. The theory of evolution is mathematically impossible despite all your evolutionary indoctrination you have been taught. Cyborg would like to ignore these facts but thanks to Dr Schneider and Paul’s good mathematical and computer programming work, the theory of evolution by mutation and selection is now much better understood and refuted. Cyborg, I would really like to co-opt your cruft theory of evolution but I think I will let you keep that idea.

 

[kjkent1]

The difference between what you are saying and what Dr Schneider did is he applied rigorous mathematics to his argument and you have not. Dr Schneider’s model shows that with competing selection processes, evolution can be brought to a standstill.

It shows nothing of the kind, and Dr. Schneider's paper suggests no such competition. Ev slows down as the genome lengthens, because there is more space for spurious binding mistakes to exist within a longer genome. Humorously, this was your original argument, back in the evolutionisdead forum. Somewhere along the line, you've invented a completely unsupported hypothesis suggesting that there is some inhibiting competition taking place within the ev genome. Why you decided that you need this additional argument is beyond me. Regardless, it's just your imagination.

I haven’t run the java version of ev for a while. Has Paul posted the version that allow weighting of different errors?

I've never seen the java version when it didn't have this weighting option, so yes.

Do you want to explain to us how increasing the weights of both spurious binding and successful binding equally will alter selection?

There are three mistakes in the java version -- not two. You can overweight spurious bindings inside the binding site region, or outside. When you overweight the mistakes outside the binding site region, it means that the area of the genome into which more mistakes will randomly fall, simply because of its greater size, will obtain greater negative weight, and thus creatures with more non-binding site mistakes will be killed off quicker. If you add Unnamed's algorithm, that will kill them off even quicker, because the mistake weight is increased by the sum of the weights of the mistakes. And that is why Unnamed's algorithm converges faster -- not because it ignores mistakes in the non-binding site region -- but because it overemphasizes their importance.

It is not just the defining of realistic selection process, even Dr Schneider’s contrived selection process with two selection conditions demonstrates an important mathematical principle for mutation and selection, that is two different selection conditions leads to a slowing and ultimately the stopping of the evolutionary process. This effect is seen in reality.

Well, your audience would very much like you to state this mathematical principle in mathematical symbols, rather than just repeating it continuously, in the hope that we will all suddenly fall to our knees with a "Praise Jesus!"

 

[fishbob]

What is particularly entertaining is that your own computer model shows why the theory of evolution is mathematically impossible.

All the other evidence supporting evolution means that your math might just be wrong. Refusal to even consider this possibility means that your arguments are weaselly. Tenacity in dementia is not an admirable trait.

 

[Mr. Scott]

Amusing Creationists

The problem for you is your own mathematics is contradicting your theory. In fact your own mathematics is showing why your theory is impossible.

I don't know why you keep repeating this when it's been explained repeatedly and with perfectly logical clarity that it's incorrect.

If you don't come up with some new lies I'll have to start wacking at that crumbling manuscript again. Every time creationists lie, they make the baby Jesus cry, for it is the devil that is the inventor of all lies. Look it up!

 

[Taffer]

They don’t have to be fatal, they just have to interfere with the other selection processes and slow down evolution. That is what happens with ev with its simple two selection conditions as the genome length is increased until the spurious selection condition dominates and stops evolution of the binding sites.

Evolution works on phenotypes. If the overall phenotype of a range of mutations is beneficial, then it doesn't matter how harmful any of the individual mutations are. What matters is the sum total of the organism's fitness.

 

[Dr Adequate]

Where are microbes in the bible? Genes? Where is micro-evolution??? The bible reports nothing but what ordinary people knew when it was written. Nothing only observable with telescopes or microscopes was reported in the bible.

Oh, come on, there's lots of good science in the Bible:

* God makes thunder by shouting.
* God makes earthquakes by shaking the Earth.
* God makes rainbows by magic.
* The Earth is supported on pillars.
* The Earth doesn't move.
* Insects have four legs.

 

[Dr Adequate]

Lie #1.

Truth #1.

See how much easier my way is?

 

[Paul C. Anagnostopoulos]

I just don't want to see any Truth #1.3.2(D).iii.q. I hate those deep truths!

~~ Paul

 

[kleinman]

Annoying Creationists

The difference between what you are saying and what Dr Schneider did is he applied rigorous mathematics to his argument and you have not. Dr Schneider’s model shows that with competing selection processes, evolution can be brought to a standstill.

It shows nothing of the kind, and Dr. Schneider's paper suggests no such competition. Ev slows down as the genome lengthens, because there is more space for spurious binding mistakes to exist within a longer genome. Humorously, this was your original argument, back in the evolutionisdead forum. Somewhere along the line, you've invented a completely unsupported hypothesis suggesting that there is some inhibiting competition taking place within the ev genome. Why you decided that you need this additional argument is beyond me. Regardless, it's just your imagination.

The reason Dr Schneider’s paper says nothing about such competition is that Dr Schneider published only a single case which used an extremely short genome. If you carefully read Dr Schneider’s web site you would have seen this quote from his http://www.lecb.ncifcrf.gov/~toms/paper/ev/faq-for-ev.html page”

If you had a reasonable sized genome would you find that there won't be an information gain? No. Don't be lazy,

go try it yourself! But notice that it will take a lot more computation, and the runs may take some years unless you write a version that uses parallel processors.

