Annoying creationists

[Paul C. Anagnostopoulos]

Sometimes these annoying creationists just piss me off:

http://www.evolutionisdead.com/forum/viewtopic.php?p=11670&sid=3406e76df02b7fb9f60af262a63c3a63#11670

~~ Paul

[pounce]

sometimes?

you are more generous than i am.

[LostAngeles]

Aww, I thought this was going to be on ways to ignore them and I was going to suggest the archaeological record! Damn it!

[joobz]

Hi Paul, can you cater to my laziness and briefly describe the 16 binding site arguement they are making?

Are they considering mutations in transcription factors? If you consider these proteins to be sources of mutation, HUGE changes in phenotype can be expected. So, I don't see how punctuated rapid evolution is not explainable at a genetic level.

[Paul C. Anagnostopoulos]

That entire thread is a discussion of the simulation of the evolution of genetic binding sites by the Ev program, described here:

http://www.lecb.ncifcrf.gov/~toms/paper/ev/

Kleinman is attempting to convince us that Ev demonstrates that there was not enough time for binding sites to develop. Actually, his thesis is that there was not enough time for macroevolution to occur. What that has to do with genetic binding sites I cannot imagine. He claims that various results that we got from running experiments with Ev support his thesis. He throws around numbers like 4^1000.

That's all well and good. He can discuss this if he wants. But I really get annoyed when he starts misrepresenting what I said.

~~ Paul

[joobz]

Thanks Paul.
not knowing the generational life span of the first organisms to develop, this is a pretty weak argument. Presumably, a lot of the initial life forming molecules were a series of microenvironment biochemical reactions. In these settings, there would be a ton of binding site type generational experiments that could have occured with unknown kinetics.

We don't know if life started as prions that assembled into viruses that started to incorporate dna... In such a series, DNA would only be selected if it possessed a binding. As such, there wouldn't be a random generation of binding sites.


Oh well. I'll give him this much, It is interesting to think how fast life did progress in relation to the span of the earth.

[CapelDodger]

Aww, I thought this was going to be on ways to ignore them and I was going to suggest the archaeological record! Damn it!
I also hoped it was about ways to annoy creationists. I'll sign up for that, I thought. No such luck.

Creationists are impenetrable, much like Trotskyists and ... lets take a very long list as read.

eta : Catholic apologists are high on that list. I shouldn't let them off without a mention.

[CapelDodger]

... this is a pretty weak argument.
Get outa here! A weak argument from a creationist? Heaven forbid! :)

[CapelDodger]

not knowing the generational life span of the first organisms to develop, this is a pretty weak argument. Presumably, a lot of the initial life forming molecules were a series of microenvironment biochemical reactions. In these settings, there would be a ton of binding site type generational experiments that could have occured with unknown kinetics.
This is something creationists/IDists miss. They start from the unlikelihood of life as it is, ignoring the astronomical number of equally unlikely systems that didn't make it but might have. At the base of their thinking, IMO, is the assumption that life was meant to be as it's turned out, specifically with humans as its crowning achievement. From that initial assumption of meaning ID necessarily derives.

We don't know if life started as prions that assembled into viruses that started to incorporate dna... In such a series, DNA would only be selected if it possessed a binding. As such, there wouldn't be a random generation of binding sites.
Viruses are actually very advanced parasites, they need cellular mechanisms to expolit. They're DNA renegades.

The prion thing is more apt. Prions have a catalytic effect which reproduces the prion. Pre-cellular proto-life (or whatever) must have had the same kind of catalytic effect, one that acted to reproduce the original, randomly-generated catalyst. Not necessarily by one step; the catalyst could produce a different catalyst which in turn produced the original, or produced yet another catalyst which produced the original ... The circular chain can get indefinitely long in theory, although there are obvious practical constraints. The players need to be kept in reasonably close proximity, for instance. In life as we know it the cell does that.

We may never know exactly how it happened, but I like Black Smokers as a good bet for the location. They're hugely fractal, have vast numbers of tiny niches that could confine sets of quite complex molecules, the walls of the niches could themselves have a catalytic effect, they sit in the middle of a very steep energy gradient (life is all about the energy gradient) and there all sorts of energy-rich chemical building-blocks streaming through that could eddy into the niches. The complex molecules could seep out and congregate again in other niches. If the reproduction was inexact - which it surely would be - evolution by natural selection kicks in. Before you know it we've got income tax and rice-pudding.

It could be happening today. Potential chemical ancestors of life might be popping up every day, every hour. What our chemical ancestors didn't have was predation by established life-forms. Newbies are toast these days.

Oh well. I'll give him this much, It is interesting to think how fast life did progress in relation to the span of the earth.
It is indeed. To me it speaks of the likelihood - not to say inevitabliity - of life emerging where it can, rather than the IDers' unlikliehood crutch.

[CapelDodger]

Between "quote" and "post reply" everything went frickin' weird. Is this the "change for the sake of it" event I've been dreading?

[Soapy Sam]

It's the technillogical Singularity.

[CFLarsen]

Sometimes these annoying creationists just piss me off:

http://www.evolutionisdead.com/forum/viewtopic.php?p=11670&sid=3406e76df02b7fb9f60af262a63c3a63#11670

~~ Paul

Down, boy! Down! :D

[alfaniner]

I posted the Top Ten list from the latest Commentary on a board where people brought up a new thread every few hours, it seemed. Totally killed all discussion of it.

[CapelDodger]

I hate change for change's sake :mad: .

[CapelDodger]

I only posted that last so that I can add it to my sig. :)

[fuelair]

Rats, I came looking for ways to annoy them.

[Paul C. Anagnostopoulos]

I hate change for change's sake.
Why? Change is good for you.

~~ Paul

[Zep]

Not...LOOSE Change...?? :eek:

[CapelDodger]

Why? Change is good for you.

~~ Paul

One moment you've "Alive" status, the next it's changed to "Dead", no obvious benefit there. One day your best girl adores you, the next she's run off with a lawyer. Not all change is good, and I happen to be a rather conservative chap. I'm even nostalgic for the Cold War (as least you knew where you stood in those days, it's been bloody mayhem ever since).

[Yahzi]

Not all change is good
Change is bad.

(Assuming you worked hard to get where you are.)

:)

[CapelDodger]

Change is bad.

(Assuming you worked hard to get where you are.)

:)

:D

If it was good enough to make my father rich ... and good enough to make his father rich ... it should be good enough to make me rich. Not referring to hard work, of course.

I have a Computer Science degree from 1976, in no small part because I saw it as the best ticket to buy. I've been de-skilled in my own lifetime. Go on someone, pass me the gun and tell me again that change is good.

[Verde]

Change is bad.



Spare some change, guv?

[Taffer]

Sometimes these annoying creationists just piss me off:

http://www.evolutionisdead.com/forum/viewtopic.php?p=11670&sid=3406e76df02b7fb9f60af262a63c3a63#11670

~~ Paul

Just...ew. :(

[Belz...]

Annoying creationists

Is there any other kind ?

[briandunning]

The best part about annoying a creationist is that you then get to go to hell. I hear the chicks there are hot.

[Fnord]

There is one sure-fire way to annoy Creationists -- IGNORE them!

Really, many 'creos' seem to engage 'evos' (and vice-versa) in pointless arguments for the attention alone. Since nothing offends a fanatic so much as indifference to their particular idealistic cause, ignoring them is a mortal offense.

And by 'pointless,' I mean that neither side is ever going to convince the other of the truth and validity of their argument. Even if their facts are in order and their reasoning sound, no-one will win. So, why bother?

BTW: This is my first post on JREF.

- Fnord of Dyscordia -

[Dark Jaguar]

Fnord, I disagree with your last point. While one who believes what they believe regardless of the amount of evidence may not ever be convinced by any argument, one who belives what they believe entirely because of evidence, who can and does change their mind as new evidence comes in, would certainly be willing to hear the other side's arguments if they are in fact sound and valid. So no, I'd say a rational person who came to believe in evolution for rational reasons WOULD in fact be convinced of creationism IF they had valid evidence and arguments for it. As of yet, they have not.

As to ignoring them, that's fun too. Unfortunatly, ignoring them has led to this point where they are trying to get it taught in public schools. Ignoring is no longer an option.

[Fnord]

I was referring to the extreme cases on both sides. Of course, there is somewhere in the middle where a dichotomy of thought can be held.

As for wanting to teach Creationism in public schools -- let them try. But give those kids an earlier start on Philosophy and Reason, especially when it comes to recognizing fallacious statements and unsubstantiated data.

You know; the "Scientific Method."

Once people know how to think for themselves, they should reach the rational conclusions on their own. Otherwise, they are innocents caught in the middle of a doctrinal war, getting fired upon from both sides. Sooner or later, they'll shut everything out and muddle along without reason or thought to their own existance.

THAT is the tragedy.

-Fnord of Dyscordia-

[CapelDodger]

Are we missing an "O" in fnoord, or is my brain screwed? Or neither?

I do not need to see fnoords right after watching someone get chased down my street in Torchwood. Gimme a break.

[CapelDodger]

More reasons for head-frick : both election episodes of West Wing Series 7 in succession. Said episodes arriving on DVD accompanied by a bottle of 10-year-old Jamieson's Malt. And the following earlier in the day when everything seemed to be pretty normal :

There's this excellent pub up the way that was known as the Poet's Corner since forever, way before Dylan Thomas got thrown out for mine-sweeping. About ten years ago the name was changed to the thoroughly innapropriate Tut 'n' Shive (immediately re-christened the Twp and Swive, look it up). Fortunately the pub remained essentially the same. Even when there was scaffolding in the pool-room to hold up the roof well, hey, there was never open access. Three tables in what's essentially an attic, waddya gonna expect?

The bullet had to be bit in the end. The pub has re-opened - and the name has been changed again. Now it's the Poet's Corner. Where will it end? Do we just have to put up with it? Have we no say?

[Bronze Dog]

I've got an annoying Creationist (http://rockstarramblings.blogspot.com/2006/10/interesting-thought.html). Feel free to deal with him so I won't have to waste my time when you can do the same.

[CapelDodger]

I've got an annoying Creationist (http://rockstarramblings.blogspot.com/2006/10/interesting-thought.html). Feel free to deal with him so I won't have to waste my time when you can do the same.
You could at least demonstrate how a master does it. Whether Paul felt he needed to be unleashed by you before he had a try is for Paul to say. If he decides he should bother. I can't, off the top of my head, imagine why he would.

[McCulloch]

As for wanting to teach Creationism in public schools -- let them try. But give those kids an earlier start on Philosophy and Reason, especially when it comes to recognizing fallacious statements and unsubstantiated data.

You know; the "Scientific Method."

Once people know how to think for themselves, they should reach the rational conclusions on their own. Otherwise, they are innocents caught in the middle of a doctrinal war, getting fired upon from both sides. Sooner or later, they'll shut everything out and muddle along without reason or thought to their own existance.
Aren't they trying to stop the teaching of how to think in the education system in the USA?

[a_unique_person]

Sometimes these annoying creationists just piss me off:

http://www.evolutionisdead.com/forum/viewtopic.php?p=11670&sid=3406e76df02b7fb9f60af262a63c3a63#11670

~~ Paul

Now that's a side of you I haven't seen before.

[Mashuna]

Are we missing an "O" in fnoord, or is my brain screwed? Or neither?

I do not need to see fnoords right after watching someone get chased down my street in Torchwood. Gimme a break.

Hee! I've had fun recognising areas where I've worked in Torchwood, but watching your street on TV must be slightly disturbing.

On a side note, the Urdd Eisteddfod was held in the field behind our house this year, and I had the strange experience of waking up to see the Tardis out of my bedroom window.

[Fnord]

Aren't they trying to stop the teaching of how to think in the education system in the USA?

Who or what do you mean by "they"?

a) The Government.
b) The Gnomes of Zurich.
c) The Limosine Liberals.
d) The Ivory-Tower Conservatives.
e) The Feminists, Feminazis, and/or Feministas.
f) The Public School Boards.
g) The Religionists.
h) The Atheists.
i) All of the above.
j) None of the above.

Personally, I choose "i) All of the above."

[CapelDodger]

Who or what do you mean by "they"?

I'm not one for the "they" term either, it lacks rigour.

There are always interests in any society that do not welcome independant thought because their status and other privileges are founded on diktat, not persuasion. Be it aristocracy, religion, or economic oligarchy. Which do tend to fade into each other. "He's the lord because his father was, the church says that's right and proper, and he owns your ass". So shut up.

I don't doubt the forces of anti-rationality have been gaining momentum over the last decade or three. I'm fifty-something, I remember the days when science was on a roll (where's my jet-pack?!) and superstition apparently reeling. It's different now. To my mind there was a cusp around 1973-76 in the Anglo-Saxon world, which is my arena of experience. It was later in the Muslim world, starting weakly in 1979 - Iranian Revolution, Soviet invasion of Afghanistan and Zia ul-Haq Islamising Pakistan - but catching a fair wind in its sails. The Soviet block suppressed anti-rationality unintentionally by making every citizen a cynic, and the post-Soviet experience has carried on the good work. China's social trajectories have never been closely synced to the West, Western impressions notwithstanding. I've given up trying to understand Japan, life's too short.

The world is in the early stages of a Great Crisis, the sort of thing that has occurred before at a regional level. At each such crisis the region is larger; at this one it's reached global. That hasn't happened before. And at each such crisis period the irrational and anti-rational gain ground because the rational says you're screwed. And who wants to hear that.

[CapelDodger]

Hee! I've had fun recognising areas where I've worked in Torchwood, but watching your street on TV must be slightly disturbing.
It's not as if I live in Los Angeles, you know? Initial reaction : how did I not notice the filming? I work from home, I shop locally, I chat regularly with neighbours. Then it occurred to me that none of us would raise - or do raise - an eyelid when somebody is chased past our window by a copper. And todays's filming technology means you can shoot it almost as quickly as you do it.

The spooky gas-mask double in first series New Who (as it's known round here) meant the crew were encamped on the old (closed) Cardiff Royal Infirmary for a week or so, everybody knew it was going to feature. I turned into the Hayes a few months ago to find it decked out for Xmas, I was fazed for a few seconds there, then recalled the special Xmas episode to introduce the new side-kick. But twenty seconds of pursuit shots? Wouldn't leave a mark.

