Annoying creationists

[joobz]

Very revealing! Kleinman is only a computer simulation/model of a creationist, and was never intended to model the whole landscape of creationist nonsense. .

I don't know if that is true. It seems that the Kleinman Simulator is modeling the entire landscape of creationist thought. this is a much simulation task to acheive since you only need to code in "God did it."

Any new evidence that wasn't accounted for was because god did it and evidence doesn't matter.

 

[kjkent1]

No, every position in the entire genome is evaluated and used to tally mistakes.


Now I'm confused. You appear to have contradicted yourself here.

I think I misunderstood what you wrote.

~~ Paul

I think I mis-wrote what you understood. Regardless, and contrary to kleinman's protestations, ev doesn't "effectively ignore" the non-binding site region -- either in it's original form, or with Unnamed's mods. Rather, both algorithms treat the entire genome identically.

 

[Ichneumonwasp]

As for mathematical models of the evolutionary landscape, here are a google search and a Pubmed search showing thousands. Most are not relevant but there are an obvious many that are:

Google search

Pubmed search

You have to sift through all the "social evolution" garbage, but there are plenty of applicable sources, especially those that relate to the mathematical modelling of alternative means of gaining information (other than mutation and selection).

 

[Paul C. Anagnostopoulos]

You have to sift through all the "social evolution" garbage, ...

Garbage, you say? Are you suggesting that human civilization is entirely a product of genetic evolution?

~~ Paul

 

[Ichneumonwasp]

Garbage, you say? Are you suggesting that human civilization is entirely a product of genetic evolution?

~~ Paul

Why, how could you possibly come to any other conclusion?



It's true!

 

[Dr Adequate]

I just saw a creationist website telling me that the Greek for "serpent" is "spakov".

The whole of creationism is epitomised in that one word.

It made me think of kleinman immediately. Mathematics, computer science, evolution, genetics, thermodynamics --- it's all Greek to him. But he thinks he knows what it says.

 

[Mr. Scott]

Annoying Genes

Alan Kleinman has pasted a statement like "there is no selection process for evolving a gene de novo" perhaps a hundred times. I wonder if he would commit to that assertion that every gene in existence today or in the history of life on Earth was created by divine intervention (or perhaps now by human bio-engineering). If he would, then a single gene proven to have evolved naturally would shatter his entire creationist stance. I seem to recall someone posting a number of articles about actual de novo gene creation.

What do you think of this angle, guys? Has it been mathematically proven that all genes were deliberately engineered by god? One single verified exception and...

 

[Ichneumonwasp]

I had a revelation this weekend, during the fifty seventh trip wheelbarrowing 6 yards of mulch to the proper beds.

T.S. Eliot's poetry is not difficult. You simply need the proper way to look at it, much like Kleinman's view of evolution.

Look at "The Love Song of J. Alfred Prufrock". It's all right there in the first stanza -- "evening is spread out against the sky like a patient etherised upon a table". It's obvious, "etherized". He was a couch potato. Women coming and going talking of Michelangelo? -- obviously objects of scorn and derision. Why else would he repeat that line over and over, almost hypnotically? Coming and going, no way. He wanted to stay on the divan.

You know, Eliot always feared that he drove Vivien mad. I think he did.

Vivien: Tom, the crocuses need planting.
Tom: I'll get to it, dear.
Vivien: Tom, dearest, did you rake the leaves?
Tom: I'll get to it, dear.

Think about "The Wasteland"? You needn't sift through the arcane references to vegation myths and fisher kings and Madame Sosostris' this and that. It's all right there in the first line -- "April is the cruellest month".

T.S. Eliot hated gardening. All of his poetry concerns this intense hatred of gardening. He drove his wife mad because of his hatred of gardening.

I think I have a new appreciation for the old boy. I'll be publishing in "Poetry Quarterly" later this year. It's all so obvious to me now.

 

[Dr Adequate]

Alan Kleinman has pasted a statement like "there is no selection process for evolving a gene de novo" perhaps a hundred times. I wonder if he would commit to that assertion that every gene in existence today or in the history of life on Earth was created by divine intervention (or perhaps now by human bio-engineering). If he would, then a single gene proven to have evolved naturally would shatter his entire creationist stance. I seem to recall someone posting a number of articles about actual de novo gene creation.

It's in the FAQ: see my sig for details.

 

[Mr. Scott]

Annoying Proof of De Novo Gene Creation

It's in the FAQ: see my sig for details.

Read through your FAQ again and laughed out loud several times. Thanks!

Also, I particularly liked the artice THE ORIGIN OF NEW GENES: GLIMPSES FROM THE YOUNG AND OLD which has so many beautifully detailed examples and even observed instances of spontaneous de novo gene creation. I think creationists are obliged to dispute the article point by point to remain in the game.

 

[kleinman]

Annoying Creationists

Ugh, Dr. Kleinman, you've become boring again. You've reverted to your original goalpost lies which have already been exposed and discounted.

Pardon me; I will try to comply with the wishes of a myopic evolutionist. Are there any other kinds of evolutionists but myopic evolutionists? Since you are having trouble seeing the goalposts, I have decided to introduce a visual aid to help you with your myopia.

********************************************
* *
* |M| |I| *
* |A| |T| *
* |T|____________________________|S| *
* |H Multiple Selection Pressures | *
* |E| |I| *
* |M| |M| *
* |A| |P| *
* |T| |O| *
* |I| |S| *
* |C| |S| *
* |A| |I| *
* |L| |B| *
* |L| |L| *
* _|Y|_ ___|E|___ *
* slows evolution *
* *
* This is what ev shows. *
* This is what reality shows. *
********************************************

Do you want to borrow the Hubble telescope in order to see the goalposts?

Please be a little more inventive. Otherwise, this thread will die.

Didn’t you know? The theory of evolution is already dead, ev shows this and reality shows this. There are only a few components of the theory useful as cadaver transplants to a real scientific and mathematical theory of mutation and selection.

It's really a pity that you don't take anyone seriously other than yourself. You might actually help make a contribution to society, if you weren't so dead set on trying to overcome your self esteem issues.

That’s not an accurate statement kjkent1. I take Dr Schneider’s ev work very seriously. It is the best mathematical model of mutation and selection available and it properly captures the mathematics of mutation and selection. Now your string cheese theory of evolution I also take seriously, that is seriously silly.

