Annoying creationists

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Kleinman said:
These scientists are trying to isolate and identify the mutations that give resistance to particular drugs. Why would they introduce other selection pressures which would interfere with what they are trying to identify? They grow their populations in incubators with plenty of resources needed by the population and introduce the drugs slowly so as not to kill the entire population.
Okay, I'll take your word that they've got it completely under control. Who's got it under control in the real world?

Paul, you are not going to make a point here by being cute. Ev is a collection of equations and conditional statements which produces data from its sorting/optimization algorithm which simulates the mutation and selection process. Dr Schneider’s equations are there, I have seen the code and it does a good job of simulating how the mutation and selection process works.
And you're not going to make a point by saying "Ev does present the math." in response to my statement "Presumably you have mathematics to show that in the real world the situation is such that only certain (unspecified) biological mechanisms could have evolved in the time available, while other extant mechanisms could not have evolved." Note how I use the term "real world."

Stop being silly Paul, there is no function being evolved in ev. There are only sequences of bases which satisfy the selection conditions determined by matches to the weight matrix evolving in ev. Of course you can claim that ev is evolving real binding sites, then you can explain to us what the function of a binding site is for a gene that evolves binding sites. That would be an amusing story for you to tell us.
I didn't claim that Ev is evolving real binding sites, did I? I claimed that it is evolving a function, which is to match binding sites but no other positions on the chromosome. Then, when you turn off one or two selection conditions, it is not evolving that function. You have got to stop harping on my use of the word function, Alan.

2 : the action for which a person or thing is specially fitted or used or for which a thing exists : PURPOSE

~~ Paul
 
Kleinman said:
You can run the numbers in Dr Schneider’s model. To evolve all three selection conditions simultaneously for a 16k genome takes more than 5,000,000 generations while each of the individual selection pressures when applied singly only take at most 100 generations. Your hunch is wrong.
Let's reword this so that it actually describes what happens:

You can run the numbers in Dr Schneider’s model. To evolve [the ability to distinguish binding sites from all other positions] for a 16k genome takes more than 5,000,000 generations while [to evolve matching at every position or no position] only takes at most 100 generations. Your hunch is wrong.

You're comparing apples and sardines.

Furthermore, these observations emphasize that sequential antiviral therapy with nucleoside analogues may allow the rapid selection of drug-resistant strains.
You know, you're emphasizing that simultaneous selection pressures make evolution more difficult, but you've cited mostly controlled lab experiments. Does your mathematical proof against evolution include the part where pressures can't happen sequentially in the real world?

~~ Paul
 
You can run the numbers in Dr Schneider’s model. To evolve all three selection conditions simultaneously for a 16k genome takes more than 5,000,000 generations while each of the individual selection pressures when applied singly only take at most 100 generations. Your hunch is wrong.

You mean like setting the mistake points for each condition? I tried it with the default settings, first with one at 10 and the other two at 1 -- on average 1000 generations to convergence. With 2 out of 3 set to 10, on average it took 700 generations to convergence. With all three set to 10, it took on average 650 generations to convergence.

Does this somehow help your theory out?
 
Delphi, the mathematics of mutation is not that complex, you have some understanding of the problem; otherwise you wouldn’t have posted the Wikipedia reference to fitness landscape.
Sorry, your rant here is totally irrelevant to my point.
Why don’t you tell us how a temperature change can transform hundreds, perhaps thousands of genes simultaneously?
Scarecrow-m.jpg

How festive! Unfortunately, Halloween was last week.
 
Circles and Circles.

He believes evolution is wrong, therefore, it MUST be wrong.

If you are so certain, Kleinman, ignore the Jref, and submit your data to a reputable, peer reviewed publication.
 
It is not a correct interpretation if you want to claim that your argument has any scientific basis. Mutation and selection does not work that way either empirically or mathematically.

In no way does this answer refer to what I asked. I was asking if you would clarify a theoretical and admittedly tangential point for me. But of course you are correct: asking you to explain anything will never result in anything with a scientific basis. I withdraw my question, and let your refusal or avoidance of answering it speak for itself.

Until you present something that is measurable and repeatable, you present nothing more than mush. The hundreds of citations which I have posted identify explicitly what the selection pressures are, the target genes for the selection pressures and often times identify the specific loci and mutations required for adaptation to the selection pressures. So far, all you have presented is mush.

The fact that several different groups of animal have countered more or less the same set of selection pressures in different ways alone shows that the process is repeatable. When faced with the selection pressures I listed before (or a subset thereof, or a combination of these, or the subset, with unlisted ones), animals will evolve a way to get from tree to tree easier, for instance to get away from an arboreal predator. Some have solved this by flying, some by gliding, some by jumping, and so on.