The Torchwood Cardiff looks so amazing I'm considering moving there :) .

On a side note, the Urdd Eisteddfod was held in the field behind our house this year, and I had the strange experience of waking up to see the Tardis out of my bedroom window.
I've had nights like that too.

[Dark Jaguar]

It's not as if I live in Los Angeles, you know? Initial reaction : how did I not notice the filming? I work from home, I shop locally, I chat regularly with neighbours. Then it occurred to me that none of us would raise - or do raise - an eyelid when somebody is chased past our window by a copper.

How often are people chased by your window by cops?! I'd certainly give it a second thought, and would certainly be VERY interested.

[CapelDodger]

Examination of the original text confirms that there is only one "O" in fnord. My recollection was that there were two. Which, given the context, is downright disturbing.

[CapelDodger]

How often are people chased by your window by cops?! I'd certainly give it a second thought, and would certainly be VERY interested.
I'd have been the same in some places I've lived. I've lived out in the sticks where a strange face draws attention. A face such as mine, for instance. Normally unremarkable.

The full Torchwood pursuit is actually quite credible, it goes around Adamsdown Square (making it look a lot bigger than it is), comes across the Black Bridge, and dives into the back-to-back geometry of Splott. The Black Bridge is a footbridge, so joyriders and such that are under motorised pursuit habitually ditch the vehicle on one side and leg it across to the other. Pursued by Cardiff's finest.

It's all about location. location and location :) . We have a low local crime-rate, but a high throughput.

[Fnord]

I had the second "O" surgically removed, and all records thereof destroyed.

The following statement is false:
The previous statement is true.
Welcome to my corner of the universe.

-Fnord of Dyscordia-

[Paul C. Anagnostopoulos]

We may be graced with the presence of the annoying creationist I mentioned in the OP. He has admonished himself "... to remember to bring my raincoat so that when all you evolutionist crybabies start throwing your pabulum it will be easier to clean up."

~~ Paul

[kleinman]

Sometimes these annoying creationists just piss me off:
One of the reasons Paul says this is that he believes when I quote him, I twist his words, so a figure I may as well start twisting.

Paul has done a very poor job presenting my arguments about Dr Tom Schneider’s ev computer program when he said the following:
Kleinman is attempting to convince us that Ev demonstrates that there was not enough time for binding sites to develop. Actually, his thesis is that there was not enough time for macroevolution to occur. What that has to do with genetic binding sites I cannot imagine. He claims that various results that we got from running experiments with Ev support his thesis. He throws around numbers like 4^1000.

That's all well and good. He can discuss this if he wants. But I really get annoyed when he starts misrepresenting what I said.

Before I present my basic argument, let the readers know that unlike most creationists and IDers, I find Dr Schneider’s computer model of the evolution of binding sites by random point and natural selection a plausible representation of this phenomenon.

My argument is that the ev computer program shows that this process is so profoundly slow when realistic parameters are used in the model that macroevolution by this mechanism is mathematically impossible. In addition, Dr Schneider in his publications on ev concludes that ev demonstrates evolution by punctuated equilibrium as described by Stephen Gould. Dr Schneider’s conclusions are likewise impossible since Gould’s thesis of punctuated equilibrium states that evolution occurs over short time spans in small sub-populations. The mathematical results from the ev model directly contradict these two conditions.

So the theory of evolution started without any mathematical foundation and continues to suffer from the same deficiency. The theory of evolution is modern mythology, not hard mathematical science.

[Paul C. Anagnostopoulos]

Welcome! Now that you're here on this fresh, new forum, you will present us the mathematical proof that macroevolution is impossible, won't you? After you define macroevolution, of course. Thanks so much.

~~ Paul

[kleinman]

Welcome! Now that you're here on this fresh, new forum, you will present us the mathematical proof that macroevolution is impossible, won't you? After you define macroevolution, of course. Thanks so much.

You are very welcome, I’m glad you enjoy being annoyed.

I like to keep it simple for you evolutionists. Since you already asked me to define macroevolution on the Evolutionisdead forum, I referred you to wikipedia. You asked me to summarize that definition and I will repeat my summary here.

Macroevolution is big change, microevolution is small change. I am still working on my abridged summary for evolutionists with short attention spans, but my grammar checker keeps underlining it in red.

Now let’s start with the mathematics of ev and explain why it shows macroevolution is impossible. Consider the computation Dr Schneider used in his publication of ev Evolution of Biological Information available at Dr Schneider’s web.

In this paper, Dr Schneider says the following:
Likewise, at this rate, roughly an entire human genome of ~4x10^9 bits (assuming an average of 1 bit/base, which is clearly an overestimate) could evolve in a billion years, even without the advantages of large environmentally diverse worldwide populations, sexual recombination and interspecies genetic transfer.


Dr Schneider arrived at this estimate of the evolution of an entire human genome in the following manner. Dr Schneider used the rate of acquisition of information from his 256 base case with a mutation rate of 1 mutation per 256 bases per generation. That case evolved 16 binding sites, each 6 bases wide in about 1,000 generations. The rate of acquisition of information for that case is about 1 bit per 11 generations. Dr Schneider then extrapolated that rate of acquisition of information of 1 bit per 11 generations to a human size genome. If you take Dr Schneider’s published example of the 256 base genome and simply use a realistic mutation rate of 1 mutation per 1,000,000 bases per generation, it requires 4,000,000 generations to evolve the same 16 binding sites. The rate of acquisition of information declines from 1 bit per 11 generations to about 1 bit per 40,000 generations. Dr Schneider’s estimate of the evolution of the human genome goes from a billion years to four trillion years. Dr Schneider’s extrapolation becomes more ridiculous when you examine the rate of acquisition of information for genomes larger than 256 bases.

[Paul C. Anagnostopoulos]

So is the evolution of binding sites to be considered microevolution or macroevoluion? Sounds like microevolution to me, in which case what does it have to do with problems with macroevolution?

~~Paul

[kleinman]

So is the evolution of binding sites to be considered microevolution or macroevoluion? Sounds like microevolution to me, in which case what does it have to do with problems with macroevolution?

I believe you hold the view that if you have enough microevolutionary steps you can obtain a macroevolutionary change. So I think it is worthwhile to try to get some perspective on your question. With respects to Dr Schneider’s single published case of the evolution of the 16 binding sites (96 loci) on a 256 base genome in 1,000 generations, I think you could call this a macroevolutionary process (greater that 1/3 of the genome is evolving). With respects to the case you did in which you evolved these 16 binding sites on a 100,000 base genome in 200,000,000 generations, this would represent more of a microevolutionary process. I tend to agree with you conceptually that in theory enough microevolutionary steps can be combined to obtain a macroevolutionary change. Where I think we differ in this view point is that I think that natural selection will limit these microevolutionary changes and not allow an organism to diverge too far from its genetic optimum. We see this effect for example with dog breeding. Particular traits are selected for by breeders and in this process, peculiar health problems often arise from this human induced selective pressure. As soon as that pressure is removed and these “pure bred” dogs are allowed to breed with mutts, these features (and peculiar health problems) tend to disappear.

You need to remember that Dr Schneider used his result from his single published case using an unrealistic genome length and unrealistic large mutation rate to predict the evolution of a human genome. Dr Schneider clearly is demonstrating that he believes that his model explains macroevolution. The peer reviewers from Nucleic Acids Research must also believe that as well since they published this result.

[Cuddles]

Macroevolution is big change, microevolution is small change. I am still working on my abridged summary for evolutionists with short attention spans, but my grammar checker keeps underlining it in red

Now define "big" and "small" and we might be able to get somewhere.

[Paul C. Anagnostopoulos]

Where I think we differ in this view point is that I think that natural selection will limit these microevolutionary changes and not allow an organism to diverge too far from its genetic optimum.
Ah, so now macroevolution is prevented because of a hypothesis of "divergence from an optimum." What happened to speciation as the definition? What happened to big vs. small? This macroevolution thing seems to be a slippery concept.

What happens when the environment changes and the optimum is no longer optimum?

~~ Paul

[Mashuna]

Ah, so now macroevolution is prevented because of a hypothesis of "divergence from an optimum." What happened to speciation as the definition? What happened to big vs. small? This macroevolution thing seems to be a slippery concept.

What happens when the environment changes and the optimum is no longer optimum?

~~ Paul

There's also the implication that things are at their optimum now - that any change is inherantly inferior.

[kleinman]

Macroevolution is big change, microevolution is small change. I am still working on my abridged summary for evolutionists with short attention spans, but my grammar checker keeps underlining it in red. Now define "big" and "small" and we might be able to get somewhere.
Small is a single point mutation which I believe occurs. Big is the de novo evolution of a gene, for example the gene which codes for hemoglobin. The transition from small to big is more difficult to pin point. I tried to make this point in my previous post. Paul’s case of the evolution of 16 binding sites (96 loci) on a 100,000 base genome in 200,000,000 generations which gives a glimpse of what happens in this transition from micro to macroevolution according to Dr Schneider’s model of evolution by point mutations and natural selection.

My view on this issue is that once you get beyond a single point mutation you are already starting to enter the realm of macroevolution. Once you get to four point mutations I think you have gotten full into the realm of big evolutionary changes. This principle is used in the treatment of HIV. The strategy for treatment calls for 3 different drugs in order to avoid getting drug resistant strains. One would have to get at least three different mutations simultaneously in order to have a drug resistant virus assuming that each of the drugs are virucidal.

Where I think we differ in this view point is that I think that natural selection will limit these microevolutionary changes and not allow an organism to diverge too far from its genetic optimum.Ah, so now macroevolution is prevented because of a hypothesis of "divergence from an optimum." What happened to speciation as the definition? What happened to big vs. small? This macroevolution thing seems to be a slippery concept.
This concept of divergence from its genetic optimum is observed all the time. Consider all the genetic diseases that are due to a single point defect in a gene. Consider what happens in the laboratory when organisms are subjected to mutagens. Only in science fiction do we find super creatures arising from organisms subject to mutagens. In reality mutagens which cause divergence from the organism's genetic optimum kill the organism.

What happens when the environment changes and the optimum is no longer optimum?
You weaken your own arguments when you take a view like this. If you believe in gradualism, the selection pressure to evolve a particular characteristic must remain for long periods of time in order to achieve macroevolution. According to your calculation of the evolution of 16 binding sites (96 loci) on a 100,000 base genome using Dr Schneider’s ev program, the selection process takes 200,000,000 generations. Look back at the results from ev when you turn off selection in the model and what happens to the binding sites. The short answer to your question is; when the environment changes and the selection pressure specified by that pressure is removed, any genetic changes that were selected for under that previous selection pressure disappear.

[Paul C. Anagnostopoulos]

My view on this issue is that once you get beyond a single point mutation you are already starting to enter the realm of macroevolution. Once you get to four point mutations I think you have gotten full into the realm of big evolutionary changes.
So you're proposing that there is a biological mechanism that prevents the accumulation of more than one or two mutations? This is now your fourth definition of macroevolution.


You weaken your own arguments when you take a view like this. If you believe in gradualism, the selection pressure to evolve a particular characteristic must remain for long periods of time in order to achieve macroevolution.
Sometimes so, yes.

According to your calculation of the evolution of 16 binding sites (96 loci) on a 100,000 base genome using Dr Schneider’s ev program, the selection process takes 200,000,000 generations.
In Ev, not in real life. We have no idea how long it would take in real life. You are extrapolating statistics from Ev to real life with gleeful abandon.

Look back at the results from ev when you turn off selection in the model and what happens to the binding sites. The short answer to your question is; when the environment changes and the selection pressure specified by that pressure is removed, any genetic changes that were selected for under that previous selection pressure disappear.
I suspect it's quite rare for a selection pressure to simply disappear, as it can in Ev. So what does this have to do with real life and a "genetic optimum"?

~~ Paul

[kleinman]

There's also the implication that things are at their optimum now - that any change is inherantly inferior.
That is a fundamental principle of the theory of evolution that is selection pressure evolves the organism to some higher level. If the selection pressure is removed, the driving force for evolution is removed. The theory of evolution requires that a fixed selective pressure stays in place for huge amounts of time in order for that optimum to be reached. This effect can be demonstrated mathematically by Dr Schneider’s ev program. Evolve a set of binding sites to their optimum and then turn off selection in the program. The information in the evolved binding sites is lost when the selection pressure is removed. Not only does the selection pressure have to be in place long enough for the binding sites to evolve, the selective pressure must remain in order for the binding sites to stay evolved (at their optimum).

My view on this issue is that once you get beyond a single point mutation you are already starting to enter the realm of macroevolution. Once you get to four point mutations I think you have gotten full into the realm of big evolutionary changes. So you're proposing that there is a biological mechanism that prevents the accumulation of more than one or two mutations? This is now your fourth definition of macroevolution.
Yes I am, and that mechanism is called natural selection.

I didn’t realize a had I presented so many different definitions for macroevolution. Feel free to quote all my different definitions.

Since my summary definition for macro and microevolution seems to be too complex for you, I decided to turn off my grammar checker in order to write an abridged version of my summary definition. Here it is:

Macroevolution big change microevolution small change

Punctuation was left off this abridged summary so that evolutionists not confuse the above as an example of punctuated equilibrium. Any further reduction of this abridged summary is not possible due to the theory of irreducible complexity.

You weaken your own arguments when you take a view like this. If you believe in gradualism, the selection pressure to evolve a particular characteristic must remain for long periods of time in order to achieve macroevolution.Sometimes so, yes.
Perhaps you would explain what this selection pressure is for the formation of the hemoglobin gene and how this pressure would select for a partially formed hemoglobin gene that is non-functional and therefore offers no selective advantage.

According to your calculation of the evolution of 16 binding sites (96 loci) on a 100,000 base genome using Dr Schneider’s ev program, the selection process takes 200,000,000 generations. In Ev, not in real life. We have no idea how long it would take in real life. You are extrapolating statistics from Ev to real life with gleeful abandon.
Now Paul, you are the one who is changing your definitions. I know how much you hate when I quote you but in order to be an Annoying Creationist, I have to do something. This quote is from this site:
I think Ev rankles the IDers because it is a model of actual life, and also because Schneider is fairly good at advertising it.

