Annoying creationists

[Paul C. Anagnostopoulos]

Mr Scott, you are confusing several principles. Those principles you are confusing are selection pressures, intensity of selection pressures and extinction. The mathematics is clear; increasing the number of selection pressures slows evolution.

Hang on a mo. Did I miss something? Has Kleinman presented the mathematics of multiple selection pressures?

~~ Paul

 

[Ichneumonwasp]

I'll go with (1). If Ev's simplistic multi-pressure model happens to mimic real-world evolution of drug resistance, either that is a stunning coincidence or real-world resistance is trivial. Wait, or both.

~~ Paul

That would be the most likely, I think, too.

Either Kleinman must give up his model or give up his example. Either way it looks bad. Give up the example and he doesn't have a real world link for the model, and it becomes a nice abstraction of uncertain provenance (at least as far as the full range of evolutionary pressure/history/etc., which is what you have said all along).

 

[Ichneumonwasp]

Hang on a mo. Did I miss something? Has Kleinman presented the mathematics of multiple selection pressures?

~~ Paul

He continues to claim that he has modelled the mathematics. I haven't seen any data.

 

[kleinman]

Annoying Creationists

Modeling relative selection pressures more realistically will take much more than the strategy that you have employed. Even with your simple strategy, the relative selective pressures change as you lengthen the genome. With large genomes, the non-binding site region becomes the dominant source of spurious binding mistakes. This is why as you lengthen the genome, even with a mutation rate fixed to a number of bases, that the number of generations for convergence increases.

I agree, a realistic model of selection pressures is way more complex. Thus I would not draw any conclusions about selection pressures in the real world. The feature was added for the same reason as the tie-breaking feature: at the insistence of a creationist.

You left off an important adjective in your response. My conclusion about the effects of multiple selection pressure is not based on relative selective pressures. It is based on turning selection pressures on and off in ev. This finding is substantiated by Delphi’s Wikipedia reference to fitness landscape. By the way Delphi, how is your sock drawer coming?

And why does it take the insistence of creationists for you evolutionists to do a thorough mathematical scientific proof of your claims?

Do you want to venture a guess whether including this effect would speed or slow the evolutionary process? I’ll stick my neck out and guess that this will slow evolution by reducing populations.

Well, extinction would certainly slow the evolution of the extinct species, yes.

That’s the way to stick your neck out little turtle. I’m not so sure that it would be difficult to develop an algorithm that could be used in ev that would model relative selective pressures. Even without this feature, being able to turn on and off individual selective pressures reveals what happens to the mathematics of mutation and selection when you have multiple selective pressures.

Yes I am extrapolating this result to all possible selection pressures. Increasing the number of selection pressures is simply increasing the number of sorting conditions. It doesn’t matter what the selection conditions are. Delphi’s Wikipedia link to fitness landscape discusses the same issue. This is a basic mathematical principle of optimization. When Delphi went to sort his sock drawer; the more colors of socks he has the slower the sort proceeds. If all his socks are of a single color, any two socks he grabs randomly out of the drawer gives a match.

So you're claiming that there is no possible way we could have two orthogonal selection pressures to which an organism adapts in parallel?

You need to reread again what I have said again. I’m not sure what you mean by orthogonal selection pressures but additional selection pressure slow the evolution of each of the individual selection condition when compared to evolution based on an individual selection pressure alone.

Also, I can sort any number of sock colors at the same speed: I look at each sock and drop it in the correct pile. Perhaps you really mean to discuss selection speed?

You are making my point. You first sort your socks by color and then put them in pairs. If all the socks are a single color, you don’t have to do the work of the sort, you simply put them in pairs. With a single selection condition, a mutation is determined to be beneficial or detrimental and the ability to reproduce is known. If you have multiple selection conditions, a mutation may be beneficial for one selection condition and detrimental for another selection condition. The total selection process becomes much more complex. Ev shows how difficult this mathematics becomes for satisfying multiple selection conditions when compared to satisfying a single selection condition.

It is your terminology which is causing confusion. What you call a “perfect creature” is nothing more than a genome with a sequence of bases that satisfies all three of your selection condition. Reducing the number of selection conditions by setting selection weights to zero gives a genome with a sequence of bases that satisfies the remaining selection conditions when you click the check box – Pause on perfect creature. You can’t use your confusing terminology to obscure what is occurring mathematically.