Think of ev as an accounting tool. What ev does is keep track of beneficial, neutral and detrimental mutations. Sequencing of human and chimp DNA shows at least 35,000,000 base substitutions in the homologous regions of the genomes. You have about 500,000 generations to accomplish all these changes. Ev shows that even on short genomes, 500,000 generations are not sufficient to evolve binding sites (100 loci) on a 32k genome and human and chimp genomes number in the billions of base pairs. The mathematics just doesn’t work out.

Last time I checked you said that we should not compare apples and oranges, but that is precisely what you are doing.

Really, what’s the problem with comparing mutation and selection with mutation and selection? You were trying to compare one generation of HIV with millions of reproductions of the virus with one generation of ev with a single reproduction of the genome. Ev shows how slow the mathematics of mutation and selection is for short genomes, do think the rates of evolution accelerate on longer genomes? If you do, you are completely ignorant of the mathematics of mutation and selection.

Ev begins with random "bases" in no particular order and evolves sequences that fit predefined binding site information. It begins from scratch, so to speak, and moves toward a defined pre-set goal (as a way to determine the emergence of information).

So what is your point? The primordial world began with all kinds of sequences of bases with all kinds of information? Or is your point that if you have no pre-set goal, randomly mixing chemicals gives you life? Ev demonstrates exactly how mutation and selection works. It is a slow process that becomes even slower as you add more selection pressures. Perhaps you would tell us what the selection pressure is that transformed reptiles into birds? Or was it numerous selection pressures?

The change from chimp to human begins with approximately 25,000 to 35,000 already pre-existing genes. A small number of those genes change over time, with most of the alterations occurring in regulatory regions or in feedback loops concerned with the timing of gene expression during development. There is no "de novo evolution of binding sites". The alterations occur and if they allow more offspring to survive, then they are expressed at higher frequency. Many of the changes were in gene deletions or gene duplications with and without modification. A simple gene duplication near a promoter that is active at a different time of development you would see as no new information (same gene), but the reality is that considerable morphological change can occur with gene expressions at different times (see bone morphogenic protein for a stark example). Other changes are single base substitutions, as with FOXP2, not the evolution of completely novel binding sites from scratch using a simple mutation and selection. The comparison with ev is absolute and complete bunk. Analogies don't work when they are not analogous.

You are demonstrating the fundamental erroneous assumption from the theory of evolution. Just because living things have genetic similarities does not prove the theory of evolution. You have to show how the transformations by mutation and selection can be accomplished in the time available. This is how precise scientific and mathematical accounting is done. We know that there are at least 10’s of millions of different base differences between human and chimp genomes and that is just in the portions of the genomes that demonstrate homology. You don’t prove your theory with your sloppy speculations.

Ev basically models what the early biosphere could have been like. It has set genome lengths and only allows mutations with no other sharing of genetic material between varying entities. Yet, under these extremely restricted conditions, it shows that information can develop over time. It's relationship to evolution of primates or any animal -- almost zero.

Ev models the fundamental mechanism of mutation and selection and there are numerous real examples that we see today which show that Dr Schneider properly modeled this mechanism. What his model shows is that evolution by this process is profoundly slow when you have multiple selection pressures. Are you saying that mutation and selection was different in the early biosphere than it is now? If you are, you are ignoring reality.

Mutation and selection does not explain these differences. Does it require mutation and selection to achieve the changes you describe? Maybe you should argue these type of differences can be achieved with recombination and selection.

What is your point? You recently told me that no new information could arise from recombination and selection. Yet now you wish to tell me that increased brain size and new communications abilities arise from the very situation that you earlier claimed could not create information? What?

The point is that you evolutionists confuse the mathematical behavior of mutation and natural selection and recombination and natural selection. Recombination and natural selection can achieve rapid morphological changes in short periods of time. Consider the example of canine evolution by recombination and natural selection. You have large morphological differences (including brain size) in a very small number of generations but despite all these morphological changes, they are all still dogs. Stephen J Gould made this same error with his concept of punctuated equilibrium. This concept is applicable to recombination and natural selection not to mutation and natural selection. Darwin made the same error with his observation of finch beaks. The variations in finch beaks were due to recombination events, not due to mutation events. You can not extrapolate these types of events to the transformation of reptiles to birds or humans and chimps from a primate precursor; you don’t have the mathematical scientific basis to do this. Mutation and selection is a far slower process than recombination and selection. Mutation and selection can create new information, recombination and selection does not.

So, let's look at the actual information. FOXP2 underwent a base substitution to become the new gene that it is. So, whoops, mutation and selection can account for that change. The protocadherin story is more complicated but may well simply result from mutation as well. There are desert regions surrounding the gene family that are thought to be involved in regulatory functions. They are probably transcription factor binding sites, etc. that are involved in regulating the expression of this and other local genes. The change in protocadhedrin is not in the protein itself -- that is conserved -- but in those regulatory regions that are considered otherwise non-coding, changing the expression of this protein during development. The big changes between chimp and human brain are in the networks of proteins involved in the developmental process. If you only look at the genes and do not consider the local milieu or the extraordinary differences that arise from alternative splicing the you only will see a bare fraction of what is responsible for the difference between us and chimps.

One speculation after another, is that your idea of a scientific proof?

Mutation and selection is a bookkeeping problem. When you apply these rules of bookkeeping, you can not account for all the genetic differences between living things. In particular, multiple selection pressures slow the evolutionary process. This is a mathematical fact shown by ev and there are numerous real examples of this including the use of combination therapy to treat HIV.

So, you've just shot yourself in the foot? Yes, mutation and selection cannot account for all the genetic differences between living things. That is one of the things I am trying to tell you. Thank you for arguing my side. What this shows is that your "mathematical fact" of ev is no fact at all, but complete bunk. If you cannot account for all the genetic differences by use of your model that uses only mutation and selection, then the answer is clear. The model cannot account for all genetic differences. The model is insufficient. You cannot use the model to argue the impossibility of evolution. You have just proved wrong your entire premise and hung yourself with your own words.

If you can’t account for all the genetic differences between living things by mutation and selection, I haven’t shot myself in the foot; I have shot the theory of evolution in the heart. How are you going to account for these differences?

End of story.

End of the story for the theory of evolution.