There are an abundance of quotes from Dr Schneider’s web site that also say he believes that ev models real life. Which words of yours am I twisting?

Look back at the results from ev when you turn off selection in the model and what happens to the binding sites. The short answer to your question is; when the environment changes and the selection pressure specified by that pressure is removed, any genetic changes that were selected for under that previous selection pressure disappear. I suspect it's quite rare for a selection pressure to simply disappear, as it can in Ev. So what does this have to do with real life and a "genetic optimum"?
I don’t think that this phenomenon is rare at all. Take the selection pressure off pure bred dogs and see what happens. Consider what happens when the selective pressure of a particular antibiotic is removed from a population of bacteria. After some time, that antibiotic becomes effective again. Sulfa antibiotics are a good example. Wide spread resistance to that class of antibiotics was seen a while back and these antibiotics became less widely used. The selective disadvantage of maintaining sulfa resistance in a non-sulfa selective environment caused the sulfa resistant bacteria to be selected out. Sulfa drugs are again more commonly used and we again seeing the emergence of sulfa resistance. Consider what Hemoglobin-S does for the individual in a non-malaria endemic environment. If you want, I will give you more examples of this phenomenon. I think ev is a very good simulation of this effect. I also think that ev is a good simulation of macroevolution when realistic parameters such as genome lengths and mutation rates are used. Macroevolution can’t happen, it is mathematically impossible according to ev. So now your argument to this has degraded to changing your view on ev, you now say it now longer simulates reality. Would you make up your mind.

[Paul C. Anagnostopoulos]

That is a fundamental principle of the theory of evolution that is selection pressure evolves the organism to some higher level.
Does it say somewhere that selection always drive an organism to some single "optimum"?


Now Paul, you are the one who is changing your definitions. I know how much you hate when I quote you but in order to be an Annoying Creationist, I have to do something. This quote is from this site:

I think Ev rankles the IDers because it is a model of actual life, and also because Schneider is fairly good at advertising it.
You're absolutely right. I should have said "... it is a model of an aspect of actual life." Of course, that is patently obvious.


I didn’t realize a had I presented so many different definitions for macroevolution. Feel free to quote all my different definitions.


I like to keep it simple for you evolutionists. Since you already asked me to define macroevolution on the Evolutionisdead forum, I referred you to wikipedia. ["Macroevolution refers to evolution that occurs above the level of species, ..."]

Macroevolution is big change, microevolution is small change.

Where I think we differ in this view point is that I think that natural selection will limit these microevolutionary changes and not allow an organism to diverge too far from its genetic optimum.

My view on this issue is that once you get beyond a single point mutation you are already starting to enter the realm of macroevolution.
Color me confoosed.

~~ Paul

[kleinman]

That is a fundamental principle of the theory of evolution that is selection pressure evolves the organism to some higher level. Does it say somewhere that selection always drive an organism to some single "optimum"?
I don’t think I ever said that a particular selection pressure would drive an organism to a single “optimum”. In fact dog breeders might breed animals for a good sense of smell and good vision simultaneously.

You're absolutely right. I should have said "... it is a model of an aspect of actual life." Of course, that is patently obvious.
And that “aspect of actual life” is the cornerstone of the theory of evolution, that is random point mutations and natural selection. Ev shows that this process of evolution is profoundly slow, far too slow to explain macroevolution.

I didn’t realize a had I presented so many different definitions for macroevolution. Feel free to quote all my different definitions.
And Paul quotes my four different definitions for macroevolution:
I like to keep it simple for you evolutionists. Since you already asked me to define macroevolution on the Evolutionisdead forum, I referred you to wikipedia. ["Macroevolution refers to evolution that occurs above the level of species, ..."]

Macroevolution is big change, microevolution is small change.

Where I think we differ in this view point is that I think that natural selection will limit these microevolutionary changes and not allow an organism to diverge too far from its genetic optimum.

My view on this issue is that once you get beyond a single point mutation you are already starting to enter the realm of macroevolution.
Paul, I only see at most two definitions, the first is the wikipedia definition and the second is the summary you asked me to write of the wikipedia definition which I have attempted to quantify.

Color me confoosed.
Paul the only paint I give to evolutionists is to paint themselves into a corner. Don’t worry about being confoosed. I’ll be patient with you.

[Yahzi]

So the theory of evolution started without any mathematical foundation and continues to suffer from the same deficiency. The theory of evolution is modern mythology, not hard mathematical science.
The theory of evolution started from observations of the real world.

The fact that mathematicians cannot simulate these observations is a comment on mathematics, not evolution.

Now let’s start with the mathematics of ev and explain why it shows macroevolution is impossible.
And this argument will conclude that a sky-god using magic is therefore the logical answer?

If your standard is impossibility, then how is ID an answer? If you assert that evolution must be false because it violates the known laws of physics and mathematics, then how can you suggest any other answer that also violates the laws of physics and mathematics?

Is this the same old trick used to stop infinite regress - "But God is defined as not having a beginning, so he doesn't need one!" Will you tell us that since magic is a defined characteristic of God, it's ok for ID to work by magic?

Where I think we differ in this view point is that I think that natural selection will limit these microevolutionary changes and not allow an organism to diverge too far from its genetic optimum.
I call Platonism! :D

When an evolutionist says "genetic optimum," he means, "best suited to its current environment."

When you say "genetic optimum," you mean, "closest to its Platonic form."

Once you rid yourself of the Theory of Forms, you will be able to see how ludicrous your answer is.

Since my summary definition for macro and microevolution seems to be too complex for you
The definitions are not to complex; they are simply useless. What do you mean by "big" and "little" change? From the viewpoint of evolution, there is only... change. Fold a protein to the wrong side, and suddenly your entire species dies. Is that a big change or a little change?

Macroevolution can’t happen, it is mathematically impossible according to ev.
Is anyone else reminded of when they said bumblebees can't fly becuase it was mathematically impossible?

Again, an interesting comment on mathematics, but not really helpful to understanding bees or evolution.


"There are two kinds of people in the world: those who think the world derives from truth, and those who think truth derives from the world." - Yahzi Coyote

[kleinman]

So the theory of evolution started without any mathematical foundation and continues to suffer from the same deficiency. The theory of evolution is modern mythology, not hard mathematical science.
The theory of evolution started from observations of the real world. The fact that mathematicians cannot simulate these observations is a comment on mathematics, not evolution.
And the evolutionist interpretation of these observations fit no mathematical model, so blame the mathematician.

Now let’s start with the mathematics of ev and explain why it shows macroevolution is impossible. And this argument will conclude that a sky-god using magic is therefore the logical answer?
I doubt that, I think the way this argument will conclude is with the evolutionist saying that the random process god can do anything.

If your standard is impossibility, then how is ID an answer? If you assert that evolution must be false because it violates the known laws of physics and mathematics, then how can you suggest any other answer that also violates the laws of physics and mathematics?
No, it is evolutionist Dr Tom Schneider, head of computational microbiology at the National Cancer Institute, whose peer reviewed published computer model of random point mutations and natural selection that sets the standard.

Yahzi, you need to pay attention, I am the annoying creationist that Paul was talking about when he started his thread.

Is this the same old trick used to stop infinite regress - "But God is defined as not having a beginning, so he doesn't need one!" Will you tell us that since magic is a defined characteristic of God, it's ok for ID to work by magic?
Who are you quoting?

Where I think we differ in this view point is that I think that natural selection will limit these microevolutionary changes and not allow an organism to diverge too far from its genetic optimum. I call Platonism! When an evolutionist says "genetic optimum," he means, "best suited to its current environment." When you say "genetic optimum," you mean, "closest to its Platonic form." Once you rid yourself of the Theory of Forms, you will be able to see how ludicrous your answer is.
Sorry, I don’t know what you mean by Platonic optimum.

Since my summary definition for macro and microevolution seems to be too complex for you The definitions are not to complex; they are simply useless. What do you mean by "big" and "little" change? From the viewpoint of evolution, there is only... change. Fold a protein to the wrong side, and suddenly your entire species dies. Is that a big change or a little change?
Since you blame mathematicians for the failure of the theory of evolution to have a mathematical foundation, I can see why when I quantify micro and macroevolution that you would see this as useless.

With respects to a protein folding to the wrong side, natural selection is much better at selecting out a single harmful mutation then selecting in the hundreds of mutations required to evolve a single gene. Dr Schneider’s ev program demonstrates this.

Macroevolution can’t happen, it is mathematically impossible according to ev. Is anyone else reminded of when they said bumblebees can't fly becuase it was mathematically impossible? Again, an interesting comment on mathematics, but not really helpful to understanding bees or evolution. "There are two kinds of people in the world: those who think the world derives from truth, and those who think truth derives from the world." - Yahzi Coyote
I don’t think you can attribute that statement about bumblebees to me. In fact, I have worked in the aerospace industry and the thinking there was that you put a big enough engine on anything and you can make it fly. The problem with the theory of evolution is that it doesn’t have a big enough engine. Dr Schneider thought he found the engine with his ev computer model but when you use realistic parameters in the model, the theory of evolution doesn’t get off the ground. Yahzi, perhaps you can find the engine that will get the theory of evolution off the ground.

Yahzi, one thing I can tell you about the truth is that it can withstand mathematical scientific examination. So you have to do better than blame the mathematicians for the lack of a mathematical basis for the theory of evolution.

[fishbob]

The annoying part is that this particular one has decided that a simulation proves or disproves something or other. The other annoying part is that no response gets this one past this point. The really annoying part is that facts, evidence, reason, logic, observation, repetition, data - none of these mean anything because of the results of a simulation.

[kleinman]

The annoying part is that this particular one has decided that a simulation proves or disproves something or other. The other annoying part is that no response gets this one past this point. The really annoying part is that facts, evidence, reason, logic, observation, repetition, data - none of these mean anything because of the results of a simulation.
fishbob, have you read evolutionist Dr Tom Schneider’s papers and looked at his simulation? Have you looked at his evidence, reasons, logic, observation, repetition, data - claims? This is a peer review, published computer model of random mutation and natural selection which when realistic parameters are used in the model show three things. They are, huge populations don’t speed up the evolutionary process markedly as shown by the results from ev, punctuated equilibrium as proposed by Stephen Gould is contradicted by the results from ev, and macroevolution is impossible when realistic genome lengths and mutation rates are used in ev.

I told Dr Schneider that when evolutionists became aware of what his program shows when realistic parameters are used that evolutionists would discredit his work. fishbob, you have just joined that crowd.

The theory of evolution started without a mathematical foundation and remains that way.

[Roboramma]

I tend to agree with you conceptually that in theory enough microevolutionary steps can be combined to obtain a macroevolutionary change. Where I think we differ in this view point is that I think that natural selection will limit these microevolutionary changes and not allow an organism to diverge too far from its genetic optimum. We see this effect for example with dog breeding. Particular traits are selected for by breeders and in this process, peculiar health problems often arise from this human induced selective pressure. As soon as that pressure is removed and these “pure bred” dogs are allowed to breed with mutts, these features (and peculiar health problems) tend to disappear.

I think I see the point you're trying to make. Here's another example of it - there are populations in Africa where sickle-cell anemia has become quite prevalent. Because of the local environment, sickle-cell anemia is selected for. When those people leave that environment for one where the selective pressure is different, and there is very little malaria for instance, the gene for sickle-cell anemia is selected against.

Sure. What I don't quite get is how you decide which population - the one with a high incidence of the sickle-cell gene, or the one with a low incidence, is the one at the "optimum". Taking the former, for instance, it's entirely possible that they will continue to co-evolve with the parasite responsible for malaria for millions of years. In those millions of years, the physiology of these individuals will have changed enough that some genes might arise that can make use of this new physiology in other ways, unrelated to malaria, that are selected for. If a population carrying these genes then finds itself in an environment free of malaria, those genes that were originally selected because they conferred an advantage against malaria, but which are now relied upon for these new physiological processes (whatever they may be it makes no difference, except that they be adaptive for some reason other than conferring resistance to malaria) will not necessarily be selected against.

Looking at the latter, the opposite is also true - they could continue to evolve free of malaria for millions of years. Genes that couldn't arise in an environment in which malaria is a major danger, because their benefit is outweighed by the added danger they cause by making you even more prone to malaria (maybe some sort of change to the immune system that makes you better at fighting some diseases, but worse at fighting others, including malaria) could arise here.
After time, other genes will be arising in an environment in which this new gene already exists, and some will become dependent upon the physiology that it creates.
So that, again, if a population of individuals carrying all of these new genes is exposed to malaria, some of the genes that initially would have made individuals more prone to malaria (and perhaps still do), won't necessarily be selected against, because the benefit they confer to other new genes is now more important than the harm they confer by making you less resistant to malaria.

In dogs, I doubt there has been time for the evolution of genes that rely upon say, the genes responsible for being very large in great danes, for instance, but which themselves just code for some digestive enzyme or other, to have evolved.

[Paul C. Anagnostopoulos]

They are, huge populations don’t speed up the evolutionary process markedly as shown by the results from ev,
My big experiment with population variation showed that the generations required to evolve a perfect creature varied as $p^{-.4}$ I'd say that was a marked speed up.

punctuated equilibrium as proposed by Stephen Gould is contradicted by the results from ev,
You keep lying about this. Could you site the peer-reviewed journal article where Gould stated the timeframe for punctuated equilibrium events? Quote the relevant paragraph if you can.

and macroevolution is impossible when realistic genome lengths and mutation rates are used in ev.
This is meaningless, since you refuse to define macroevolution in anything but a slippery manner.


The theory of evolution started without a mathematical foundation and remains that way.
Yes, if you ignore all the mathematical work.

~~ Paul

[Roboramma]

I told Dr Schneider that when evolutionists became aware of what his program shows when realistic parameters are used that evolutionists would discredit his work. fishbob, you have just joined that crowd.
I think fishbob has a decent point. I think it's not that the simulation is meaningless. Rather, a model is only useful when it's interpretted within the confines of it's acuracy.