Yes, my terminology is causing confusion. Therefore, you should not employ my terminology in making your point. We all agree that different numbers of selection pressures will cause Ev to arrive at a zero-mistake creature in different numbers of generations. But to refer to all those various creatures as "perfect creatures" obscures the issue.

If you think of a “perfect creature” as one which has satisfied all the selection conditions placed on it then this terminology is understandable. You just don’t like when I co-opt anything of yours.

I don’t agree that you have creatures that have evolved different functions. The creatures have evolved to satisfy each of the selection conditions. In the case of three selection conditions your “perfect creature” has evolved a genome to satisfy all three selection condition. When you set some of the selection conditions to zero, you evolve a genome to satisfy the remaining selection conditions.

And thus, those two creatures have evolved different functions. One distinguishes binding sites from all other sites. The other does not.

So what! Define any three selection conditions and evolving the conditions one at a time will occur much more quickly than trying to evolve all three selection conditions simultaneously.

Mr Scott, you are confusing several principles. Those principles you are confusing are selection pressures, intensity of selection pressures and extinction. The mathematics is clear; increasing the number of selection pressures slows evolution. The number of selection pressures and the intensity of selection pressures determine whether extinction occurs. When you treat patients with HIV and use selection pressures that are insufficient to cause extinction of the virus, you will get resistant strains of the virus to those selection pressures. The fewer the number of selection pressures, the more rapidly the resistant strains appear.

And the intensity of those selection pressures doesn't matter? Three mild pressures will always result in "slower evolution" than two brutal pressures?

Of course the intensity of selection pressures can determine extinction but the point is that selection pressure and selection intensity are independent variables in the mathematics of mutation and selection. In ev, it is not the intensity of the selection pressures that makes evolution so slow, it is the number of selection pressures which makes evolution so slow. Varying the intensity of the selection pressures is not going to reverse the huge number of generations required to evolve the three selection conditions in ev. The dominant variables in the mutation selection mechanism of evolution are genome length and the number of selection pressures. This is what ev shows. Other variables including population and mutation rate have much less profound effect on the mathematical behavior of the model.

This is why I like debating ev. The definitions are mathematical and the assumptions used at arriving at these definitions can be easily scrutinized. If you are going to continue on in this discussion, you had better familiarize yourself with ev. This thread is about the mathematics of mutation and selection.

The very issue of this thread is whether or not ev serves as a proper model for what you think it does. You cannot assume that ev properly models the mathematics of evolution (as it exists in the real world). You provided as support for this idea (that ev does model evolutionary change properly) HIV triple therapy as directly analogous to ev's functions. In your assessment of ev you have claimed that ev proves that evolution is so slow when three selection pressures are used that it could never have accounted for the bounty that surrounds us. However, if HIV triple therapy is analogous to the function of ev, as you have proposed, then your theory is wrong. Resistance develops in the presence of HIV triple therapy when the potency of this therapy is taken into account -- specifically when the potency is not as strong as the currently used treatments. And this resistance develops relatively quickly on an evolutionary time scale.

The basic approach evolutionists have to ev is that if it shows something that supports your theory it is a valid, if it shows something that contradicts your theory, the model is not valid. You evolutionists are filled with prejudices and biases. But let’s see what Dr Schneider has said about his model:

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.

Dr Schneider’s model shows important essential relationships between genome length, selection conditions, mutation rates and population. If you take the time to study the model, you will find that genome length and the number of selection conditions are the dominant variables in the mathematics of mutation and selection.

I am forced to conclude either: (1) ev does not adequately model three selection pressures as they relate to the development of resistance or (2) ev does not adequately model the development of resistance in a realistic time frame, which may simply be an issue of population size (which ev cannot handle).

I'll go with (1). If Ev's simplistic multi-pressure model happens to mimic real-world evolution of drug resistance, either that is a stunning coincidence or real-world resistance is trivial. Wait, or both.