I'll get to the rest later. This looks like it will need to be a very long post, though I'm not sure there is much sense in continuing since even you seem to see that your argument is fundamentally flawed. An inadequate model is an inadequate model. The model (ev) was very good for what it was designed to to -- in fact I think it was brilliantly conceived -- but it is, even by your own admission, inadequate for the task you have set it.

You have no shortage for words; you do have a shortage of mathematics. The only thing you have demonstrated so far is that you are ignorant of the mathematics of mutation and selection and that you think you know more about the mathematics of mutation and selection than Dr Schneider and the peer reviewers at Nucleic Acids Research.

Mutation and selection can accomplish small events such as drug resistance with microbes. There are real examples of these phenomena. However, to extrapolate these types of phenomena to the evolution of birds from reptiles or humans and chimps from a primate ancestor by mutation and selection has no mathematical foundation. You simply do not have sufficient number of generations and populations to accomplish all the genetic changes required. In the real world, the books have to balance. In addition to the fact that multiple selection pressures slow down evolution, there are no selection pressures that can evolve a gene from the beginning. You are the one ignoring the real world and you do this by extrapolating mutation and selection far beyond what it is mathematically capable of doing.

Load of bunk. Mutation and selection can accomplish small events, big events, grand events, deathly events, whatever. It all depends on what genes and gene networks are involved. You are again showing your incredibly one-dimensional view of the genome. Single base changes in regulatory genes or in regions for promoter or transcription factors can have a huge impact on morphology. It is absolute and complete misrepresentation to say anything else.

You have a zero-dimensional view of the mathematics of mutation and selection. If you had any knowledge of the mathematics of mutation and selection, you would realize that multiple selection pressures slow the process. You think your speculations will overcome this mathematical fact. Do you think that single base changes in regulatory genes caused the transformation of reptiles to birds? What a strange and contorted view of reality you evolutionists have.

I am not extrapolating mutation and selection beyond what it is mathematically incapable of doing. You seem to have no grasp whatsoever of the actual genome of actual living beings. We have seen huge changes in organisms over time that you seem to think are impossible mathematically. Yet you do not fault the mathematical model? Why? Because you have a preset notion that evolution cannot occur. Schneider based his model on a subset of information from living creatures. He did not model the genomic behavior of all living beings. I'm sure we can contact him about this issue?

Of course you are extrapolating mutation and selection beyond what it is capable of doing. This is a simple bookkeeping problem. You have to account for the differences between the genomes of living things and the mathematics of mutation of selection can not do this. It is you who has the preset notion about evolution and that mutation and selection can accomplish these huge genetic transformations in limited time. You have no mathematical scientific basis for this belief.

Hey, Paul, would you mind asking Schneider if he designed his model to cover all living beings?

Yes Paul, ask Dr Schneider what he has advertised ev to model? In particular, ask him what he was trying to do when he computed the amount of time to evolve a human genome.

You're beginning to screech, Dr. Kleinman. Your argument from a model against reality. That's a truly stupid thing to do.

Oh really, ev doesn’t show how mutation and selection works and that multiple selection pressures slows evolution? Well let’s see, combination therapy of HIV demonstrates this, combination therapy of TB demonstrates this, combination pesticides demonstrates this, combination, combination herbicides demonstrates this, combination rodenticides demonstrates this and let’s not forget that combination cancer therapies demonstrates this. Of course, you have all kinds of mathematical scientific proof that Barney evolved to Big Bird. You are really smart Ichneumonwasp. Too bad that doesn’t extend to the mathematics of mutation and selection.

Where is this mathematics of mutation and selection you are talking about?

Your biases are showing Dr. Kleinman. I said there were plenty of mathematical models of the current theory of evolution, not merely of mutation and selection. You, who are the mathematical genius of the century, are aware of all this work, are you not, Dr. Kleinman? I can barely read a paper on evolutionary theory without being inundated with mathematical modelling of this, that, and the other.

That’s very interesting, does all this mathematical modeling include the modeling of mutation and selection?

I have the mathematics of a peer reviewed and published computer model of mutation and natural selection. Now where is this mathematical cornucopia that forms the foundation of your theory?

You haven't read any of the literature, have you? OK, I'll start posting links in the morning as I pull up individual articles. How many do you want? There are mathematical models galore. You know this. Why are you acting dumb about it?

Feel free to point us to models of mutation and selection that prove your point. As it stands, it appears you don’t understand ev yet. If you did, you would understand how the mathematics of mutation and selection works.

Crossing over does not increase information in a genome; it is simply a rearrangement of existing genes in the gene pool. You not created any new genes.

Pseudogenes, not previously expressed in an organism, now expressed in the presence of a promoter, repeat, rinse. Move transcription factor to new gene so that it is expressed in new milieu and suddenly the protein balance is changed. We're talking morphological changes here, Dr. Kleinman. You know, the stuff that natural selection actually works on.

So are you arguing this is how reptiles evolved to birds? How did all these pseudogenes come into existence? What is the selection pressure that gives rise to pseudogenes?

What you continue to have difficulty with is the mathematics of mutation and selection. The massive number of differences between reptile and bird genomes can not be accomplished by mutation and selection. Not only is there no selection pressure that would do this, there is no way to account for all the required changes needed by mutation and selection.

Well gosh and golly jeepers, name me one person who actually thinks that all the changes between reptile and bird occurred by simplistic models of mutation and selection. I'd actually like to meet this mythical creature rarer than a phoenix-unicorn hybrid. Your mathematics are useless in this situation, Dr. Kleinman. Just how far do you intend to carry this straw man?

Oh, now I understand your theory of evolution. Reptiles evolved to birds by a complex, mathematically inexplicable mechanism. How could anyone doubt your scientific explanations of the theory of evolution?

One unique gene difference between birds and reptiles is enough to prove the impossibility of evolution. What is the selection pressure that would evolve this unique gene?

What? I have no idea what you are on about now.

What is the selection pressure that would evolve a gene from the beginning?

This seems to be the sum total of the evolutionist argument, you don’t know how it happened but you know it did. Well, I know it didn’t happen by mutation and selection, ev shows how slow this process is and that the theory of evolution by mutation and selection is mathematically impossible.

Well, isn't that nice. We agree on something. I know it didn't happen according to the simple outline you propose too. Evolution is much more complex than simple mutation and selection. There is no argument here.