If I were to use a climate model designed to model the climate over the course of a century to try find an accurate description of the climate over the course of a million years, I'd be making a mistake. If I were to make conclusions based upon doing so, I'd likely make incorrect conclusions. This doesn't mean the model is "wrong", nor does it mean it's meaningless.
It just means that we have to be careful to interpret models within the parameters that they are designed for.

No model is going to be a perfect representation of the real thing. It may be a good representation of one aspect of that thing. But we have to be careful to understand how to apply that.

To that much, I can agree with fishbob. If he takes it further than that, I'll have to disagree.

[Paul C. Anagnostopoulos]

The annoying part is that this particular one has decided that a simulation proves or disproves something or other. The other annoying part is that no response gets this one past this point. The really annoying part is that facts, evidence, reason, logic, observation, repetition, data - none of these mean anything because of the results of a simulation.
What is the antecedent of "this one"?

~~ Paul

[kleinman]

Sure. What I don't quite get is how you decide which population - the one with a high incidence of the sickle-cell gene, or the one with a low incidence, is the one at the "optimum".
First thing you have to be aware of is that the sickle-cell gene represents an example of microevolution which I believe occurs. The optimum is determined by the selective pressure. What people who believe in macroevolution have failed to explain is the de novo evolution of the hemoglobin gene. What kind of selective pressure could be sustained for a long enough period of time that would cause a series of microevolutionary steps to generate such a gene, especially when virtually all the preliminary steps would not yield a molecule that can selectively bind oxygen and carbon dioxide based on the partial pressures. Random mutations and natural selection do not explain the formation of such a gene and corresponding protein. Dr Schneider’s ev computer model shows how slow random point mutations and natural selection is.

In dogs, I doubt there has been time for the evolution of genes that rely upon say, the genes responsible for being very large in great danes, for instance, but which themselves just code for some digestive enzyme or other, to have evolved.
Recombination without error can never create a new gene. Recombination with natural selection can cause the loss of alleles.

They are, huge populations don’t speed up the evolutionary process markedly as shown by the results from ev, My big experiment with population variation showed that the generations required to evolve a perfect creature varied as p^-.4 I'd say that was a marked speed up.
Ok, Paul, let’s go down this road. Post your data that you used to arrive at your curve fit.

punctuated equilibrium as proposed by Stephen Gould is contradicted by the results from ev, You keep lying about this. Could you site the peer-reviewed journal article where Gould stated the timeframe for punctuated equilibrium events? Quote the relevant paragraph if you can.
Paul, I already have on the Evolutionisdead web site but I guess you didn’t read it very carefully, so I’ll do it again.

Start with the following from Dr Schneider’s web page:
http://www.lecb.ncifcrf.gov/~toms/paper/ev/blog-ev.html (http://www.lecb.ncifcrf.gov/~toms/paper/ev/blog-ev.html)
Punctuated equilibrium correlates directly with information gain. Further, punctuated equilibrium has not addressed the more specific and fundamental problem of explaining the origin of the new biological information (whether genetic or epigenetic) necessary to produce novel biological form.This is incorrect since the Ev program demonstrates clearly the gain of biological information as a punctuated equilibrium. See Figure 2b (http://www.lecb.ncifcrf.gov/~toms/paper/ev/latex/node6.html#fig.curves), which shows a rapid increase in the information in binding sites up to the predicted amount of information ("punctuation") followed by noisy stability ("equilibrium").

Then we go to Dr Schneider’s publication in Nucleic Acids Research, where he said the following:
This roughly-sigmoidal rapid transition corresponds to (and the program was inspired by) the proposal that evolution proceeds by punctuated equilibrium [18 (http://www-lecb.ncifcrf.gov/~toms/paper/ev/latex/node7.html#Gould1977.sigmoid),19 (http://www-lecb.ncifcrf.gov/~toms/paper/ev/latex/node7.html#Gould.Eldredge1993)], with noisy `active stasis' clearly visible from generation 705 to 2000 (Fig. 2 (http://www-lecb.ncifcrf.gov/~toms/paper/ev/latex/node6.html#fig.curves)b, Fig. 3 (http://www-lecb.ncifcrf.gov/~toms/paper/ev/latex/node6.html#fig.logos)).
Reference 18 and 19 refer to these two documents:
18Gould, S. J. (1977) Is the cambrian explosion a sigmoid fraud?. In Ever Since Darwin, Reflections in Natural History N. Y.: W. W. Norton & Co. pp. 126-133.
19 Gould, S. J. and Eldredge, N. (1993) Punctuated equilibrium comes of age. Nature, 366, 223-227.
Gould said the following on page 127 of his Ever Since Darwin publication.
Complex life did arise with startling speed near the base of the Cambrian. (Readers must remember that geologists have a peculiar view of rapidity. By vernacular standards, it is a slow fuse indeed that burns for 10 million years. Still, 10 million years is but 1/450 of the earth's history, a mere instant to a geologist.)

Paleontologists have spent a largely fruitless century trying to explain this Cambrian "explosion"—the steep rise in diversity during the first 10 to 20 million years of the Cambrian period.

Gould said the following in his Punctuated equilibrium comes of age. publication:

As a neonate in 1972, punctuated equilibrium entered the world in unusual guise. We claimed no new discovery, but only a novel interpretation for the oldest and most robust of palaeontological observations: the geologically instantaneous origination and subsequent stability (often for millions of years) of palaeontological 'morphospecies'. This observation had long been ascribed, by Darwin and others, to the notorious imperfection of the fossil record, and was therefore read in a negative light--as missing information about evolution (defined in standard palaeontological textbooks of the time 9 as continuous anagenetic transformation or populations, or phyletic gradualism).
Gould further adds the following:
Mayr's 10 peripatric theory or speciation in small populations peripherally isolated from a parental stock, would yield stasis and punctuation when properly scaled into the vastness of geological time--for small populations speciating away from a central mass in tens or hundreds of thousands of years, will translate in almost every geological circumstance as a punctuation on a bedding plane, not gradual change up a hill of sediment, whereas stasis should characterize the long and recoverable history of successful central populations.
Later in this paper Gould applies the concept of punctuated equilibrium to Homo Sapiens:
Homo sapiens is a young species, perhaps no more than 200,000 years old. If most of our increment accrued quickly at our origin, but we then express this entirety from our origin to the present time as a darwin rate, we calculate a high value because our subsequent time of stasis has been so short. But if the same speciation event, with the same increment in the same time, had occurred two million years ago (with subsequent stasis), the darwin rate for the identical event would be much lower.
Cope's rule, the tendency for phyletic increase in body size, had generally been attributed to selective value of large size within anagenetic lineages, but is probably better interpreted 44,45 as greater propensity for speciation in smaller species, for whom increasing size is the only 'open' pathway (see Martin 46 on the negative correlation of generic species richness and body size).

From these quotes from Gould’s writings on punctuated equilibrium, it is clear that Gould is attempting to explain the lack of transitional forms in the fossil record. In addition, Gould sets the upper limit on the duration of the time span for punctuated equilibrium at 20 million years. However Gould then talks about much shorter time spans for punctuated equilibrium in the tens or hundreds of thousands of years time spans.

The value for the time span according to Gould and used as a reference in Dr Schneider’s paper is much less than 20 million. Gould says that ” small populations speciating away from a central mass in tens or hundreds of thousands of years,” is his proposed time scale.

These statements are in direct contradiction to the results from ev. Not only does your estimate of 575 million years to evolve 16 binding sites (96 loci) on a 100k genome far exceed the upper limit of punctuated equilibrium mentioned by Gould, Gould says macroevolutionary processes can occur in time spans of tens or hundreds of thousands of years.

Again, Gould says that this process occurs in small populations which is in direct contradiction to the results from ev which show that reducing population increases the generations required for evolution of binding sites.

Even though ev demonstrates a sigmoidal convergence curve, the scale of this curve far exceeds the requirements for Gould’s hypothesis of punctuated equilibrium. The results from ev are a direct contradiction to Gould’s hypothesis of macroevolution.

Paul, you keep calling me liar and I’m going to start thinking you don’t care for me.

and macroevolution is impossible when realistic genome lengths and mutation rates are used in ev. This is meaningless, since you refuse to define macroevolution in anything but a slippery manner.
Poor Paul, not only is the math confoosing you, now the words are confoosing you. That’s ok, I’ll continue working with you until you get it right.

The theory of evolution started without a mathematical foundation and remains that way. Yes, if you ignore all the mathematical work.
Paul, I’m shocked, how could I ignore all the good mathematical work that you and Dr Schneider have put into ev, that would be rude.

I told Dr Schneider that when evolutionists became aware of what his program shows when realistic parameters are used that evolutionists would discredit his work. fishbob, you have just joined that crowd.I think fishbob has a decent point. I think it's not that the simulation is meaningless. Rather, a model is only useful when it's interpretted within the confines of it's acuracy.
That’s a fair enough argument, why wasn’t this raised by evolutionists when Dr Schneider predicted the evolution of a human genome in a billion years based on unrealistic parameters in his model? If you study this model, I think you will find it difficult to find inaccuracies. Dr Schneider has been defending his model for years from arguments like this from IDers. The only thing this demonstrates is that evolutionists can not recognize their own biases. When Dr Schneider first published his results, it was welcomed without close scrutiny by other evolutionists as a mathematical proof of how evolution occurs. Now that it has been demonstrated that his model shows something completely different, evolutionists start questioning the validity of the model.


If I were to use a climate model designed to model the climate over the course of a century to try find an accurate description of the climate over the course of a million years, I'd be making a mistake. If I were to make conclusions based upon doing so, I'd likely make incorrect conclusions. This doesn't mean the model is "wrong", nor does it mean it's meaningless.
It just means that we have to be careful to interpret models within the parameters that they are designed for.
Dr Schneider used his model to predict the evolution of a human genome. This result was published in the peer reviewed journal, Nucleic Acids Research. Evolutionist Dr Schneider and his evolutionist peer reviewers have seen fit to apply the results from ev to long time spans and macroevolution. If you believe that Dr Schneider and the peer reviewers at Nucleic Acids Research were incorrect in applying this model in this manner you should tell them.

No model is going to be a perfect representation of the real thing. It may be a good representation of one aspect of that thing. But we have to be careful to understand how to apply that.
I think I will let Dr Schneider’s defense of ev speak to this point you have raised.
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.

[Paul C. Anagnostopoulos]

What kind of selective pressure could be sustained for a long enough period of time that would cause a series of microevolutionary steps to generate such a gene, especially when virtually all the preliminary steps would not yield a molecule that can selectively bind oxygen and carbon dioxide based on the partial pressures.
The presence of oxygen in the atmosphere?


Ok, Paul, let’s go down this road. Post your data that you used to arrive at your curve fit.
genome 1024
sites 16
widths 5/6
1 mu / genome

Population, Generations

4, 95600
8, 43400
16, 22000
32, 14800
64, 18000
128, 4400
256, 4000
512, 3900
1024, 2700
2048, 1800
4096, 1140
8192, 1180
16384, 1144
32768, 1148
46200, 1709
65536, 863
92680, 708
110000, 1177


Paul, I’m shocked, how could I ignore all the good mathematical work that you and Dr Schneider have put into ev, that would be rude.
Go ahead and ignore it. There's plenty more where that came from.


That’s a fair enough argument, why wasn’t this raised by evolutionists when Dr Schneider predicted the evolution of a human genome in a billion years based on unrealistic parameters in his model?
What he said was [emphasis mine]:

Likewise, at this rate, roughly an entire human genome of ~4 x 10^9 bits (assuming an average of 1 bit/base, which is clearly an overestimate) could evolve in a billion years, even without the advantages of large environmentally diverse worldwide populations, sexual recombination and interspecies genetic transfer.
Did he say somewhere that he necessarily thinks the rate of evolution demonstrated by Ev is a realistic rate for the complete evolution of H. sapiens?

~~ Paul

[kleinman]

What kind of selective pressure could be sustained for a long enough period of time that would cause a series of microevolutionary steps to generate such a gene, especially when virtually all the preliminary steps would not yield a molecule that can selectively bind oxygen and carbon dioxide based on the partial pressures. The presence of oxygen in the atmosphere?
Since the purpose of hemoglobin is to transport oxygen longer distances more quickly than can occur by diffusion then hemoglobin would have evolved when there were multicellular organisms. Why would a single cell organism need hemoglobin? You have also introduced a complication for abiogenesis. Doesn’t oxygen interfere with abiogenesis?

Ok, Paul, let’s go down this road. Post your data that you used to arrive at your curve fit. genome 1024
sites 16
widths 5/6
1 mu / genome
Population, Generations
4, 95600
8, 43400
16, 22000
32, 14800
64, 18000
128, 4400
256, 4000
512, 3900
1024, 2700
2048, 1800
4096, 1140
8192, 1180
16384, 1144
32768, 1148
46200, 1709
65536, 863
92680, 708
110000, 1177
I like that data, between a population of 4096 and 110,000 there is essentially no change in the generations for convergence. The data appears to have reached a plateau after a population of 4096. Why not try your curve fit algorithm on the data between population of 4096 and 110,000? In the several population series I have done, using different parameters, the same type of trend is observed. From the population of 64 to populations up to 1,000,000 you see only about an order of magnitude decrease in the generations for convergence.

Paul, I’m shocked, how could I ignore all the good mathematical work that you and Dr Schneider have put into ev, that would be rude.Go ahead and ignore it. There's plenty more where that came from.
Do you know of a better model for random point mutations and natural selection than Dr Schneider’s ev model? If so, point me to it, I’ll do some creationist research on it.