Well Paul, you have your own model of the mathematics mutation and selection which reveals something about genome lengths and selection pressures and you dismiss it out of hand because it doesn’t agree with your world view. Dr Schneider thinks that ev models reality, you used to think this until you finally studied the behavior of the model. Well, I’m still with you Dr Schneider. Your evolutionists partners may deny the validity of your work but we creationists will stick with you. I will any way.

Mr Scott, you are confusing several principles. Those principles you are confusing are selection pressures, intensity of selection pressures and extinction. The mathematics is clear; increasing the number of selection pressures slows evolution.

Hang on a mo. Did I miss something? Has Kleinman presented the mathematics of multiple selection pressures?

Paul, you must have missed something. Didn’t you read Delphi’s Wikipedia link to fitness landscape? Don’t you see what happens to the convergence of ev when you reduce the selection conditions to one? Multiple selection conditions slow evolution, your program shows this and Delphi’s link shows this very nicely.

I'll go with (1). If Ev's simplistic multi-pressure model happens to mimic real-world evolution of drug resistance, either that is a stunning coincidence or real-world resistance is trivial. Wait, or both.

That would be the most likely, I think, too.

What makes you think the mathematics of real-world evolution of drug resistance is any different than from the mathematics of any other mutation and selection process?

Either Kleinman must give up his model or give up his example. Either way it looks bad. Give up the example and he doesn't have a real world link for the model, and it becomes a nice abstraction of uncertain provenance (at least as far as the full range of evolutionary pressure/history/etc., which is what you have said all along).

Ichneumonwasp, this is not my model of mutation and natural selection. This is the peer reviewed and published model of mutation and natural selection, written by Dr Tom Schneider, head of computational molecular biology and the National Cancer Institute. This model shows that three selection pressures simultaneously slow the evolution process for each of the conditions. While single selection conditions evolve much more rapidly. This is exactly what we see when combination therapy is used for treating HIV and TB and what results with monotherapy with the treatment of MRSA, Gonorrhea, pseudomonas and cancers as well. So it is not my model to give up and my examples work just fine, thank you.

Hang on a mo. Did I miss something? Has Kleinman presented the mathematics of multiple selection pressures?

He continues to claim that he has modelled the mathematics. I haven't seen any data.

Dr Schneider modeled the mathematics. The reason you haven’t seen any data is you haven’t read this thread or the Evolutionisdead forum where this discussion started. Here is some new data for you.

The following data from ev is based on a mutation rate of 1 mutation/256 bases/generation, G was varied, and the weight factors were set to 0 or 1 for the following series of cases. All other parameters were left at default values. The top row in the table gives the weight factors for missed binding sites, spurious binding sites in the gene and spurious binding sites outside the gene.

G \111 \110 \101 \011 \100 \010 \001
8192 \20237 \881 \22324 \20 \1 \13 \19
16384 \49963 \424 \41260 \20 \1 \21 \28
32768 \140958\436 \284,000+\20 \1 \9 \20

There are a couple of interesting numbers in this table highlighted in red. These two cases with two selection conditions actually took more generations to evolve than the three selection condition case. However, the single selection condition cases are able to converge thousands of times more quickly than the three selection condition cases for any of the three selection conditions. It is amazing how quickly a single selection condition can evolve, even on a lengthier genome.

 

[delphi_ote]

Has Kleinman presented the mathematics of multiple selection pressures?

Yes.

Delphi + EtOH -> Wikipedia & fitness landscape -> organize sock drawer

 

[kleinman]

Annoying Creationists

Has Kleinman presented the mathematics of multiple selection pressures?

Yes.

Delphi + EtOH -> Wikipedia & fitness landscape -> organize sock drawer

I hope my mathematics is not too obscure. Delphi, if you have any trouble organizing your sock drawer, Paul will help you. He’s very good at the mathematics of sorting socks.

 

[delphi_ote]

I hope my mathematics is not too obscure. Delphi, if you have any trouble organizing your sock drawer, Paul will help you. He’s very good at the mathematics of sorting socks.

Obscure? Heavens no! Your capacity for mathematical reasoning is abundantly clear. Please, show us more of these "equations." I'm sure they'll further elucidate your "insight" into this complicated subject.