Yes, we all now know that the theory of evolution is explained by a complex, mathematically inexplicable mechanism. Your inexplicable explanations obscurely clarify your consistently illogical theory. Is this the best argument for your theory of evolution, which is it is mathematically inexplicable?

What still hasn’t sunk in with you is that recombination without error can not increase information in the gene pool and that recombination with natural selection can cause the loss of information in the gene pool due to loss of alleles.

Oh, really? Yet up above you said that I should be arguing for recombination with selection for the development of the human brain. I guess the human brain is just a degenerate version of something that has lost information from that wonder of the world, the human-chimp common ancestor. I'll get the press on the line and let them know.

Recombination and natural selection is a rapid mathematical (microevolutionary) mechanism. This is a sorting problem with far fewer items (alleles) to sort where as mutation and selection is a far slower mathematical (microevolutionary) mechanism. This is a sorting problem with far more items (mutations) to sort.

Really now, do you think this occurs with reproduction? You are now extrapolating the production of immunoglobins to reproduction. And do you want to explain how coping promoters all over the place speeds up the evolutionary process?

Didn't even mention immunoglobulins or hypervariable regions, but we could go there next. How do I explain it? I already have. You obviously didn't understand. Do you know what a promoter region is? Do you know what a transcription factor site is?

Now you make this ridiculous extrapolation. Why do children have to be immunized if parents have been immunized?

If a promoter is placed near a pseudo gene, then that pseudogene can lose its paltry pseudo status and join the rest of the club in the smoking car, the place where all the big boy genes hang out.

Oh, now I understand how reptiles evolved into birds.

Copy a gene and you have two copies of the same gene. A new gene requires mutation. So now you have a copy of a gene that is slightly altered and low and behold, it performs an entirely new function like growing feathers on a lizard. It requires mutations to make a new gene and ev shows this is a profoundly slow process even if you have a selection process that could make the new gene and you don’t. You are in complete denial of the mathematics of mutation and selection and how it works. Study ev and learn how the mathematics of mutation and selection works instead of making your wild unscientific extrapolations.

I'm in complete denial of your lunacy for thinking you have "the mathematics of mutation and selection". Copy a gene and its expression can increase. It can also be associated with different transcription factors so that it is expressed at different times. You know, the whole proteomics bit. Making completely different morphologies -- having genes expressed in different places, different times.

Let’s not forget that you have the inexplicably complex mathematics to explain your theory. Dr Schneider’s simple mathematics which shows that multiple selection pressures slow evolution can not stand up to your inexplicably complex mathematics. Are different transcription factors the new inexplicable explanation for the evolution of reptiles to birds?

And yes, single gene mutations in newly copied genes works too. But, again, there is no analogy to ev, since ev models numerous changes in the same place and all those changes have to fit a pre-determined state. The new mutation in a gene copy only has to advance survival. Ev does not model that behavior.

Oh, now gene duplication is your inexplicable explanation for the evolution of reptiles to birds? Could you explain to us the selection pressure that gave the original gene?

A gene is to evolve. The first base in the sequence for the gene is laid down on the genome. One base codes for nothing so there is nothing for natural selection to act upon. A second base added by random chance is laid down in the sequence. Still nothing to code for, natural selection can not act on this sequence. A third base in the sequence is laid down. You now have enough bases to form a codon for a single amino acid. A single amino acid has no functional use so there is still nothing for natural selection to act upon. So bases must be added randomly until you have a long enough sequence of bases to produce a functional polypeptide and then natural selection can act. Adding bases randomly yield probabilities so infinitesimally small that evolution is mathematically impossible.

What an interesting just so story.

I’m sure you have an inexplicably complex explanation for how this all happened.

And if we begin with peptides that serve as templates for RNA? There is already a relationship between amino acid and RNA in that scenario. The other way around makes no sense -- starting with RNA and/or DNA and expecting it to code for an amino acid. That is a silly story.

Are you ready to give us your inexplicable explanation for what the components of the DNA replicase system were doing before DNA could be replicated? I’d like to hear your inexplicable explanation for what helicase and gyrase were doing.

Simple enough, tell us how recombination without error can create new genes and I’ll tell you how recombination and natural selection can cause the loss of alleles. Of course you can’t tell us how recombination without error can create new genes but I can tell you how recombination and natural selection can cause the loss of alleles.

Are you an ostrich with its head in the sand. I've already given you several scenarios for this and you pretend that I haven't. Try something new. Your screeching is growing old.

Which one of your scenarios gives us the inexplicable explanation of how a gene evolved from the beginning? The only hole in the sand we have is the one where we are burying the remains of the theory of evolution.

If you had read the paper beyond the abstract you would realize that you are limiting the scope of ev because it suits your belief system, not because that was the intention of Dr Schneider. If you had read these threads you would have seen from the very beginning that I acknowledged that you can gain information by mutation and selection. The only shame in this is that you think you can understand the mathematics of mutation and selection without doing your homework. Read Dr Schneider’s works completely and read these threads completely, otherwise you reveal that you are superficial in your analysis, of course, that is the only type of analysis the theory of evolution can stand up to.

Um, no. I have read the paper completely, just today again. I see in it just how wrong you are, as reflected in some responses above. You, of course, will either not understand them or will pretend not to understand them, or will neglect the issue and continue to put your head in the sand. Whatever you want bro.

Then why do you ask Paul what Dr Schneider’s intention for ev are? Dr Schneider clearly published his intentions for ev. I wonder why Dr Schneider is not still advertising his model.

So, how about this. You publish this excellent work of yours. Put up now or shut up. You have the answer, so you think. It's time for peer review. I can't wait for the chuckles.

Now this is not a very nice thing to say about James Randi Educational forum. You don’t think this is a valid place to discuss these ideas? You don’t seem to value the peer review process of the editors of Nucleic Acids Research did for the ev computer model. You discredit Dr Schneider’s work which he describes as realistic and which went through a peer review process. Which mathematically challenged evolutionists peer reviewers do you suggest I use.

But, frankly, no one here needs me to repeat the same arguments that you have ignored since the beginning of this thread. This whole fiasco reads -- ev shows that evolution couldn't happen; no, you're wrong and here's the evidence to show where you are wrong; but ev shows that evolution couldn't happen; no, you're wrong and here's more evidence to show where you are wrong; rinse, repeat.