That’s a fair enough argument, why wasn’t this raised by evolutionists when Dr Schneider predicted the evolution of a human genome in a billion years based on unrealistic parameters in his model? What he said was [emphasis mine]:
Likewise, at this rate, roughly an entire human genome of ~4 x 10^9 bits (assuming an average of 1 bit/base, which is clearly an overestimate) could evolve in a billion years, even without the advantages of large environmentally diverse worldwide populations, sexual recombination and interspecies genetic transfer.
Let do a step by step analysis of how Dr Schneider arrived at this billion year estimate for the evolution of a human genome. The full text of his extrapolation is as follows:
The ev model can also be used to succinctly address two other creationist arguments. First, the recognizer gene and its binding sites co-evolve, so they become dependent on each other and destructive mutations in either immediately lead to elimination of the organism. This situation fits Behe's [34 (http://www-lecb.ncifcrf.gov/~toms/paper/ev/latex/node7.html#Behe1996)] definition of `irreducible complexity' exactly (``a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning'', page 39), yet the molecular evolution of this `Roman arch' is straightforward and rapid, in direct contradiction to his thesis. Second, the probability of finding 16 sites averaging 4 bits each in random sequences is 2 ^(-4*16) ~= 5*10^-20 yet the sites evolved from random sequences in only ~10^3 generations, at an average rate of ~1 bit per 11 generations. Because the mutation rate of HIV is only 10 times slower, it could evolve a 4 bit site in 100 generations, about 9 months [35 (http://www-lecb.ncifcrf.gov/~toms/paper/ev/latex/node7.html#Perelson.Ho1996)], but it could be much faster because the enormous titer (10^10 new virions/day/person [17 (http://www-lecb.ncifcrf.gov/~toms/paper/ev/latex/node7.html#Loeb.Mullins1999)]) provides a larger pool for successful changes. Likewise, at this rate, roughly an entire human genome of ~ 4*10^9 bits (assuming an average of 1 bit/base, which is clearly an overestimate) could evolve in a billion years, even without the advantages of large environmentally diverse worldwide populations, sexual recombination and interspecies genetic transfer. However, since this rate is unlikely to be maintained for eukaryotes, these factors are undoubtedly important in accounting for human evolution.
Dr Schneider’s rate of accumulation of ~1 bit per 11 generation is obtained from his case of the evolution of 16 binding sites on a 256 base genome with an unrealistic mutation rate of 1 mutation per 256 bases per generation. Simply the use of a mutation rate of 1 mutation per 1,000,000 bases per generation (a realistic mutation rate) in that case and the generations for convergence increases from ~1,000 generations (using the unrealistic mutation rate) goes to ~4,000,000 generations (using the realistic mutation rate). The ~1 bit per 11 generations (using the unrealistic mutation rate) goest to ~1 bit per 40,000 generations (using the realistic mutation rate). The evolution of the human genome in ~a billion years (using the unrealistic mutation rate) goes to ~4 trillion years (using the realistic mutation rate). Dr Schneider’s extrapolation becomes more preposterous when you start using a larger genome than 256 bases.

Dr Schneider’s qualifications of this extrapolation also contradict his own case of punctuated equilibrium. Large environmentally diverse populations contradicts Gould’s hypothesis of punctuated equilibrium which Gould states occurs in small isolated sub-populations in short time spans. Your own data above shows that increasing population does not offer the kind of advantage that Dr Schneider is implying. Recombination without error cannot create a new gene, recombination with natural selection can cause the loss of alleles. Even interspecies gene transfers do not create new genes. The initial gene must still be formed by some mechanism. You are back to random point mutations and natural selection for forming the original gene that is somehow transferred to the human genome.

Perhaps Dr Schneider would like to clarify his statements.

Did he say somewhere that he necessarily thinks the rate of evolution demonstrated by Ev is a realistic rate for the complete evolution of H. sapiens?
Is this the depends on meaning of is is defense?
Dr Schneider did say the following:
The following quotes were taken from Dr Schneider’s blog web page: http://www.lecb.ncifcrf.gov/~toms/paper/ev/blog-ev.html (http://www.lecb.ncifcrf.gov/~toms/paper/ev/blog-ev.html)

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

"Schneider's paper is misleadingly titled: "Evolution of biological information". But it is just a *computer* simulation. No actual *biological* materials (e.g. genomes of nucleic acids, proteins, etc) were used, nor does Schneider propose that his simulation be tested with *real* genomes or proteins Actual biological materials were used to determine the original hypothesis. Read the literature: Schneider1986 (http://www.lecb.ncifcrf.gov/~toms/paper/schneider1986)

It only becomes *real* biological information and random mutation and natural selection, when the simulation is tested in the *real* world, using *real* DNA, proteins, with *real* mutations and a *real* environment does the selecting. It is significant that Schneider does not propose this, presumably because he knows it wouldn't work.You are very bad at reading my mind, I have considered doing this experiment. Given the right conditions, it WILL WORK. Do you have th gumption to do the experiment yourself? That's the way real science works! FURTHERMORE, if you read the literature, you will recognize that related experiments have been repeatedly done for 20 years. Look up SELEX.

In the rest of the paper he uses the single word "selection". I take this as a tacit admission that his model is not a simulation of *real* biological natural selection. No. A rose is a rose by any other name. Selection is selection whether it be natural (generally meaning the environment of earth), breeding (by humans usually, though perhaps some ants select their fungi), SELEX or in a computer simulation. Of COURSE it is a simulation of natural selection! The paper would not be relevant to biology and would not have been published in a major scientific journal if it were not!

Schneider lets slip that there is another unrealistic element in his (and indeed all) computer simulations in that it (they) "does not correlate with time": So? Run the program slower if you want. Make one generation per 20 minutes to match rapid bacterial growth. THIS WILL NOT CHANGE THE FINIAL RESULT!

Well, when Schneider's simulation is actually tested with *real* "life" (e.g. a bacterium), and under *real* mutation and natural selection it gains information, then, and only then, would "creationists" be favourably impressed. But if they are like me, they would already be impressed (but unfavourably) that Schneider does not mention in his paper that his simulation should now be so tested in the *real* "biological" world.1. The simulation was of phenomena in the "real" world.
2. Dr. Jones is invited yet again to do an experiment.

The following is a response Dr Schneider made to a statement made by David Berlinski (http://www.discovery.org/scripts/viewDB/index.php?command=view&id=51&isFellow=true).

Where attempts to replicate Darwinian evolution on the computer have been successful, they have not used classical Darwinian principles, and where they have used such principles, they have not been successful. The ev program disproves this statement since it uses classical Darwinian principles and was successful.

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

[fishbob]

fishbob, have you read evolutionist Dr Tom Schneider’s papers and looked at his simulation? Have you looked at his evidence, reasons, logic, observation, repetition, data - claims? This is a peer review, published computer model of random mutation and natural selection which when realistic parameters are used in the model show three things. They are, huge populations don’t speed up the evolutionary process markedly as shown by the results from ev, punctuated equilibrium as proposed by Stephen Gould is contradicted by the results from ev, and macroevolution is impossible when realistic genome lengths and mutation rates are used in ev.

I told Dr Schneider that when evolutionists became aware of what his program shows when realistic parameters are used that evolutionists would discredit his work. fishbob, you have just joined that crowd.

The theory of evolution started without a mathematical foundation and remains that way.

A simulation is a method for visualizing data or processes. A model or a simulation is a glorified, computerized diagram.
A simulation proves or disproves nothing, so your entire effort on this thread has value only as excercise for your typing skills.

[fishbob]

What is the antecedent of "this one"?

~~ Paul

Creationist. Involved in this discussion.

[Paul C. Anagnostopoulos]

A simulation proves or disproves nothing, so your entire effort on this thread has value only as excercise for your typing skills.
A simulation can prove something, as long as you're willing to agree that the same assumptions can be made about the real world. Ev shows that information can evolve, as long as you're willing to assume that mutations and selection happen in the real world. However, I certainly agree that it's quite easy to pile on the assumptions past a reasonable point.

~~ Paul

[Paul C. Anagnostopoulos]

I like that data, between a population of 4096 and 110,000 there is essentially no change in the generations for convergence. The data appears to have reached a plateau after a population of 4096. Why not try your curve fit algorithm on the data between population of 4096 and 110,000?
That restricted data is too noisy to fit any curve to it. I'll have to run more experiments in that population range.

~~ Paul

[kleinman]

I like that data, between a population of 4096 and 110,000 there is essentially no change in the generations for convergence. The data appears to have reached a plateau after a population of 4096. Why not try your curve fit algorithm on the data between population of 4096 and 110,000?That restricted data is too noisy to fit any curve to it. I'll have to run more experiments in that population range.
What did you say? I can’t hear you, too much noise in the data.:)

[Paul C. Anagnostopoulos]

What did you say? I can’t hear you, too much noise in the data.
If I run the same population multiple times, which generation count should I use in the curve fit? I think I'll use the minimum. Any objection?

~~ Paul

[fishbob]

A simulation can prove something, as long as you're willing to agree that the same assumptions can be made about the real world. Ev shows that information can evolve, as long as you're willing to assume that mutations and selection happen in the real world. However, I certainly agree that it's quite easy to pile on the assumptions past a reasonable point.

~~ Paul

OK - I accept that proof given that the assumptions are correct is possible. However, in the real world we often get our assumptions handed to us on a platter.

[kleinman]

What did you say? I can’t hear you, too much noise in the data.If I run the same population multiple times, which generation count should I use in the curve fit? I think I'll use the minimum. Any objection?
That should be alright, my first impression to this question is that when looking at population effect in the ev model, trends in convergence are more important than the absolute numbers of generations. If I think something look strange in the data, I will probably ask you to post all your runs for the series.

[Yahzi]

And the evolutionist interpretation of these observations fit no mathematical model, so blame the mathematician.
You have the cart before the horse.

Nobody is blaming the mathematician. It is your mathematician who is yelling at biologists - "I can't explain your observations, so they must be false!'

I doubt that, I think the way this argument will conclude is with the evolutionist saying that the random process god can do anything.
The fact that you characterize evolution as random is really all we need to know about your qualifications to discuss evolution.

Yahzi, you need to pay attention, I am the annoying creationist
Trust me. I know.

Who are you quoting?
Are you unaware of what a "literary device" is?

]Sorry, I don’t know what you mean by Platonic optimum.
You don't even understand your own argument. But that won't stop you from yammering on about it.

I don’t think you can attribute that statement about bumblebees to me.
And I did not. Perhaps you mean some other word than "attribute."

The problem with the theory of evolution is that it doesn’t have a big enough engine. Dr Schneider thought he found the engine with his ev computer model but when you use realistic parameters in the model, the theory of evolution doesn’t get off the ground.
Given that evolution is an observed fact, ordinary people would conclude that it was the model that failed to get off the ground.

But no: your mind is of a entirely different caliber. You are one of those people who build a wind tunnel, stick a model plane in it, and when the model plane crashes... you tear down the wind tunnel and re-build it.

I can say, with all honesty, that a mind like yours is a rarity in the scientific world.

So you have to do better than blame the mathematicians for the lack of a mathematical basis for the theory of evolution.
Is there a matematical basis for the stock market? I guess the stock market doesn't exist... Come to think of it, the incompleteness of String theory shows that there is no mathematical basis for reality. So I guess reality must be wrong, too!

Heck, there's no mathematical model for me, so I guess that means I don't

[kleinman]

And the evolutionist interpretation of these observations fit no mathematical model, so blame the mathematician. You have the cart before the horse. Nobody is blaming the mathematician. It is your mathematician who is yelling at biologists - "I can't explain your observations, so they must be false!'
Yahzi, it is an evolutionist’s mathematical model of random point mutation and natural selection that argues against your own theory. I figure it is going to take a month or two of these preliminaries before you will be ready to learn how this model works and why I make these claims.
I doubt that, I think the way this argument will conclude is with the evolutionist saying that the random process god can do anything.The fact that you characterize evolution as random is really all we need to know about your qualifications to discuss evolution.
Sorry, did I miss name your god, it’s the random mutation and natural selection god.
Yahzi, you need to pay attention, I am the annoying creationistTrust me. I know.
If you stick with this discussion, you will get beyond annoyed and become pissed off like Paul. That happens when your find out that your favorite theory not only has no mathematical foundation, when you try to apply mathematics to the theory, the theory is refuted.
The problem with the theory of evolution is that it doesn’t have a big enough engine. Dr Schneider thought he found the engine with his ev computer model but when you use realistic parameters in the model, the theory of evolution doesn’t get off the ground. Given that evolution is an observed fact, ordinary people would conclude that it was the model that failed to get off the ground. But no: your mind is of a entirely different caliber. You are one of those people who build a wind tunnel, stick a model plane in it, and when the model plane crashes... you tear down the wind tunnel and re-build it. I can say, with all honesty, that a mind like yours is a rarity in the scientific world.
Don’t confuse your observations with your interpretations of the observations. I don’t argue with evolutionist observations, what I do argue is the contorted interpretation they have to resort to in order for their observations to fit their theory.

I have worked on wind tunnels but I have never done what you attribute to me.
So you have to do better than blame the mathematicians for the lack of a mathematical basis for the theory of evolution. Is there a matematical basis for the stock market? I guess the stock market doesn't exist... Come to think of it, the incompleteness of String theory shows that there is no mathematical basis for reality. So I guess reality must be wrong, too! Heck, there's no mathematical model for me, so I guess that means I don't
We’ll continue to do these preliminaries for a while then I’ll show how Dr Schneider’s model of evolution by random point mutations and natural selection contradicts your theory of evolution.

Yahzi, you would be surprise what kind of mathematical models exist for you, I am sure you

[Yahzi]

I figure it is going to take a month or two of these preliminaries before you will be ready to learn how this model works and why I make these claims.
I wish I could be so optimistic. But I am quite confident that no amount of time is sufficient for you to understand your error.

I did not come to accept the theory of evolution because of this model. Thus, this model's failure to explain evolution will not matter to me. All it can do is convince me the model is flawed.

I came to accept evolution because of observations of the real world. To discredit evolution, you must demonstrate an observation of the real world that contradicts it.

What you are doing right now has a name: it is called voodoo. You are creating a model of your enemy, sticking pins in it, and fully expecting the enemy to fall over and die.

That happens when your find out that your favorite theory not only has no mathematical foundation, when you try to apply mathematics to the theory, the theory is refuted.
Remember when I cited the "bumblebee" example? You simply did not understand the point.

You seem to think that because there is no mathematical model of evolution right now, there can never be. Why do you think this?

Oh, right, for us to assert that they'll figure it out someday is "faith in science." Your position seems to be that anything that is not completely understood right now is, by definition, never understandable.