 

[Paul C. Anagnostopoulos]

You are making my point. You first sort your socks by color and then put them in pairs. If all the socks are a single color, you don’t have to do the work of the sort, you simply put them in pairs. With a single selection condition, a mutation is determined to be beneficial or detrimental and the ability to reproduce is known. If you have multiple selection conditions, a mutation may be beneficial for one selection condition and detrimental for another selection condition. The total selection process becomes much more complex. Ev shows how difficult this mathematics becomes for satisfying multiple selection conditions when compared to satisfying a single selection condition.

The sock drawer is a silly analogy. What if you have no a priori knowledge that all the socks are the same color? Then you always have to sort them and it takes the same amount of time regardless of the number of colors.

If you think of a “perfect creature” as one which has satisfied all the selection conditions placed on it then this terminology is understandable. You just don’t like when I co-opt anything of yours.

Okay, misuse the term. But then you have to address Kjkent's point that a "perfect creature" arises instantaneously with no selection pressures at all. Don't you see that you're just shooting yourself in the foot?

So what! Define any three selection conditions and evolving the conditions one at a time will occur much more quickly than trying to evolve all three selection conditions simultaneously.

You can't use Ev to demonstrate this. If you turn on one pressure until the mistake count is zero, then turn it off and turn on a second pressure, you won't end up with a creature that distinguishes binding sites from other sites. You'll end up with a creature that performs a different function.

~~ Paul

 

[Paul C. Anagnostopoulos]

There are a couple of interesting numbers in this table highlighted in red. These two cases with two selection conditions actually took more generations to evolve than the three selection condition case. However, the single selection condition cases are able to converge thousands of times more quickly than the three selection condition cases for any of the three selection conditions. It is amazing how quickly a single selection condition can evolve, even on a lengthier genome.

Well then, at least you admit there is nothing special about three or more pressures. Note how even more amazing it is when there are zero selection conditions.

What you are doing here is extrapolating the rather degraded case of a single selection pressure in Ev to cover the entire real world of evolution. You are claiming there is not a single case of evolution accommodating two selection pressures more quickly than one pressure. You are making a claim about the entire landscape of biochemistry. You have some seriously enlarged gonads there, my friend.

~~ Paul

 

[Dr Adequate]

He's still telling Lie #5?

Kleinman, what part of "particularly effective" are you too dumb to understand?

 

[Dr Adequate]

And Adequate, if you can’t keep it decent, at least don’t be dull and boring.

You are lecturing people on decency? Well, that's good for a chuckle.

If you find reality "dull and boring", I suggest that you crawl off and read the Bible. You'll like that, it has magic talking animals, and none of that nasty mathematics that you have such difficulty in understanding.

Now, is that your sole riposte to my expose of Lie #5, or do you have anything to say in your defense?

C'mon, I want to see you try to twist the words "particularly effective". What's the point of keeping a tame creationist if it won't do the Silly Dance for us?

 

[Schneibster]

And Adequate, if you can’t keep it decent, at least don’t be dull and boring.

Looks like another one for the "did he really say that" file.

Dr. Adequate, that was an excellent summation on the last page. Just in case anyone missed it, here's a linky-poo.

 

[kjkent1]

Okay, misuse the term. But then you have to address Kjkent's point that a "perfect creature" arises instantaneously with no selection pressures at all. Don't you see that you're just shooting yourself in the foot?

I don't believe that the real Dr. Alan Kleinman is on the other end of this argument. It's got to be someone else, because no one with a Ph.D and MD could possibly be so ignorant.

You've defined a perfect creature as one substantially free of both missed or spurious bindings. If we turn the pressure off that selects for one of these features, then the resulting creature cannot possibly meet the original definition -- it's not the same creature.

For some reason, kleinman appears to believe that because ev reports a perfect creature, that the resulting creature must therefore necessarily be perfect.

That's great. Here, let's do this, then:

main()
{
printf("Evolution is true.");
}

Game over.

 

[joobz]

Hang on a mo. Did I miss something? Has Kleinman presented the mathematics of multiple selection pressures?

~~ Paul

No, but Dr. Kleinman has presented many other facinating scientific "facts".

I can compose a list to add to Dr. Adequate's Kleinman FAQ if need be.

 

[Dr Adequate]

No, but Dr. Kleinman has presented many other facinating scientific "facts".