And ev shows why it couldn’t happen. That is multiple selection pressures slow the evolutionary process. Mutation and selection is a profoundly slow mechanism for change and information acquisition. Evolutionists have inappropriately extrapolated this mechanism to the huge number of genetic changes required to make the transformation of reptiles to birds or humans and chimpanzees from a primate precursor. You simply do not have enough generations to accomplish the huge number of genetic changes. Of course you have an inexplicably complex explanation of how it does occur. Now that works as well as kjkent1’s string cheese theory of evolution.

My only contribution was to argue against your use of HIV. I've served that purpose. You are now returning to arguments that began on page 2 of the thread and needn't be rehashed.

And your argument against my use of combination therapy for the treatment of HIV as an example of how multiple selection pressures slow the evolution of resistant strains of the virus completely failed. Ev demonstrates how multiple selection pressures slow evolution and combination therapy for the treatment of HIV demonstrates this in reality. Of course, your argument that the evolution of reptiles to birds by an inexplicably complex mathematical mechanism is a striking example of the power of evolutionary logic. I put this argument on par with the string cheese theory of evolution.

Peer review. A wonderful tradition. It works.

And what is your problem with writing about this topic in the James Randi Educational Forum? You don’t show much respect for the ev model despite the fact that it was peer reviewed.

Yes, and this is the equation that does this:

sv += Math.abs(valuation[p] - threshold);

valuation[p] (the value of the dot product of the weight matrix with the positions on the genome) will almost always be a small number in the nonbinding site region of the genome. This is equivalent of ignoring the spurious binding in the nonbinding site region.

Why do you always speak in absolutes when things aren't absolute? At the beginning of a run, the valuations of loci are almost immediately all less than the threshold. I'd be happy to discuss this further if someone can refresh my memory about Unnamed's selection method, but I don't think he's ignoring anything.

Here are the changes Unnamed made to ev:

// This constructor is used to create creatures at the beginning

// of a run. Each creature's chromosome is random.
@@ -710,19 +710,25 @@

gene = param.getInt(Param.spuriousGene),
nongene = param.getInt(Param.spuriousNongene);

- mistakes = spuriousHits = 0;
+ float sv;
+ sv = mistakes = spuriousHits = 0;
for (int p = 0; p <= chromosome.length - width; ++p) {
if ((valuation[p] = siteValuation(p, width)) >= threshold) {
if (!siteInd[p]) {
if (p < availablePos) mistakes += gene; else mistakes += nongene;
+ sv += Math.abs(valuation[p] - threshold);
++spuriousHits;
}
} else {
- if (siteInd[p]) mistakes += missed;
+ if (siteInd[p]) {
+ mistakes += missed;
+ sv += Math.abs(valuation[p] - threshold);
+ }
}
}

- sortValue = mistakes; // We will sort on the mistake
+ sortValue = (int)(Math.min(sv, Integer.MAX_VALUE));
+ //sortValue = mistakes; // We will sort on the mistake
// count, unless randomized.
}

Why don’t you post a version of ev with these changes online so everyone can study the behavior of these changes?

He must have meant that only variations that support the theory of evolution should be investigated. Paul, I love it when you squirm.

He must have meant that? You're a psychologist now?

Paul, Dr Schneider was quite clear what he intended ev to be used for when he said the following:

Variations of the program could be used to investigate how population size, genome length, number of sites, size of recognition regions, mutation rate, selective pressure, overlapping sites and other factors affect the evolution.

You don’t have to be a psychologist to understand what Dr Schneider was saying here. When you study the behavior of these parameters you find the following:

Population sizes reduce the generations for convergence but at a decreasing rate with increasing population.

Genome length increases the generations for convergence at an increasing rate with increasing population.

Number of sites has a slight decreasing effect on the generations for convergence.

Size of recognition region has only a small effect on the generations for convergence except that it appears that larger recognition regions allow larger genomes to converge.

Mutation rate has a paraboloid behavior when tested over a wide range but with realistic mutation rates the behavior is fairly linear. That is mutation rate is inversely proportional to the generations to the generations for convergence.

Selection pressures, ev converges much more rapidly with single selection pressures than with all three selection pressures.

Overlapping sites were not investigated. Hey Ichneumonwasp, maybe that’s how reptiles evolved into birds.

Just what does ev show now? You certainly aren’t saying the same thing that the author of the program has said which is unfortunate because I think he got this mathematical model of mutation and selection correct. Since random point mutation and natural selection represents 1/100 of 1% of your theory of evolution, care to tell us what the other 99.99% is?

Everything else.

That must be the inexplicably complex mathematical stuff that Ichneumonwasp is talking about.

Very revealing! Kleinman is only a computer simulation/model of a creationist, and was never intended to model the whole landscape of creationist nonsense. That explains why he seems to be failing the Turning Test: no matter how much new information evolutionists present, he just keeps repeating the same old lies. He's a creationist-bot.

Just call me HAL, pussycat.

It seems that the Kleinman Simulator is modeling the entire landscape of creationist thought. this is a much simulation task to acheive since you only need to code in "God did it."

I keep telling you that I am not proving that “God did it.” I’m only showing you that “evolution didn’t do it.” As a little bonus, we are learning how mutation and selection really works. We need to thank Dr Schneider for his very good peer reviewed mathematical model of mutation and selection and Paul’s very good online java version of the model. Now if we can only get you evolutionists to believe your own model.

You have to sift through all the "social evolution" garbage, but there are plenty of applicable sources, especially those that relate to the mathematical modelling of alternative means of gaining information (other than mutation and selection).

So not only do I have to sift through your stuff, I have to sift through all this stuff? You are the one who said there are all kinds of mathematics that supports your arguments of mutation and selection. Post a URL and quotes from the URL that support your arguments.

Also, I particularly liked the artice THE ORIGIN OF NEW GENES: GLIMPSES FROM THE YOUNG AND OLD which has so many beautifully detailed examples and even observed instances of spontaneous de novo gene creation. I think creationists are obliged to dispute the article point by point to remain in the game.

Ok, let’s start with this one:

De novo origination: a coding region originates from a previously non-coding

genomic region

and this:

Rare for whole gene origination; might not be rare for partial gene origination

I think evolutionists need to explain point by point how the original hemoglobin gene, insulin gene, Krebs cycle genes, coagulation cascade genes, DNA replicase genes… arose de novo in order to remain in the game. Is that fair pussycat?