Why does it take more time to run a reasonable length genome? It is the competing selection processes in his model that profoundly slow the rate of information gain.

I haven’t run the java version of ev for a while. Has Paul posted the version that allow weighting of different errors?

I've never seen the java version when it didn't have this weighting option, so yes.

Now isn’t that interesting. Paul’s online version does not have this feature. I guess Paul is too fatigued to put that version up on the net.

Do you want to explain to us how increasing the weights of both spurious binding and successful binding equally will alter selection?

There are three mistakes in the java version -- not two. You can overweight spurious bindings inside the binding site region, or outside. When you overweight the mistakes outside the binding site region, it means that the area of the genome into which more mistakes will randomly fall, simply because of its greater size, will obtain greater negative weight, and thus creatures with more non-binding site mistakes will be killed off quicker. If you add Unnamed's algorithm, that will kill them off even quicker, because the mistake weight is increased by the sum of the weights of the mistakes. And that is why Unnamed's algorithm converges faster -- not because it ignores mistakes in the non-binding site region -- but because it overemphasizes their importance.

Now why don’t we have Paul put the same version up on the net so we can all generate identical data and compare results?

It is not just the defining of realistic selection process, even Dr Schneider’s contrived selection process with two selection conditions demonstrates an important mathematical principle for mutation and selection, that is two different selection conditions leads to a slowing and ultimately the stopping of the evolutionary process. This effect is seen in reality.

Well, your audience would very much like you to state this mathematical principle in mathematical symbols, rather than just repeating it continuously, in the hope that we will all suddenly fall to our knees with a "Praise Jesus!"

The failure of ev to converge is demonstrated in what calls the Rcapacity problem. This problem occurs when spurious bindings dominate the selection process. This effect is seen and used in reality when physicians use multiple antimicrobials to prevent the evolution of resistant strains of microbes. A particular example of this is the use of triple anti-HIV drugs for the treatment of this disease. If you want to see this written in mathematical symbols, read Dr Schneider’s papers, he did this properly. The only thing he did not do is a thorough analysis of his equations. Why should I expect that showing you the mathematical truth about your theory should make you fall on your knees with a “Praise Jesus”?

What is particularly entertaining is that your own computer model shows why the theory of evolution is mathematically impossible.

All the other evidence supporting evolution means that your math might just be wrong. Refusal to even consider this possibility means that your arguments are weaselly. Tenacity in dementia is not an admirable trait.

This is not my mathematics. This is Dr Schneider’s mathematics and it was peer reviewed and published in Nucleic Acids Research. I only did what Dr Schneider called for in his publication and the results show that your theory is mathematically impossible.

With respects to your other evidence, perhaps you better start reconsidering your interpretation of this evidence since your foundation concept of mutation and selection is mathematically impossible. Isn’t your theory in a sad state when a demented person can show that your theory is mathematically impossible with your own mathematics.

The problem for you is your own mathematics is contradicting your theory. In fact your own mathematics is showing why your theory is impossible.

I don't know why you keep repeating this when it's been explained repeatedly and with perfectly logical clarity that it's incorrect.

I keep repeating it because it is true. You have two basic reasons why your theory is mathematically impossible. You don’t have a selection process that can evolve a gene from the beginning and competing selection processes is what slows and ultimately stops evolution in ev. This effect is seen and used in reality.

If you don't come up with some new lies I'll have to start wacking at that crumbling manuscript again. Every time creationists lie, they make the baby Jesus cry, for it is the devil that is the inventor of all lies. Look it up!

You only wish these were lies that I am saying about ev but these results are easily reproducible. You don’t have a selection process that can evolve a gene from the beginning and multiple selection process slow and ultimately stop evolution. This is shown by ev and exists in reality. Evolutiondidn’tdoit.

They don’t have to be fatal, they just have to interfere with the other selection processes and slow down evolution. That is what happens with ev with its simple two selection conditions as the genome length is increased until the spurious selection condition dominates and stops evolution of the binding sites.

Evolution works on phenotypes. If the overall phenotype of a range of mutations is beneficial, then it doesn't matter how harmful any of the individual mutations are. What matters is the sum total of the organism's fitness.

Do you want to explain how the overall fitness will evolve a gene from the beginning? How do you include what you have just said in a mathematical model of mutation and selection?

What ev reveals about competing selection processes is demonstrated with the use of multiple antimicrobials. Evolution is slowed if not halted in the HIV by using the three antimicrobials. The prevention of the changes in the genotype prevent the change in the phenotype.

I just don't want to see any Truth #1.3.2(D).iii.q. I hate those deep truths!

Especially when those truths contradict your belief system.

What happen, did you find enough strength to post again on this thread, Mr Rcapacity?

 

[Paul C. Anagnostopoulos]

Now isn’t that interesting. Paul’s online version does not have this feature. I guess Paul is too fatigued to put that version up on the net.

Lie #39. Look harder, dude.

~~ Paul