I can compose a list to add to Dr. Adequate's Kleinman FAQ if need be.

You mean stuff like the "Kleinman Lectures On Probability Theory"?

You are confusing the probability of a particular event occurring which must have a value between 0 and 1 with probability that a particular event may occur by a series of mutually exclusive events which can have probabilities greater than 1 ...

The probability of throwing a 1 in either of two rolls of a die is 1/6 + 1/6 = 1/3.

Yeah, that's funny.

And then he wishes to tell us what he thinks is "mathematically impossible".

 

[BPScooter]

OK, I bow out and really didn't contribute much. I felt a little creepy when the people I tend to trust were all-of-a-sudden called "dumbass." That's nearly like calling me a "dumbass," which takes me so far aback that I went back and a-back in this thread and realized I have no rationale for being reading this in the first place.

 

[joobz]

You mean stuff like the "Kleinman Lectures On Probability Theory"?

I forgot about that. The great part was with with the notion that probability can exceed 1.

I was considering these gems:

Since natural selection is a restatement of the 1st law of thermodynamics, what selection pressure would lead to the formation of a self replicating ligase?

In case You were wondering 1st law, which states that heat and work are equivilent/interchangable (dE=dQ-dW) is identical to saying that the species best adapted for survival will survive.

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.

This one had me rolling. classical thermodynamics is a study of heat(thermo) and work (dynamics). the newer work in non-equilibrium thermo is a kinetic study, but requires additional arguments not handled by what kleinman is refering to.

This would be honest mistakes for anyone, but coupled with his assertion of his fine engineering and mathematics background and claims of having taught thermodyanmics, it is a quite funny.

 

[articulett]

This is not my primary reason though for doing this thread. That reason is none of your business.

Umm....let me guess...to get some extra credit heaven bonus points?

 

[Taffer]

Well, looks like I'm not needed. Kleinman hasn't changed his argument one bit. Oh well.

/me wonders off to do something more productive.

 

[Ichneumonwasp]

The basic approach evolutionists have to ev is that if it shows something that supports your theory it is a valid, if it shows something that contradicts your theory, the model is not valid. You evolutionists are filled with prejudices and biases. But let’s see what Dr Schneider has said about his model:

You may continue to conjure any straw man you wish, but here is, once again, the point:

You have a computer model (Dr. Schneider's model, so that you will stop harping on trivial minituae as though you are making a point). You claim this computer simulation models the reality of evolution in all its particulars. You have argued that the intersection of this simulation and reality is the behavior of HIV in the presence of triple therapy. You argued that three selection pressures in ev demonstrate that evolution cannot occur on a realistic time scale. You have been shown with the very example you cite as the intersection of reality and your computer model that what you think the model proves is incorrect. The model does not win in this situation. Reality does. And since the model was not intended to simulate this issue, I'm not the least surprised.

For the nth time, I am not claiming anything about ev except that it was designed to show one thing -- that information can increase in a very simple model of mutation and selection. That is all that the model was designed to do and that is what it does.

There is no conspiracy to quell the demons of ev. Your entire argument depends on ev modelling the reality of evolution in all its particulars (not just one aspect of reality -- information gain -- as it was designed to do). When it fails to model all of evolutionary reality, reality wins, not the model. The model only goes so far as it can explain anything in the real world. It's the same with all models. The only thing I have denied is the ability of ev to do what you said it does. It simply does not model what you propose. Your own, hand-picked, example -- the only real-world example you have offered -- demonstrates this fact.

Dr Schneider’s model shows important essential relationships between genome length, selection conditions, mutation rates and population. If you take the time to study the model, you will find that genome length and the number of selection conditions are the dominant variables in the mathematics of mutation and selection.

How nice. Need I remind you, again, that the model does what it was designed to do and not what you argue it does. Nothing else in this argument matters. You can argue till you're blue in the face and your fingers cramp at the keyboard that ev models important relationships between genome length, selection conditions, mutation rates, and population and we will all sit back and say "Well, yeah, that is how it is designed, so tell us something we don't know." What it doesn't model is the reality of triple therapy for HIV under all treatment conditions. If you have no real-world analogy, then the model is useless for that purpose. Dr. Schneider provided his real world analogy for what the model was created to do -- demonstrate the emergence of information under Darwinian conditions.