 

[Ichneumonwasp]

Really, what’s the problem with comparing mutation and selection with mutation and selection?

What's the problem with comparing a generation and a generation?

You were trying to compare one generation of HIV with millions of reproductions of the virus with one generation of ev with a single reproduction of the genome.

No, I wasn't. I was pointing out the errors in your logic. You're just comparing mutation and selection. OK. I'm just comparing generation and generation. Same words, different ideas behind what actually transpires.

So what is your point? The primordial world began with all kinds of sequences of bases with all kinds of information?

My point is that ev models a possibility at the onset of life, not the creation of new information in already existing genes that need to alter to escape a particular selection pressure. How could you fail to see that? You are comparing apples and oranges.

HIV and three selection pressures cannot be modelled by ev. We leave aside again the issue of there being more than three selection pressures and concentrate on triple therapy and its effect on HIV. When triple therapy is used and the potency of that therapy is not terrible great, resistance develops and it develops relatively quickly. Resistance develops by mutations within an already existing gene that must alter in a few places in order to escape the applied selection pressures. This is not what ev models.

Ev begins with random bases and demonstrates that pre-defined information can be created by the same forces that result in drug resistance for HIV.

Apples. Oranges. You lose.

 

[kleinman]

Annoying Creationists

The forum editor modified the goalposts so here it is again in proper format.
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[kleinman]

Annoying Creationists

Really, what’s the problem with comparing mutation and selection with mutation and selection?

What's the problem with comparing a generation and a generation?

It’s a huge problem comparing generation with generation when one generation of HIV has up to 10^9 reproductions and ev’s generation has only a single reproduction per creature. One point mutation in ev is equivalent to one point mutation in an HIV virus.

You were trying to compare one generation of HIV with millions of reproductions of the virus with one generation of ev with a single reproduction of the genome.

No, I wasn't. I was pointing out the errors in your logic. You're just comparing mutation and selection. OK. I'm just comparing generation and generation. Same words, different ideas behind what actually transpires.

It is your logic and language that is inconsistent. What you are describing as a generation with HIV is not mathematically equivalent to a generation with ev, however a point mutation of an HIV virus is equivalent to a point mutation in ev. You have to take into account that a generation with HIV has up to 10^9 viral reproductions. You can’t use semantics to alter the mathematics of mutation and selection.

So what is your point? The primordial world began with all kinds of sequences of bases with all kinds of information?

My point is that ev models a possibility at the onset of life, not the creation of new information in already existing genes that need to alter to escape a particular selection pressure. How could you fail to see that? You are comparing apples and oranges.

Ev models the mathematics of mutation and selection. It shows that multiple selection pressures slow the evolutionary process and there are numerous real examples of this phenomenon. This is how mutation and selection works.

HIV and three selection pressures cannot be modelled by ev. We leave aside again the issue of there being more than three selection pressures and concentrate on triple therapy and its effect on HIV. When triple therapy is used and the potency of that therapy is not terrible great, resistance develops and it develops relatively quickly. Resistance develops by mutations within an already existing gene that must alter in a few places in order to escape the applied selection pressures. This is not what ev models.

Ev models three selection pressures, they are missed binding sites where they should be constitutes an error which affects the fitness of that creature to reproduce, spurious binding sites in the gene region which constitutes an error which affects the fitness of that creature to reproduce and spurious binding sites in the non-binding site region which constitutes an error which affects the fitness of that creature to reproduce. Set any two of the three selection conditions to zero and the remaining selection condition evolve much more quickly than all three selection conditions simultaneously. None of these selection conditions cause extinction. This is exactly analogous to combination therapy to treat HIV vs monotherapy. In the former, the evolution of resistant strains of the virus is much slower than the evolution of resistance to monotherapy alone. Ev and combination therapy of HIV are analogous cases of mutation and selection. Ev is a mathematical simulation and combination therapy of HIV is a real case of this phenomenon.

Ev begins with random bases and demonstrates that pre-defined information can be created by the same forces that result in drug resistance for HIV.

It doesn’t matter that ev starts with a random genome. What matters is that at the end of the selection process you have sequences of bases that satisfy the selection conditions. What ev shows is that satisfying all three selection conditions simultaneously slows the evolution process. You don’t understand the mathematics of mutation and selection. You aren’t even in the game yet.

 

[Ichneumonwasp]

So what is your point? The primordial world began with all kinds of sequences of bases with all kinds of information?

That was the whole friggin' point.

If you want to compare what ev does to the "reality" of HIV and triple therapy, then HIV would be required to create de novo all of its genes in the presence of three selection pressures. That is what ev models.

HIV already has its genes. It only has to solve the problem of three selection pressures applied to one, or two depending on the regimen, issues. That is the case with almost everything in evolution -- solving one problem at a time (that is, if we define a selection pressure as a problem), not recreating a new genome with every "experiment".

Apples. Oranges.

ETA
There are two big issues. The one is that generally only one or two sites change in any length of time in nature, not multiple sites over the genome. The other is that the site changes in evolution only need to escape the selection pressure. They needn't look like a pre-arranged "binding site".

 

[kleinman]

Annoying Creationists

So what is your point? The primordial world began with all kinds of sequences of bases with all kinds of information?

That was the whole friggin' point.

Did all this information come about by selection or are we talking about random combinations of bases?

If you want to compare what ev does to the "reality" of HIV and triple therapy, then HIV would be required to create de novo all of its genes in the presence of three selection pressures. That is what ev models.

Why would you assume that? According to Paul, ev does not even evolve binding sites de novo.

HIV already has its genes. It only has to solve the problem of three selection pressures applied to one, or two depending on the regimen, issues. That is the case with almost everything in evolution -- solving one problem at a time, not recreating a new genome with every "experiment".

Where did you come up with this notion? There are numerous selection pressures acting on living things all the time. If you think evolution only has to solve one problem at a time, describe the problem of evolving a reptile to a bird.

You still have no idea of the mathematics of mutation and selection. I’m not sure whether it’s because the mathematics of ev is too difficult for you to understand or whether it’s due to you are in denial of what it shows.

Apples. Oranges.

The theory of evolution is that, nuttier than a fruit cake.

There are two big issues. The one is that generally only one or two sites change in any length of time in nature, not multiple sites over the genome. The other is that the site changes in evolution only need to escape the selection pressure. They needn't look like a pre-arranged "binding site".