I have worked on wind tunnels but I have never done what you attribute to me.
I think this explains a lot. No, seriously, I do.

You have consistently failed to recognize or understand "literary devices." You have demonstrated a repeated inability to grasp abstractions, metaphors, and similes. And the discussion at hand is about your inability to distinguish between a simulation and the real world.

What we are dealing with here appears to be simply a cognitive deficiency.

[Paul C. Anagnostopoulos]

What you are doing right now has a name: it is called voodoo. You are creating a model of your enemy, sticking pins in it, and fully expecting the enemy to fall over and die.
Uh oh. Multiple sig lines by the same person.

~~ Paul

[T'ai Chi]

A simulation can prove something, as long as you're willing to agree that the same assumptions can be made about the real world.


In that case, why don't you just use the real world? Do a lot of stuff with flys in jars.

[Level]

So let me get this straight, Kleinman is saying evolution is bunk because it is incompatible with certain results of a simulation? That's rich.

[Paul C. Anagnostopoulos]

In that case, why don't you just use the real world? Do a lot of stuff with flys in jars.
I don't know, same reason you use a computer to balance your checkbook? Why not do a lot of stuff with paper and pencil?

Seriously, here's the problem:

Creationist: Not enough time, 2nd law, fossil record, blah, blah, blah. You can't creation information.

Schneider: Sure you can. Look at genomes.

Creationist: No information created. God put it there.

Schneider: Let me write this program ... Look! Did God put the information in my simulated genome?

Dembski: You snuck it in somehow!

http://www.ccrnp.ncifcrf.gov/~toms/paper/ev/dembski/claimtest.html


~~ Paul

[Paul C. Anagnostopoulos]

So let me get this straight, Kleinman is saying evolution is bunk because it is incompatible with certain results of a simulation? That's rich.
Not evolution as a whole, but macroevolution. Whatever macroevolution is, there is not enough time for it to happen, because Ev's simulation of 1/1000 of 1% of the evolutionary landscape shows that it can't happen in the unspecified timeframe of punctuated equilibrium. Something like that.

~~ Paul

[kleinman]

So let me get this straight, Kleinman is saying evolution is bunk because it is incompatible with certain results of a simulation? That's rich.
That’s a simulation written by evolutionist Dr Tom Schneider, head of computational molecular biology at the National Cancer Institute and peer reviewed and published in the Oxford University Press journal Nucleic Acids Research. The java version of the program is available online and was written by Moderator Paul Anagnostopoulos. Paul is an excellent java programmer but we have got to work on his arithmetic.

Warning, this ride is not for evolutionists who are faint of heart.
For the fearless evolutionist, here is the URL: where you can access and run the program:
http://www.ccrnp.ncifcrf.gov/~toms/paper/ev/evj/evjava/index.html (http://www.ccrnp.ncifcrf.gov/~toms/paper/ev/evj/evjava/index.html)
Use this program at your own risk.
So let me get this straight, Kleinman is saying evolution is bunk because it is incompatible with certain results of a simulation? That's rich. Not evolution as a whole, but macroevolution. Whatever macroevolution is, there is not enough time for it to happen, because Ev's simulation of 1/1000 of 1% of the evolutionary landscape shows that it can't happen in the unspecified timeframe of punctuated equilibrium. Something like that.
You almost got it right. This is a three trick pony. Ev shows that huge populations do not markedly accelerate evolution by random point mutations and natural selection. Ev shows that evolution by random point mutations and natural selection is far too slow for punctuated equilibrium as described by Stephen Gould to be mathematically possible. Ev shows that macroevolution by point mutations and natural selection is mathematically impossible.

[Paul C. Anagnostopoulos]

You almost got it right. This is a three trick pony. Ev shows that huge populations do not markedly accelerate evolution by random point mutations and natural selection.
With sufficient computing resources, you could run Ev with huge populations and determine how many generations are required. Neither you nor I have run Ev with any more than about 128,000 creatures. Furthermore, Ev does not simulation multiple nearly-independent populations.

Ev shows that evolution by random point mutations and natural selection is far too slow for punctuated equilibrium as described by Stephen Gould to be mathematically possible.
This is absurd. How long did Gould say that punctuated equilibrium episodes last, what sort of biological mechanisms was he talking about, and how many generations of Ev simulation is equivalent to that time period?

Ev shows that macroevolution by point mutations and natural selection is mathematically impossible.
This is so absurd it's not even worth analyzing.

~~ Paul

[Level]

That’s a simulation written by evolutionist Dr Tom Schneider, head of computational molecular biology at the National Cancer Institute and peer reviewed and published in the Oxford University Press journal Nucleic Acids Research. The java version of the program is available online and was written by Moderator Paul Anagnostopoulos. Paul is an excellent java programmer but we have got to work on his arithmetic.

Warning, this ride is not for evolutionists who are faint of heart.
For the fearless evolutionist, here is the URL: where you can access and run the program:
http://www.ccrnp.ncifcrf.gov/~toms/paper/ev/evj/evjava/index.html (http://www.ccrnp.ncifcrf.gov/%7Etoms/paper/ev/evj/evjava/index.html)
Use this program at your own risk.



Thank you for the link. So if this proves, as you keep claiming, that large-scale evolution is impossible, what steps will you be taking in order to prove this to the scientific community? Are you going to organize a formal argument or is posting in a few online forums the extent of your evolution rebuttal?

[kleinman]

You almost got it right. This is a three trick pony. Ev shows that huge populations do not markedly accelerate evolution by random point mutations and natural selection. With sufficient computing resources, you could run Ev with huge populations and determine how many generations are required. Neither you nor I have run Ev with any more than about 128,000 creatures. Furthermore, Ev does not simulation multiple nearly-independent populations.
That’s not quite accurate, I have been able to run a 1000 base genome with a population of just over 1,000,000 using the pascal version of ev. In theory you can run larger cases but my computer only has 512 meg of memory and larger cases use a disk page file which slow the calculations a 1000 fold and would probably destroy my hard drive.
Ev shows that evolution by random point mutations and natural selection is far too slow for punctuated equilibrium as described by Stephen Gould to be mathematically possible. This is absurd. How long did Gould say that punctuated equilibrium episodes last, what sort of biological mechanisms was he talking about, and how many generations of Ev simulation is equivalent to that time period?
I posted Gould’s estimates for punctuated equilibrium, earlier on this thread. He uses a range of values up to 20 million years but as low as 10-100,000 years. In one of Gould’s publications he even supposes a length of time of only 5-10,000 years. Read the quotes I posted from Dr Schneider’s references from his ev publication. If you consider your case of the evolution of 16 binding sites (96 loci) on a 100,000 base genome in 200,000,000 generations (over 500,000 years at one generation per day), you have already exceeded a large portion of the time span that Gould proposes and you still haven’t reached a realistic genome length. If you are talking about reptiles evolving into birds, not only will you have a genome much larger than 100,000 bases, you will have much longer generation times than 1 per day.
Ev shows that macroevolution by point mutations and natural selection is mathematically impossible. This is so absurd it's not even worth analyzing.
That’s ok, I’ll post the data from ev that shows this.
Thank you for the link. So if this proves, as you keep claiming, that large-scale evolution is impossible, what steps will you be taking in order to prove this to the scientific community? Are you going to organize a formal argument or is posting in a few online forums the extent of your evolution rebuttal?
The first thing I did was discuss this directly with Dr Schneider and Paul Anagnostopoulos who is Dr Schneider’s java programmer for ev. Paul is the one who started this thread. I then asked Dr Schneider if he was willing to discuss this publicly because he had in the past but said no to my request, however Paul was willing to take up the banner. Dr Schneider had started a thread on the Evolutionisdead web site so I went ahead and started a discussion there. That went on for several months and there were a couple of evolutionists (including Paul) who were willing to debate this issue but they ran out of ideas on how to counter the data that was coming out of the model. Paul’s argument has gone from saying that ev simulates reality to it simulates a small portion of the rich evolutionary landscape. I also contacted the editors of Nucleic Acids Research who originally published Dr Schneider’s results based on unrealistic parameters in his model. I hoped to submit a letter to the editor. I told them that when realistic parameters are used in his model that it predicts that random point mutation and natural selection is too slow to account for macroevolution. They gave the usual evolutionist argument and said I was setting up a strawman, in addition they don’t take letters to the editor and to publish in their journal costs over $1000. So here we are James Randi educational forum.

My plan is to give an explanation of how Dr Schneider’s program works, give a little bit of the theory behind the model and then present series of cases that demonstrates the mathematical behavior of the model. In addition, I will mix in some of the voluminous quotes Dr Schneider and Paul have made about the model. This really annoys Paul but it reveals how convoluted evolutionist thinking has become. I don’t know whether I will write a formal paper. I don’t think any mainline scientific journals would take it at this time. The evolutionist community has a real problem with this computer simulation. This is not a model written by IDers. In fact IDers have been attacking this model for years. When I first saw this model the evolutionist community thought they had the mathematical proof for the theory of evolution. I happen to believe the model is a plausible simulation for random point mutations and natural selection unlike the IDers who have criticized the model. The problem for evolutionists is that one of their own has produced a mathematical model that puts their theory in a mathematical vise that I don’t think they can get out of without discrediting 20 years of work by the head of the computational molecular biology lab at the National Cancer Institute. It also reveals a very poor peer review process at Nucleic Acids Research. Tomorrow I’ll post the first steps of my proof and walk the readers through this very interesting computer model.

[gopi]

Pardon me if I'm a bit confused here, but...

It seems to me that it is much easier to prove that something is possible with a simulation than to prove it is impossible.

In the case of Ev, its author has (in my understanding) said, "This, this and this characteristic and behaviour can create result X."

The fact that Ev can't produce result Y does not mean that Y is impossible. It could simply be that Ev doesn't model the physical world accurately enough to simulate that.

Ev demonstrates one way things _could_ work. To prove that something is _impossible_ requires that you prove there is _no_ way it could work. This discussion reminds me of another poster on this forum, who's trying to use a physical modelling program to design a perpetual motion machine.

All models have limits. They can be very useful when used within their limits, but if you go outside the limits, the results are usually utterly meaningless.

To argue that Ev disproves the possibility of macroevolution requires two things:
1. You must demonstrate that a simulation done with Ev shows the impossibility of macroevolution.
2. You must demonstrate that none of the differences between Ev and the real world are significant enough to matter.

All of the discussions I have seen so far have centered on (1). The only arguments I have seen for (2) reference that Ev has been accepted as a reasonable modelling tool for microevolution. Can somebody justify the use of Ev for macro-evolution?

[Roboramma]

First thing you have to be aware of is that the sickle-cell gene represents an example of microevolution which I believe occurs. The optimum is determined by the selective pressure. What people who believe in macroevolution have failed to explain is the de novo evolution of the hemoglobin gene. What kind of selective pressure could be sustained for a long enough period of time that would cause a series of microevolutionary steps to generate such a gene, especially when virtually all the preliminary steps would not yield a molecule that can selectively bind oxygen and carbon dioxide based on the partial pressures. Random mutations and natural selection do not explain the formation of such a gene and corresponding protein. Dr Schneider’s ev computer model shows how slow random point mutations and natural selection is.
What does any of this have to do with what I posted?
You suggested that the fact that dogs tend to revert to a more wolf-like state when they are put back into an ancestral "pre-dog" environment suggests that new traits picked up by micro-evolution will also tend to be lost quickly if the selective pressure that favoured those traits goes away.

I pointed out how and why that won't always be the case. I also suggested that for dogs, there simply hasn't been enough time for the other factors that I'm talking about to come into play. To which you responded:
Recombination without error can never create a new gene. Recombination with natural selection can cause the loss of alleles.
I may be stupid, but I don't see how that addresses what I said at all.

It's quite possible that I just need things spelled out for me. It's happened before.

[T'ai Chi]

I don't know, same reason you use a computer to balance your checkbook? Why not do a lot of stuff with paper and pencil?


Although you must realize a computer spreadsheet is not a simulation of a checkbook- it is in fact doing the same exact thing as a checkbook. Programs that model real world evolution, on the other hand, have many assumptions built in for simplification purposes.

Why would you shy away from doing experiments on real biology to prove your point? Wouldn't that be more effective than appealing to an intelligently designed assumption laden simulation?

[Roboramma]

Although you must realize a computer spreadsheet is not a simulation of a checkbook- it is in fact doing the same exact thing as a checkbook. Programs that model real world evolution, on the other hand, have many assumptions built in for simplification purposes.

Why would you shy away from doing experiments on real biology to prove your point? Wouldn't that be more effective than appealing to an intelligently designed assumption laden simulation?

The experiments are "intelligently designed" as well. The reason to use a computer simulation is that there are some things that are much easier to do with a computer. You just have to know what it is you're trying to show, and the limits of the model.

Do you object to computer models in general?

[Cuddles]

Kleinman, I suggest you read this thread ("http://forums.randi.org/showthread.php?t=48951). I would be interested to know your views on AgingYoung, and if you believe a perpetual motion machine is possible. The argument is exactly the same as this one, that a simulation of one small part of the world is more accurate at representing the world than the world is itself.

[Paul C. Anagnostopoulos]

That’s not quite accurate, I have been able to run a 1000 base genome with a population of just over 1,000,000 using the pascal version of ev. In theory you can run larger cases but my computer only has 512 meg of memory and larger cases use a disk page file which slow the calculations a 1000 fold and would probably destroy my hard drive.
Ooh, cool. Exactly which parameters did you use and how many generations did it take?

~~ Paul

[kleinman]

An Introduction to the ev computer program
In the following postings, I will introduce the reader to the ev computer simulation of evolution of binding sites by random point mutations and natural selection. This initial discussion will be limited to a description of the model, how the model is used and some of the key parameters that are used in the model. Later, I will discuss some of the theory behind the derivation of the model and give series of cases which show that this model of evolution by random point mutations and natural selection is far too slow to explain macroevolution and the results from this computer model also contradict Stephen Gould’s hypothesis of punctuated equilibrium.