But I will present you, again, with the Brassica example. When different diploid species of Brassica were cross-bred, polyploid progeny occurred. These were cross-bred again, according to certain patterns (1), for five generations, and the resulting polyploid hybrids are analogous to two species of natural hybrids. In five generations of inbreeding, the plants acquired several morphological and physiological changes, including changes in leaf shape and colour, branching patterns, number of side shoots, and differences in fertility. The genetic distance between the F5 generation and the F2 generation varied between 3.7% and 9.6%. The selection pressures included having to cope with two different copies of the same gene within the same genome, having to cope with sudden polyploidisation, and several other factors which are present for all plants, such as microbial and other parasitism, pathogens, and so on. The authors used 82-89 nuclear DNA probes to detect changes in the genome, and detected changes with 23-59 of these probes, indicating, again, that no specific genes were targeted.

There are of course more details in the paper, but as you never read details and instead only post stock answers and lies, I see no reason to elaborate further.

Kotatsu, you are trying to make connections where none exist. You don’t have selection pressures which would make these transformations.

How on Earth can you make such a categorical statement? Am I to understand that you believe that regardless of what group of animal is under study, the researcher never knows any selection pressures operating on that group? Regardless of what gene he/she is working with?

The relevant selection pressures would of course change depending on the gene, the organism, and other factors. The same selection pressures wouldn't necessarily operate on a EF-1α tree as on an 18S tree. And in trees based on other genes, it is often possible to be very specific on at least some of the selection pressures operating on the gene in that organism.

Just because you don't understand phylogenies --- and this is becoming abundantly clear --- doesn't mean that the people who work with them don't.

Kotatsu, you are in denial. Mutation and selection is not an incomprehensible process mathematically. If you ever come to understand that this process is nothing more than a sorting/optimization problem, you would realize that your belief system is wrong. The empirical evidence of how mutation and selection works verifies this. The pictures you draw are based on a mathematically impossible theory.

This, again, has nothing to do with my post. I was simply making the same observation as several other people have done before me, that your arguments are changing gradually as you are overwhelmed by evidence.

For some reason I don’t think I’ll ever pass your class in evolutionism or joobz’s class in alchemy.

No, I would imagine reading comprehension would be needed for both.

---
(1) This can all be found in the paper, Song et al., 1995 (see earlier posts for complete reference).
 
Ok I wrote a little simulation for use in investigating Kleinman's claim. I will post the source code on my website later today after I clean it up a bit.

The results show his theory to be wrong -- multiple pressures, of the same strength, eventually speed up the rate of evolution.

At first, it appeared as though Kleinman might be right -- adding selective pressures in low numbers really does slow the average rate of fixation way down. However, once a "critical mass" has been reached, adding pressures actually drives the rate back up. Eventually, with enough pressures, you get to a point where the average rate of fixation is equal to or faster than it is under only a single pressure.
 
rocketdodger (Dude!!!)

As a reader of this thread, I will await this long-anticpated battle of simulations. (YEAH! Dude!)

I truly hope the best simulation wins, and I will learn something about the ultimate questions that trouble my soul. (GRRR Go for it)

[I suffer from a strange disorder, I appear to type a left parenth and lose my mind, I type a right parenth and appear to be normal again. (Take Klein's simulation and give it a little selection pressure...")] Oh poops, I have a bracket problem, too...
 
As a reader of this thread, I will await this long-anticpated battle of simulations. (YEAH! Dude!)

Of course, all it takes for Kleinman to ignore this is to state that it doesn't do a good job of simulating how mutation and selection really works, and all your work will have been in vain.

Nevertheless, would it be possible for you and Paul to make your simulations into robots? They could fight each other with large laser axes or something. It would be much more convincing that way.
 
The point you are missing Belz is that Dr Schneider’s model shows that the reason it so slowly converges is the three selection conditions.

I don't see how this could be the point, since this is not what we were talking about. We were talking about how understanding and posting were two different things.

The mere fact that you're talking about a subject doesn't mean you know what you're talking about.

If you set two of the three selection conditions to zero in the model then the remaining selection condition can evolve much, much more rapidly.

But why the hell would you want to do this ? What happens, instead, if you set two of the three conditions to a relatively low, non-zero value ?

That same behavior of mutation and selection is seen in reality in the numerous citations posted.

No, because you have not shown that those real-life examples have a number and relative strength of selection pressures that you can define.

That is how mutation and selection works mathematically and that is how it works empirically.

Actually, I've pointed out to you before that real things don't work mathematically.

Mutation and selection is simply a sorting/optimization problem.

You'd like that to be true, wouldn't you ?

You can try to say that I don’t understand how mutation and selection works but I can produce data from a peer reviewed and published computer simulation of random point mutations and natural selection and hundreds of empirical examples which shows the same thing

Actually, that's precisely what I'm saying. You don't understand how mutation and selection works but you can produce data from a peer reviewed and published computer simulation of random point mutations and natural selection and hundreds of empirical examples which shows the same thing according to you.

Paul, do I have to spell this out for you?

Oh, you don't need to. You've been very, very helpful at debunking your own theory. Thank you.
 
rocketdodger said:
You mean like setting the mistake points for each condition? I tried it with the default settings, first with one at 10 and the other two at 1 -- on average 1000 generations to convergence. With 2 out of 3 set to 10, on average it took 700 generations to convergence. With all three set to 10, it took on average 650 generations to convergence.
Kleinman is talking about setting two out of three of them to 0. Then it'll converge in only a few generations. The problem, then, is that we're not evolving a creature who distinguishes bindings sites from other positions.