You are correct that there are two big issues but you are wrong about what they are. The two big issues are the number of selection pressures, the more pressures the slower the evolutionary process and the other is the genome length, the longer the genome, the slower the evolutionary process.

If a binding site does not change in nature over time it most likely due to that creature being selected out immediately if the site is altered. What makes you think any mutation escapes the effects of selection?

 

[kjkent1]

That’s not an accurate statement kjkent1. I take Dr Schneider’s ev work very seriously. It is the best mathematical model of mutation and selection available and it properly captures the mathematics of mutation and selection. Now your string cheese theory of evolution I also take seriously, that is seriously silly.

You have an poor understanding of the important distinctions between the terms "serious" vs. "silly," in my view.

Ev does capture the basic mathematics of mutation and selection. However, ev does not model any mutational mechanisms other than random point mutation, and ev does not make any attempt to accurately weight the selective value of any mutations which occur, based upon how such mutations would affect a real-world living organism.

And, without both of the above-stated issues being resolved, it is unscientific for you to conclude that ev is too slow.

Considering your esteemed credentials, I wonder why you would voluntarily choose to draw an unscientific conclusion. Perhaps, because you have a personal bias?

You may respond that Dr. Schneider has drawn similar unscientific conclusions. However, that is irrelevant. If you value the scientific method, and you believe that Dr. Schneider has been unscientific in his approach, then your goal should be to demonstrate why Schneider's approach is unscientific -- not to use what you view as his unscientific behavior to justify your own similar actions.

To the extent that ev is too slow, using random point mutation and a very simple selective method, I would agree with you that the conclusion that ev proves the entire human genome could evolve within the time available since life purportedly appeared on Earth, is a stretch.

However, the stated purpose of ev in the NAR paper was to demonstrate information gain, via random mutation and natural selection, and you admit that ev does prove this.

That really should end the discussion. However, you continue to try to extrapolate ev to disprove all evolution as impossible. This activity is unscientific, unless you first accurately model all of the other mutational mechanisms and selective behaviors -- and ev remains too slow.

Your conclusion is simply unsubstantiated, because you haven't done any science to support it. Meanwhile, your competitors continue to do research and publish their findings. So, while you sit alone in your room, certain that you have entirely destroyed the theory of evolution, in reality, you fall further and further behind in the race.

And, that, my friend, is REALLY silly.

 

[Ichneumonwasp]

Did all this information come about by selection or are we talking about random combinations of bases?

I haven't the slightest idea how you are making the connections that you seem to be making. The whole friggin' point is that you are comparing apples to oranges.

Why would you assume that? According to Paul, ev does not even evolve binding sites de novo.

I'm not assuming it. That is what ev does. It begins with random collections of bases and evolves information in pre-specified sites. What constitutes information is a site that can bind a pre-selected signal. The analogy with HIV would be the de novo creation of new genes, not the alteration of an already existing one.

Where did you come up with this notion? There are numerous selection pressures acting on living things all the time. If you think evolution only has to solve one problem at a time, describe the problem of evolving a reptile to a bird.

We aren't talking about reptile to birds here. We are talking about HIV, the use of triple therapy, and your contention that this represents the perfect example of how ev treats three selection pressures. HIV has to get past three drugs -- it has to solve the issue of forming a new reverse transcriptase that works and is not affected by those three drugs. It does so quickly.

This is your analogy, Dr. Kleinman, not mine.

the longer the genome, the slower the evolutionary process.

Haven't you ever asked yourself the question of why this is the case with the ev program?

 

[kleinman]

Annoying Creationists

That’s not an accurate statement kjkent1. I take Dr Schneider’s ev work very seriously. It is the best mathematical model of mutation and selection available and it properly captures the mathematics of mutation and selection. Now your string cheese theory of evolution I also take seriously, that is seriously silly.

You have an poor understanding of the important distinctions between the terms "serious" vs. "silly," in my view.

Let’s see if I can help you with the word serious. Try the word “earnest” instead of “serious”. Dr Schneider has made an earnest application of the mathematics of mutation and selection while you have made earnestly silly application of the string cheese theory to mutation and selection.

Ev does capture the basic mathematics of mutation and selection. However, ev does not model any mutational mechanisms other than random point mutation, and ev does not make any attempt to accurately weight the selective value of any mutations which occur, based upon how such mutations would affect a real-world living organism.

You are correct on both of these points. When considering other mutation mechanisms, the question is whether these other mutation mechanisms will significantly alter the behavior of the mathematics of mutation and selection process. I don’t believe it will for several reasons. Point mutations are the least destructive of mutations as well as the most common type of mutation. They don’t cause frame shifts which alter large numbers of codons. If you think that other mutation mechanism will somehow accelerate the mutation selection process, feel free to prove this. With respects to Dr Schneider’s selection scheme, it is very forgiving. What I mean by this is that you don’t have the possibility of extinction. The weight factors are not tied to survival of a creature. There are many examples of single mutations which cause the death of the creature with that mutation, yet ev does not have this effect. Including these types of features in the model would only slow evolution more so. In addition, how would you formulate the selection process that would evolve a gene de novo? There is no such selection process.

And, without both of the above-stated issues being resolved, it is unscientific for you to conclude that ev is too slow.

That’s an easy one. Introduce whatever feature you want in the model and see whether you can speed up evolution sufficiently and prove your case. Since ev is already showing that it is the multiple selection conditions which slow the evolution process, the changes you advocate will not alter the fundamental mathematics already revealed.

Considering your esteemed credentials, I wonder why you would voluntarily choose to draw an unscientific conclusion. Perhaps, because you have a personal bias?

Everybody has biases. The question is whether I am drawing my conclusion based on these biases or am I drawing my conclusions based on the results from ev and the numerous real examples which show that multiple selection pressures slow evolution.

You may respond that Dr. Schneider has drawn similar unscientific conclusions. However, that is irrelevant. If you value the scientific method, and you believe that Dr. Schneider has been unscientific in his approach, then your goal should be to demonstrate why Schneider's approach is unscientific -- not to use what you view as his unscientific behavior to justify your own similar actions.

I have demonstrated why Dr Schneider improperly extrapolated the evolution of a human genome. You evolutionists refuse to acknowledge this. Instead, you look for ways to parse words to justify this type of unscientific approach. That said, Dr Schneider’s underlying simulation has properly captured the mathematics of mutation and selection. In particular, the effect of multiple selection pressures is properly revealed.