As a starting point, I refer readers to the following URL:

http://www.ccrnp.ncifcrf.gov/~toms/paper/ev/evj/evjava/index.html (http://www.ccrnp.ncifcrf.gov/~toms/paper/ev/evj/evjava/index.html)

This link will take you to the online version of ev written in the java language by the very capable programmer, a moderator on this forum and originator of this thread but confoosed evolutionist Paul Anagnostopoulos. If you only have a low speed internet hookup, you can still run longer cases with ev. Once you have started ev, you can disconnect from the net and continue running your cases.

I will not post screen shots of the program, I will assume you have followed the above link and now have the applet available to be viewed. There are two basic screens to this applet. The initial screen which presents when starting the applet is the program execution screen. The second screen is accessed by pushing the New button at the top left of the execution screen.

The layout of the first screen gives several controls, some of which are user modifiable and others which are for display purposes only. I will start from the top left and describe the controls.

The Restart button does as the title suggest, it restarts the computation from its initial point. The New button takes you to a form which allows the user to change input parameters to the model. The Help button is not functional but there is more than enough information on the screen to understand how to use this program with minimal study. The About button should be pushed and the window read. The Run/Pause button allow you to start and pause a case at any point and then continue the execution. The Step button allows the user to execute a single generation at a time. Below the Run/Pause and Step buttons are the Speed spinning list control which allows the user to vary the rate at which the program executes. If you are doing larger cases, I suggest you set this control to its maximum value of 21, however it will use 100% of your CPU time and make any other applications you happen to be running execute very slowly. Below the Speed control is the Generations display which tells the user the number of generations that have been calculated to that point. Below that is a Cycles to run control which allows the user to specify the maximum number of generations to execute and below that is a graphical gauge that displays the number of generations that have been run and will also display a message if the program has stopped due to satisfying a convergence criteria.

To the right of the controls just described are 6 controls, 5 of these controls are display only and consist of Population which is the number of creatures or genomes used in the simulation. Potential Sites which is more commonly called genome size in our discussion and is represented by the letter “G” in Dr Schneider’s calculations. This is the number of bases or loci in the entire genome. binding sites which are the portion of the genome that is evolving. This parameter is described by the Greek letter gamma in Dr Schneider’s computation. The only thing I will say about binding sites at this time is that it is the portion of the genome that resides before a gene and must be identified by the organism’s genetic control system in order for the gene to be transcribed. If you are a fisherman, you might think of the binding site as the leader on the fishing line and the fishing line as the gene. Gene are not evolving, only the binding sites for the genes are evolving.Site width is the number of bases or loci in each binding site. Note that Gamma * site width gives the total number of loci that are evolving on the genome. Mutations displays the number of mutations per genome per generation being used in the particular case you are running. The mutation rate can cause some confusion by its definition. There are several ways you can define mutation rate. If you google the terms “bacteria” & “mutation rates”, you will find papers that usually describe mutation rates as 10^-6 or 10^-8 and so on. These rates represent the probability that a mutation will occur at a certain locus per generation. Dr Schneider has used two slightly different definitions than above for programming ease and reduced computational time. I don’t believe these approximations have significant affect on the results of the simulation but you need to be aware which definition you are using. The two definitions that Dr Schneider uses is “m” mutations per genome per generation and 1 mutations per “b” bases per generation. The first definition requires genome lengths (G) of 500,000 or so to give realistic mutation rates, the second definition allows you to approximate realistic mutations on smaller genomes. A per locus rate of 10^-6 would be approximately the same as 1 mutation per 1,000,000 bases per generation. The final control in this column is the Perform selection check box which enables the user to run the simulation with or without selection. To the right of this column is a graphical control which dynamically displays the acquisition of information in a binding site. The last controls on the top portion of the screen, which are labeled at the top with Best and Worst consist of ID which you have to ask Paul what these are for, Age which gives the number of generations that that the best and worst creatures have survived, Mistakes which give the number of mistakes for the best and worst creature. Mistakes is the parameter which is used for selection. Rsequence is the amount of information that has evolved in the binding site. At the start of the computation Rsequence should be zero and according to Dr Schneider’s theory, Rsequence should evolve to the value of Rfrequency which is the amount of information required to find the binding sites. Rfrequency is computed using G and gamma and does not change during the evolutionary process. There are four user modifiable controls below which allow the user to specify convergence conditions including when a Perfect creature has evolved which occurs when the random point mutations and natural selection process has located all gamma number of binding sites on any genome without erroneously identifying a binding site where one should not exist. The Rseq>=Rfreq check box will pause the simulation if the amount of information in the binding sites in any creature equals or exceeds the Rfrequency and the third check box requires that both conditions be met to pause the program. Any none or all boxes can be checked, however Paul seems to have settled on the Perfect Creature criteria as the best convergence criteria. This sometimes gives different results than the Rseq>=Rfreq convergence condition but I see no reason at this time to argue this issue. The last user modifiable control is the Update every generation spin box. This control allows the user to vary the number of times the screen display is updated. I find if the control is set to a low number, it slows the computation, however if you are an old hippie and like to see a colorful display change rapidly, leave this spin box control at a low number. The bottom half of the screen displays the progress of the evolution on one of the genomes with lots of pretty colors.

If you have been able to keep up with this discussion to this point, and your head is not spinning too much, I’ll now describe the second screen in the program. This second screen is accessed by pushing the New button on the execution page. This is a form window that allows the user to change parameters in the model. The top line on this form Title allows you to put a title on the case you are running. This can be useful if you decide to run several cases simultaneously. The Title will show up on the taskbar. The left side of the form has 5 spin box/entry fields, Population, Potential Sites or genome length “G”, Binding sites count also called gamma, Weight width which is the mathematical representation of the binding protein which is used to identify binding sites as they evolve. Site Width is the number of loci or bases in each of the gamma binding sites. If you want a description of the control Placement, you will have to ask Paul or Dr Schneider, I have only used the default value. On the right side of this form are the two different choices for setting the mutation rate as described earlier. The Selection Parameters box repeats the same controls as on the execution screen except you can experiment with Tie Scores and vary the selection process when this occurs. The final two entry controls are the cycles to run which performs the same function as on the execution screen control and Random Seed which is used to initiate the random number generator. The buttons on the bottom of the screen are self explanatory. The Ok returns you to the execution screen with your modified parameters loaded into the model. Unless Paul has done more work on this program, you are unable to Save or Load a case.

The basic flow of the simulation once you have defined your input parameters, consists of the following: The program defines a series of random genomes equal to the population. A portion of each genome is set aside to evolve the gamma number of binding sites, each with the site width specified. Random mutations defined by the user are allowed to each genome. If the mutations enable the weight matrix (binding protein) to identify binding sites in the appropriate area of the genome, then these are not considered mistakes. If the weight matrix does not identify binding sites where they should be, these are considered mistakes. The opposite occurs in the non-binding site region of the genome. If binding sites are identified in this region it is considered a mistake. The total number of mistakes determines the selection process. The half of the population with the fewest mistakes is allowed to reproduce, the other half is selected out. The process is then repeated.

I hope I got all the details correct, if I messed up something I’m sure Paul will gently correct me.

If this discussion hasn’t completely bored you out of your mind, try running a few cases with ev. In the coming days, I will discuss how information theory is tied in with this computation and start presenting results of cases that I have run that I believe prove my case that ev shows that macroevolution by point mutation and natural selection is mathematically impossible, Gould’s hypothesis of punctuated equilibrium is mathematically impossible and that huge populations do not accelerate evolution.

[Yahzi]

So let me get this straight, Kleinman is saying evolution is bunk because it is incompatible with certain results of a simulation? That's rich.
Exactly.

That you so quickly percieved the root of the matter makes me all warm and fuzzy inside. I think I am going to enjoy your contributions to this forum. :)

[Yahzi]

An open question:

Why isn't Kleinman simply settling for proving Schnieder wrong? "Look, your response to creationism fails. Try again."

Instead, he wants to use a (possibly) failed argument by an evolutionist as a way to overturn all of evolution.

Is this just more magical thinking - the law of contagion in action (having gained a piece of evolutionary theory, it magically relates to the entire thing)? Or does he think he's doing the same thing we do when we use a Bible contradiction to overturn the inerrancy of the Bible?

[kleinman]

Pardon me if I'm a bit confused here, but... It seems to me that it is much easier to prove that something is possible with a simulation than to prove it is impossible.
That’s ok, Paul is Dr Schneider’s coworker and he is confoosed as well. Read my post #94 on this thread and I’ll walk you through the simulation.
Recombination without error can never create a new gene. Recombination with natural selection can cause the loss of alleles.I may be stupid, but I don't see how that addresses what I said at all. It's quite possible that I just need things spelled out for me. It's happened before.
If you stick with this discussion, this will make sense. You will get a little understanding of Information Theory which Dr Schneider used to write his computer simulation of evolution by random point mutations and natural selection. His simulation shows that it this mechanism can not account for macroevolution. Other evolutionists have tried to counter this finding by saying that recombination will speed up the macroevolutionary processes. Recombination can not create a new gene that is recombination can not add information to the gene pool.
Kleinman, I suggest you read ... I would be interested to know your views on AgingYoung, and if you believe a perpetual motion machine is possible. The argument is exactly the same as this one, that a simulation of one small part of the world is more accurate at representing the world than the world is itself.
I couldn’t get you link to work. I do not believe in perpetual motion machines. Dr Schneider believes his simulation represents the real world.
That’s not quite accurate, I have been able to run a 1000 base genome with a population of just over 1,000,000 using the pascal version of ev. In theory you can run larger cases but my computer only has 512 meg of memory and larger cases use a disk page file which slow the calculations a 1000 fold and would probably destroy my hard drive. Ooh, cool. Exactly which parameters did you use and how many generations did it take?
I posted the results on the Evolutionisdead forum on the following page:
http://www.evolutionisdead.com/forum/viewtopic.php?t=348&postdays=0&postorder=asc&start=285 (http://www.evolutionisdead.com/forum/viewtopic.php?t=348&postdays=0&postorder=asc&start=285)
It is on my Oct 09, 5:39PM post.
That case took about 300Mb of RAM and 4 days of cpu time.

[Timble]

There are four user modifiable controls below which allow the user to specify convergence conditions including when a Perfect creature has evolved which occurs when the random point mutations and natural selection process has located all gamma number of binding sites on any genome without erroneously identifying a binding site where one should not exist.


Surely, the point is that there is no perfect creature. By prespecifying an end point you're trying to determine the time taken and probability of reaching that end point. In the real universe, assuming ID isn't correct, there isn't an end point and evolution goes to where it goes to.

[kleinman]

An open question: Why isn't Kleinman simply settling for proving Schnieder wrong? "Look, your response to creationism fails. Try again." Instead, he wants to use a (possibly) failed argument by an evolutionist as a way to overturn all of evolution.
I think Dr Schneider’s model is essentially correct. Where Dr Schneider went wrong was using unrealistic parameters in his model. You need to ask Paul or better yet ask Dr Schneider if he believes his arguments and model is correct.

[fls]

I believe prove my case that ev shows that macroevolution by point mutation and natural selection is mathematically impossible...

Who says that macroevolution occurs by point mutation alone?

Linda

[Yahzi]

I think Dr Schneider’s model is essentially correct.
Why do you think his model is correct?

For normal people, the answer is: because it models the observed facts.

You quite clearly feel it does not model the observed facts. What, then, is your basis for asserting the model is accurate?

[Beleth]

Uh oh. Multiple sig lines by the same person.

~~ Paul
Awww man! And during a thread where the one you took out (mine) is just so freaking appropriate!

[Yahzi]

Awww man! And during a thread where the one you took out (mine) is just so freaking appropriate!
I believe the accepted and appropriate comment for me to make at this juncture is:

Nyaah nyaah nyaah!

:D :D :D

[joobz]

Let's not attack kleinman until he places his cards on the table.

Instead of the suspense building, kleinman, post the entire theory and supporting equations that make you feel that the model is wrong or that the model shows evolution is wrong. We can debate those claims once we've seen them.

So far, you've posted nothing earth shattering, nothing remotely difficult to disprove or find inaccurate. Right now, it is up to you to support your case.

We wait patiently.

I will state quite plainly, this is the first time i've ever dealt with any in science who didn't lead with their results. the cooler more dramatic the results, the more that person will shove it under your nose. Normally I know i'm gonna see something exciting when a person runs into my office sayinig, "Check this out!"

[Bronze Dog]

Is this just more magical thinking - the law of contagion in action (having gained a piece of evolutionary theory, it magically relates to the entire thing)? Or does he think he's doing the same thing we do when we use a Bible contradiction to overturn the inerrancy of the Bible?

I'd go with the voodoo hypothesis.

[kleinman]

There are four user modifiable controls below which allow the user to specify convergence conditions including when a Perfect creature has evolved which occurs when the random point mutations and natural selection process has located all gamma number of binding sites on any genome without erroneously identifying a binding site where one should not exist. Surely, the point is that there is no perfect creature. By prespecifying an end point you're trying to determine the time taken and probability of reaching that end point. In the real universe, assuming ID isn't correct, there isn't an end point and evolution goes to where it goes to.
The “perfect creature” terminology is not of my choice. What a “perfect creature” is according to the ev concept is a genome that has evolved to the point where every binding site that should be identified is identified and no binding sites are identified that should not be identified. What happens at that point is the evolutionary process plateaus. This is probably why Dr Schneider proposes this is an example of punctuated equilibrium.
I believe prove my case that ev shows that macroevolution by point mutation and natural selection is mathematically impossible... Who says that macroevolution occurs by point mutation alone?
What mechanisms do you want to propose?
I think Dr Schneider’s model is essentially correct.Why do you think his model is correct?
Tomorrow I will describe the theory behind the model and why I believe the model is essentially correct.
For normal people, the answer is: because it models the observed facts. You quite clearly feel it does not model the observed facts.
No computer model will ever accurately simulate reality when input parameters do not reflect realistic values. This is what Dr Schneider has done.
What, then, is your basis for asserting the model is accurate?
I’ll post this now since you have asked twice.

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

In the ev model, the initial ensemble is the initial random genome. In the ev model, the questioning process are the random mutations. If a random mutation hits a locus in a binding site and improves the match between the weight matrix (binding protein) and that binding site it increases the information in that binding site. So the weight matrix gives the answer. Natural selection then chooses the ensemble with the higher information (or in this model, with the fewest number of mistakes in the identification of binding sites).