~~ Paul
 
Klein said:
Now if you want to try and argue that putting a strong selection pressure on a population will make the weak selection pressures evolve more rapidly then you might have a point but the problem for you is that it is mathematically impossible.

Selection pressures do not evolve. They don't even beggaminases.
 
Klein said:
Stop being silly Paul, there is no function being evolved in ev. There are only sequences of bases which satisfy the selection conditions determined by matches to the weight matrix evolving in ev. Of course you can claim that ev is evolving real binding sites, then you can explain to us what the function of a binding site is for a gene that evolves binding sites. That would be an amusing story for you to tell us.

Well, I guess it all depends on whether or not the simulation's any good.

Of course, the only reason why you think it IS good is due to circular reasoning.

Rocketdodger, you are wrong about this, there is one thing more that you have to add to your description. How does this mutation and selection process work mathematically and empirically?

That WAS his description.

Again rocketdodger, you are wrong about this, the environment does the sort.

Then "predators" are part of the environment.
 
Belz... said:
But why the hell would you want to do this ? What happens, instead, if you set two of the three conditions to a relatively low, non-zero value ?
Here are a few experiments:

standard model with all mistake points = 1: 662 gens

with all mistake points = 10 (should be same): 662 gens

with missed site points = 10 (heavier pressure): 316 gens

with two spurious binding points = 10 (different heavier pressure): 1267 gens

with just gene spurious binding points = 10: 889 gens

with just nongene spurious binding points = 10: 1034 gens

So changing the relative pressures has some fairly obvious effects. More pressure on missed binding sites results in faster convergence. More pressure against spurious binding sites results in slower convergence.

Now let's turn off pressures:

(a) with missed site points = 0: 1 gen

(b) with just gene spurious binding points = 0: 707 gens

(c) with just nongene spurious binding points = 0: 405 gens

(d) with both spurious binding points = 0: 6 gens

In cases (a) and (d), no distinction evolves between binding sites and other positions, so it takes no time to produce a creature with zero mistakes. Essentially, there are no mistakes.

In cases (b) and (c), a distinction between binding sites and other positions evolves, but only for a portion of the genome. Not surprisingly, if the portion that matters is larger (case b), it takes longer.

~~ Paul
 
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Here are a few experiments:

standard model with all mistake points = 1: 662 gens

with all mistake points = 10 (should be same): 662 gens

with missed site points = 10 (heavier pressure): 316 gens

with two spurious binding points = 10 (different heavier pressure): 1267 gens

with just gene spurious binding points = 10: 889 gens

with just nongene spurious binding points = 10: 1034 gens

So changing the relative pressures has some fairly obvious effects. More pressure on missed binding sites results in faster convergence. More pressure against spurious binding sites results in slower convergence.

Now let's turn off pressures:

(a) with missed site points = 0: 1 gen

(b) with just gene spurious binding points = 0: 707 gens

(c) with just nongene spurious binding points = 0: 405 gens

(d) with both spurious binding points = 0: 6 gens

In cases (a) and (d), no distinction evolves between binding sites and other positions, so it takes no time to produce a creature with zero mistakes. Essentially, there are no mistakes.

In cases (b) and (c), a distinction between binding sites and other positions evolves, but only for a portion of the genome. Not surprisingly, if the portion that matters is larger (case b), it takes longer.

~~ Paul
Kleinman's entire hypothesis is built on his introducing a software "bug" into ev. Using a zero value for any of the selection weights causes the population genomes to be filled with missing and/or spurious bindings, while simultaneously reporting a "perfect" creature. However, the program population is not actually evolving towards the known natural quality shared by the genomes of all independently living organisms: RSequence ~ RFrequency.

It's analogous to trying to test Einstein's E=mc2 equation by building a nuclear weapon using lead instead of U238, and then declaring Einstein wrong, because no fission occurs.

The irony of all this is that no one would argue with kleinman that exposing a population to multiple strong selective pressures will make evolution more difficult than via exposure to one selective pressure. Three against one is definitely unfair odds. But, to suggest that this means that natural evolution cannot possibly occur is frivolous/quackery.

Evolution happens and the evidence is everywhere.
 
The irony of all this is that no one would argue with kleinman that exposing a population to multiple strong selective pressures will make evolution more difficult than via exposure to one selective pressure.

Actually, Adequate and I sort of are. My simulation shows that if you introduce enough strong pressures, and if you measure the rate of fixation on average, then fixation is just as fast (or even faster).

Of course this only applies to pressures that don't kill off 90% of the population, which seems to be the only kind of pressure Kleinman cares about.
 
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Actually, Adequate and I sort of are. My simulation shows that if you introduce enough strong pressures, and if you measure the rate of fixation on average, then fixation is just as fast (or even faster).

Of course this only applies to pressures that don't kill off 90% of the population, which seems to be the only kind of pressure Kleinman cares about.

Which is odd. When you wipe out 90% of a population and the rest has adapted to said pressure, then evolution has proceeded much more rapidly.
 
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