To the extent that ev is too slow, using random point mutation and a very simple selective method, I would agree with you that the conclusion that ev proves the entire human genome could evolve within the time available since life purportedly appeared on Earth, is a stretch.

That’s a bit of an understatement. Simply using a realistic mutation rate of 10^-6 instead of 1 mutation per 256 bases per generation in Dr Schneider’s published case makes his estimate of 1 billion years for the evolution of a human genome go to 4 trillion years. And what real living thing has a genome length of 256?

However, the stated purpose of ev in the NAR paper was to demonstrate information gain, via random mutation and natural selection, and you admit that ev does prove this.

Kjkent1, you can’t parse away this statement from the NAR paper:

Variations of the program could be used to investigate how population size, genome length, number of sites, size of recognition regions, mutation rate, selective pressure, overlapping sites and other factors affect the evolution.

That really should end the discussion. However, you continue to try to extrapolate ev to disprove all evolution as impossible. This activity is unscientific, unless you first accurately model all of the other mutational mechanisms and selective behaviors -- and ev remains too slow.

Only evolutionist cultists would end the discussion here. I have no objection to adding any feature to ev. Let’s see if it changes any of my conclusions.

Your conclusion is simply unsubstantiated, because you haven't done any science to support it. Meanwhile, your competitors continue to do research and publish their findings. So, while you sit alone in your room, certain that you have entirely destroyed the theory of evolution, in reality, you fall further and further behind in the race.

My conclusions are unsubstantiated except for the results from ev and numerous real examples of these results.

And, that, my friend, is REALLY silly.

Would you pass the red herring, string cheese and whine please.

Did all this information come about by selection or are we talking about random combinations of bases?

I haven't the slightest idea how you are making the connections that you seem to be making. The whole friggin' point is that you are comparing apples to oranges.

Ah yes, the gap theory of evolution, is there anyplace you don’t have a gap in your theory?

Why would you assume that? According to Paul, ev does not even evolve binding sites de novo.

I'm not assuming it. That is what ev does. It begins with random collections of bases and evolves information in pre-specified sites. What constitutes information is a site that can bind a pre-selected signal. The analogy with HIV would be the de novo creation of new genes, not the alteration of an already existing one.

Ev does not evolve binding sites de novo according to Paul.

Where did you come up with this notion? There are numerous selection pressures acting on living things all the time. If you think evolution only has to solve one problem at a time, describe the problem of evolving a reptile to a bird.

We aren't talking about reptile to birds here. We are talking about HIV, the use of triple therapy, and your contention that this represents the perfect example of how ev treats three selection pressures. HIV has to get past three drugs -- it has to solve the issue of forming a new reverse transcriptase that works and is not affected by those three drugs. It does so quickly.

HIV evolves resistance much more quickly if monotherapy is used. In addition you argued that evolution only has to solve one problem at a time, so why not answer what the mutation condition is that would evolve reptiles to birds?

This is your analogy, Dr. Kleinman, not mine.

The use of combination therapy for HIV is a good analogy to what ev shows. Don’t you think so?

the longer the genome, the slower the evolutionary process.

Haven't you ever asked yourself the question of why this is the case with the ev program?

Of course I have, and if you had read this thread, you would know what I have to say about it. Let’s hear your explanation.

 

[joobz]

Let’s see if I can help you with the word serious. Try the word “earnest” instead of “serious”. Dr Schneider has made an earnest application of the mathematics of mutation and selection while you have made earnestly silly application of the string cheese theory to mutation and selection.

You are correct on both of these points. When considering other mutation mechanisms, the question is whether these other mutation mechanisms will significantly alter the behavior of the mathematics of mutation and selection process. I don’t believe it will for several reasons. Point mutations are the least destructive of mutations as well as the most common type of mutation. They don’t cause frame shifts which alter large numbers of codons. If you think that other mutation mechanism will somehow accelerate the mutation selection process, feel free to prove this. With respects to Dr Schneider’s selection scheme, it is very forgiving. What I mean by this is that you don’t have the possibility of extinction. The weight factors are not tied to survival of a creature. There are many examples of single mutations which cause the death of the creature with that mutation, yet ev does not have this effect. Including these types of features in the model would only slow evolution more so. In addition, how would you formulate the selection process that would evolve a gene de novo? There is no such selection process.

That’s an easy one. Introduce whatever feature you want in the model and see whether you can speed up evolution sufficiently and prove your case. Since ev is already showing that it is the multiple selection conditions which slow the evolution process, the changes you advocate will not alter the fundamental mathematics already revealed.

Everybody has biases. The question is whether I am drawing my conclusion based on these biases or am I drawing my conclusions based on the results from ev and the numerous real examples which show that multiple selection pressures slow evolution.

I have demonstrated why Dr Schneider improperly extrapolated the evolution of a human genome. You evolutionists refuse to acknowledge this. Instead, you look for ways to parse words to justify this type of unscientific approach. That said, Dr Schneider’s underlying simulation has properly captured the mathematics of mutation and selection. In particular, the effect of multiple selection pressures is properly revealed.

That’s a bit of an understatement. Simply using a realistic mutation rate of 10^-6 instead of 1 mutation per 256 bases per generation in Dr Schneider’s published case makes his estimate of 1 billion years for the evolution of a human genome go to 4 trillion years. And what real living thing has a genome length of 256?

Kjkent1, you can’t parse away this statement from the NAR paper:


Only evolutionist cultists would end the discussion here. I have no objection to adding any feature to ev. Let’s see if it changes any of my conclusions.

My conclusions are unsubstantiated except for the results from ev and numerous real examples of these results.

Would you pass the red herring, string cheese and whine please.

Ah yes, the gap theory of evolution, is there anyplace you don’t have a gap in your theory?

Ev does not evolve binding sites de novo according to Paul.

HIV evolves resistance much more quickly if monotherapy is used. In addition you argued that evolution only has to solve one problem at a time, so why not answer what the mutation condition is that would evolve reptiles to birds?

The use of combination therapy for HIV is a good analogy to what ev shows. Don’t you think so?

Of course I have, and if you had read this thread, you would know what I have to say about it. Let’s hear your explanation.

no new lies. very, very dull. Let me know when you do something different, like tell the truth.
Until then, here's a new image.