Well Paul, you have your own model of the mathematics mutation and selection which reveals something about genome lengths and selection pressures and you dismiss it out of hand because it doesn’t agree with your world view. Dr Schneider thinks that ev models reality, you used to think this until you finally studied the behavior of the model.

And that is utter BS and another prime example of your penchant for misrepresenting others' arguments. I have yet to see Paul once claim that ev does not model something of reality. He has maintained that ev did its job -- demonstrating an increase in information. That is what Dr. Schneider claims as well -- repeatedly from the quotes you have provided of him. I have yet to see anyone but you claim that ev models all aspects of the evolutionary landscape. You have specifically stated that it predicts the inability of evolution to occur on a realistic time scale if three selection pressures are applied. Your example for this in the real world -- HIV triple therapy -- when all the information about it is considered, actually shows the opposite. Unless you can show some real-world example of how this model that you think explains what occurs in the real world functions, then I'm afraid that your argument is dead in the water. Otherwise, all you have is a model that does nothing but sit in the corner.

What makes you think the mathematics of real-world evolution of drug resistance is any different than from the mathematics of any other mutation and selection process?

First, I never said it was. The "mathematics" of real-world evolution of drug resistance shows that three selection pressures does not stop the process and does not slow it to the point that evolution cannot happen on a realistic time scale. That is what the HIV triple therapy story tells us.

But, there is no question, whatsoever, that different mechanisms play into resistance with different organisms. I am not aware of any lateral transfer of information amongst viruses (there probably is some example of this, though), but there is clear lateral transmission of information in bacteria through plasmids. That is an entirely different mechanism from random mutation and selection and a process that dramatically speeds "evolution".

Ichneumonwasp, this is not my model of mutation and natural selection. This is the peer reviewed and published model of mutation and natural selection, written by Dr Tom Schneider, head of computational molecular biology and the National Cancer Institute.

Wow, really? Please leave the rhetoric at home. We all know the facts here.

This model shows that three selection pressures simultaneously slow the evolution process for each of the conditions.

The model was designed to show increases in information. It performs that task.

It shows that three selection pressures slow the evolutionary process. Well, so does reality. Yes, of course. But that has not been your argument until very recently. If your only argument is that three selection pressures (potency held constant) slow evolution, then we all agree. Yes, for one particular definition of "evolution" -- defined as increased variability in a population -- three pressures, potency held constant, slows evolution.

That, quite simply, has not been your argument through this incredibly long series of posts. You have argued that evolution is so profoundly slowed that it could never account for significant change in realistic time frames. Have you changed that argument?

While single selection conditions evolve much more rapidly. This is exactly what we see when combination therapy is used for treating HIV and TB and what results with monotherapy with the treatment of MRSA, Gonorrhea, pseudomonas and cancers as well. So it is not my model to give up and my examples work just fine, thank you.

We have never debated whether single selection conditions evolve more rapidly than three selection conditions. I don't even see the point in arguing that. Why do you bring this up? No one that I am aware of has contended the opposite position, so what is your point? Is this simply another attempt to misrepresent my position? Should I repeat all the other instances of your attempts to misrepresent my position, Dr. Alan Kleinman?

I am not accusing you of creating the model. I am accusing you of using the model for ends it was not designed. Such post-hoc analysis may be useful in science to suggest future research but is notoriously unreliable in arriving at conclusions.

Dr Schneider modeled the mathematics. The reason you haven’t seen any data is you haven’t read this thread or the Evolutionisdead forum where this discussion started. Here is some new data for you.

That isn't what I asked for. I said that you had not provided data for the mathematics of ev. As in an equation. I have seen plenty of data from individual runs. You continue to harp on the mathematics of ev. Show me the mathematics of it. Show me the equations and let's apply them to the real world and see how they work. If the mathematics of ev models all aspects of the evolutionary landscape then we may continue to discuss it as an accurate model of the evolutionary landscape. If it doesn't, then we scrap it for that purpose and admit that it did it's job -- it showed that information can increase under Darwinian conditions of mutation and natural selection.