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

Let's not attack kleinman until he places his cards on the table.
Wait until I put my cards on the table and then attack.
Instead of the suspense building, kleinman, post the entire theory and supporting equations that make you feel that the model is wrong or that the model shows evolution is wrong. We can debate those claims once we've seen them.
I posted the basic theory above so now you can attack.
So far, you've posted nothing earth shattering, nothing remotely difficult to disprove or find inaccurate. Right now, it is up to you to support your case.
I thought it only fair to warn you that your earth was about to be shattered.
I will state quite plainly, this is the first time i've ever dealt with any in science who didn't lead with their results. the cooler more dramatic the results, the more that person will shove it under your nose. Normally I know i'm gonna see something exciting when a person runs into my office sayinig, "Check this out!"
Hey joozb, check this out! By the way, I like your new sign on your office door.
Is this just more magical thinking - the law of contagion in action (having gained a piece of evolutionary theory, it magically relates to the entire thing)? Or does he think he's doing the same thing we do when we use a Bible contradiction to overturn the inerrancy of the Bible? I'd go with the voodoo hypothesis.
Yahzi, no rabbits out of my hat, Bronze Dog, no voodoo dolls, this one is mathematics with a computer model of random point mutations and natural selection written by the head of computational molecular biology at the National Cancer Institute and published in the peer reviewed journal Nucleic Acids Research. This model has been around for years and scrutinized by numerous scientists and mathematicians. The one thing nobody has done until now is a systematic parametric study. These results put the cornerstone of evolutionary theory in a severe mathematical vise. I’m not a bad applied mathematician and computer programmer and I see no way of rescuing this aspect of the theory evolution from this mathematical conundrum.

[T'ai Chi]

The experiments are "intelligently designed" as well. The reason to use a computer simulation is that there are some things that are much easier to do with a computer.


I'd think real-life experiments are always worth more than a computer simulation of real life. Why? Because it shows directly it could happen more realistically in real life.

If Paul's program shows something could happen in X number of generations, why not just go through X number of generations of flies and see if it actually occurs in real life?

[fls]

Originally Posted by Kleinman
I believe prove my case that ev shows that macroevolution by point mutation and natural selection is mathematically impossible...
Originally Posted by fls
Who says that macroevolution occurs by point mutation alone?

What mechanisms do you want to propose

I'm guessing that in addition to showing that point mutations alone will not suffice as a mechanism for macroevolution, you want to dismiss other mechanisms that are a part of current evolutionary theory such as crossing-over and inversion.

You seem to be spending an inordinate amount of time arguing something that most people may already agree with - point mutation alone does not drive evolution. Maybe you'd make more headway if you could explain why you think it is reasonable to exclude other mechanisms from your model (other than simply dismissing them).

Linda

[Paul C. Anagnostopoulos]

Awww man! And during a thread where the one you took out (mine) is just so freaking appropriate!
I know, I'm sorry. Three sigs just don't work. For anyone who has not seen this beautiful sig:

ID has no answers. It can only make itself look palatable by making evolution look less palatable. It lives in a cardboard refrigerator box and throws rocks through the windows of evolution's unfinished mansion. ---Beleth

[Paul C. Anagnostopoulos]

Surely, the point is that there is no perfect creature. By prespecifying an end point you're trying to determine the time taken and probability of reaching that end point. In the real universe, assuming ID isn't correct, there isn't an end point and evolution goes to where it goes to.
But it's an endpoint that we know has been reached in the real world. Don't be mislead by the word perfect, it's just used to mean that the creature has no binding site errors.

~~ Paul

[kleinman]

What mechanisms do you want to proposeI'm guessing that in addition to showing that point mutations alone will not suffice as a mechanism for macroevolution, you want to dismiss other mechanisms that are a part of current evolutionary theory such as crossing-over and inversion.
How do you get the original gene to cross-over or invert? You must still have some mechanism to create the original gene.

You seem to be spending an inordinate amount of time arguing something that most people may already agree with - point mutation alone does not drive evolution. Maybe you'd make more headway if you could explain why you think it is reasonable to exclude other mechanisms from your model (other than simply dismissing them).
I don’t know if that is what most evolutionists agree on. Recombination may drive diversity but recombination can not drive macroevolution because recombination without errors can not add information (create new genes) to the gene pool. Recombination with natural selection can cause the loss of information (alleles) from the gene pool. Neither of the mechanisms (inversions and cross-over) that you propose can create a new gene these mechanisms require and existing gene that must be created by random point mutations and natural selection.

Since all you evoblogophiles now understand the basics of the basics of ev, I know give you your first homework assignment if you are willing to enter this realm of danger. Your first assignment is to take Dr Schneider’s baseline case (the case which he published in Nucleic Acids Research) which are the default values in evjava. Click both the Pause on Perfect Creature check box and Pause on Rs>=Rf check box. Also change the maximum number of generations for the program to run to 1,000,000. You only need to run any case the number of generations required to meet the convergence criteria. Then click the Run button. When either convergence criterion is met, record that number of generations required to meet that convergence criterion, unclick the corresponding check box, then click the Run button again and let the program run until the other convergence criterion is met. Record the generations required to meet this condition as well. Now click the New button. Change only the number of Potential sites (the genome length) from 256 to 512 and click either the Pause on Perfect Creature check box or Pause on Rs>=Rf check box so that both pause conditions are checked. Then click the ok button to return to the program execution screen. Click the Run button and repeat the process you just performed for the 256 base case for this 512 base case. Once both convergence criterion are satisfied for this case and you have recorded the generations for convergence, click the New button and double the genome length from 512 to 1024 and make sure both the Pause on Perfect Creature check box and Pause on Rs>=Rf are clicked on and repeat the process for potential sites (genome lengths) 2048, 4096, 8,192, … Report these result in the following format:
Genome length/Generations for Perfect Creature/Generations for Rs>=Rf
256/662/675
512/2412/2925
1024/***/***
2048/***/***
4096/***/***
8192/***/***
16384/***/***
I’ve given the first two cases in this little table so you can compare if you obtain the same results. Once someone posts their filled table, we can discuss the meaning of these results.

[Paul C. Anagnostopoulos]

I posted the results on the Evolutionisdead forum on the following page:
http://www.evolutionisdead.com/forum/viewtopic.php?t=348&postdays=0&postorder=asc&start =285
It is on my Oct 09, 5:39PM post.
That case took about 300Mb of RAM and 4 days of cpu time.
Merging your data with mine and ignoring populations below 2048, I obtain the following curve fit for a genome size of 1024 and 1 mutation / genome / generation:

$12{,}138p^{-.23}$ with r = -.92

So increased population size does help.

~~ Paul

[Roboramma]

If Paul's program shows something could happen in X number of generations, why not just go through X number of generations of flies and see if it actually occurs in real life?

Because to do so would be far more expensive? Because to do so would take much more time? Because you can run the program many many times with different conditions for less money and in less time than you could run your fruit fly experiment once.

Possibly (I don't know if this is the case or not) by building a model that focuses on one aspect of the process, we might get more insight into that specific aspect of the process than doing an experiment on complex living organisms where many more things can muddle our interpretation.

There might be other reasons as well. Certainly we have to be careful as to how to interpret the results of a computer model, but that doesn't mean they are useless.

[delphi_ote]

I'd think real-life experiments are always worth more than a computer simulation of real life. Why? Because it shows directly it could happen more realistically in real life.

If Paul's program shows something could happen in X number of generations, why not just go through X number of generations of flies and see if it actually occurs in real life?
Gee. I wonder why nobody ever thought of that.

Oh. (http://www.jstor.org/view/00143820/di000351/00p0103p/0)

[Paul C. Anagnostopoulos]

I'd think real-life experiments are always worth more than a computer simulation of real life. Why? Because it shows directly it could happen more realistically in real life.
The purpose of Ev was to show that information could evolve, and that one can predict how much information will evolve in a particular context. The program succeeds in demonstrating this. If you think it doesn't pertain to real life, it would be helpful if you could explain what part of mutation and selection real life doesn't exhibit. Heck, if you could convince us that DNA doesn't contain information, that would pretty much do it right there.

Ev was never meant to replace fruit fly labs.

~~ Paul

[kleinman]

Awww man! And during a thread where the one you took out (mine) is just so freaking appropriate! I know, I'm sorry. Three sigs just don't work. For anyone who has not seen this beautiful sig:ID has no answers. It can only make itself look palatable by making evolution look less palatable. It lives in a cardboard refrigerator box and throws rocks through the windows of evolution's unfinished mansion. ---Beleth
Beleth, it’s not an unfinished mansion, it’s a house of cards, and I’m not throwing rocks, I throwing mathematical data. And don’t make fun of my house, it happens to be a double door refrigerator box that came with built in ice-maker. I’m planning on adding a chest freezer box room addition as soon as cardboard prices drop a little.

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

We can discuss the population effect but why don’t we give the bloggers a chance to familiarize themselves with ev so that we might have more than a two way discussion on these issues.

[Paul C. Anagnostopoulos]

Paul, I didn’t say that ev doesn’t show that population helps, what I said was that huge populations don’t markedly reduce the number of generations for convergence sufficiently to allow macroevolution to occur. In addition large populations contradict Gould’s concept of punctuated equilibrium which he said occurs in small sub-populations.
We don't know this, because we haven't modeled more than a measly million creatures. You won't let me extrapolate using that fitted curve, but if I did extrapolate to a lousy billion creatures, it would require 103 generations; to a trillion creatures, 21 generations. Of course, there is some asymptote it's approaching, although I haven't the slightest idea what that is.

I think that is a sufficient reduction for macroevolution to take place. Wait, what was macroevolution, again? And how small is a small population of bacteria? Hang on, does punctuated equilibrium pertain to the evolution of an ancient mechanism such as genetic binding?

~~ Paul

[joobz]

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


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


In the ev model, the initial ensemble is the initial random genome. In the ev model, the questioning process are the random mutations. If a random mutation hits a locus in a binding site and improves the match between the weight matrix (binding protein) and that binding site it increases the information in that binding site. So the weight matrix gives the answer. Natural selection then chooses the ensemble with the higher information (or in this model, with the fewest number of mistakes in the identification of binding sites).

Unlike many IDers who have criticized Dr Schneider’s simulation, I find his basic concept plausible. What I don’t find plausible is Dr Schneider’s use of unrealistic parameters. Dr Schneider used a genome length of only 256 bases (2000 times smaller than the smallest genome known in any free living organism) and a mutation rate of 1 mutation per 256 bases per generation (4000 times higher than the average mutation rate in prokaryotes) in his publication on ev. When more realistic parameters are used in the model, the rate of acquisition of information become profoundly slow as will unfold as the data from ev is presented. This rate of information acquisition becomes so slow that it shows that it takes hundreds of millions of generations to evolve less than 100 loci on a genome of only 100,000 bases. Point mutation and natural selection is a profoundly slow process. Far too slow to evolve a gene de novo.
That's it? Um, again, Not enough time? THere are never situations where mutation rate changes? I'm sorry, the model is interesting in it's ability to show increased information with improvements in the binding site sequence.
But you ignore, not all point mutations are created equal. Some loci are not as improtant as others (consider consensus sequences).
You ignore insertion/deletion errors
You ignore genetic exchange
You ignore the ADMITTED limitations to the code presented

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

[T'ai Chi]

Because to do so would be far more expensive? Because to do so would take much more time?


Yes, it probably would be more prohibitive for various reasons. It would also be more convincing IMO, because it would deal directly with real life.

[T'ai Chi]

The purpose of Ev was to show that information could evolve, and that one can predict how much information will evolve in a particular context. The program succeeds in demonstrating this. If you think it doesn't pertain to real life, it would be helpful if you could explain what part of mutation and selection real life doesn't exhibit.


That's all good and stuff, but why not do the same with actual biology instead?

But what I'm really wondering is why, if you admit Ev shows information could evolve, and you admit that Ev is an intelligently designed program, that you are not admitting that it really shows that it takes intelligence to get information?

[joobz]

But what I'm really wondering is why, if you admit Ev shows information could evolve, and you admit that Ev is an intelligently designed program, that you are not admitting that it really shows that it takes intelligence to get information?

I agree with your desire for actual lab experiments. Models can provide insight, but they can only do so much.

BUt, I don't get this line of reasoning. You can't honestly believe that a simulation verifies ID.

[Yahzi]

I’m not a bad applied mathematician and computer programmer and I see no way of rescuing this aspect of the theory evolution from this mathematical conundrum. [/SIZE][/FONT]
Well, there you go. If the great Dr. Kleinman can't figure it out, it must not work!

But you did not answer the questoin (I notice you do this a lot).

You stated that you thought EV was an accurate model of evolution. I asked you why you thought it was accurate. Please tell us why you think it is accurate. What evidence do you have that the model accurately reflects actual evolution?

See, for the rest of us, we believe the model because when given the same parameters as real life, it produces the same results. But you argue this is not the case. So what makes you think the model is accurate?

[Yahzi]

I know, I'm sorry. Three sigs just don't work. For anyone who has not seen this beautiful sig:

ID has no answers. It can only make itself look palatable by making evolution look less palatable. It lives in a cardboard refrigerator box and throws rocks through the windows of evolution's unfinished mansion. ---Beleth
Actually, I think that's a better quote than my voodoo one. I love that imagery. In fact, that gives me an idea....

:)

[fls]

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

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

I don’t know if that is what most evolutionists agree on. Recombination may drive diversity but recombination can not drive macroevolution because recombination without errors can not add information (create new genes) to the gene pool. Recombination with natural selection can cause the loss of information (alleles) from the gene pool. Neither of the mechanisms (inversions and cross-over) that you propose can create a new gene these mechanisms require and existing gene that must be created by random point mutations and natural selection.

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

Linda

[joobz]

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



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

Linda
Will you stop presenting facts, this seems to anger the ID gods. They may see fit to send back their envoys of repetitive missinformation.

[Roboramma]

That's all good and stuff, but why not do the same with actual biology instead?

But what I'm really wondering is why, if you admit Ev shows information could evolve, and you admit that Ev is an intelligently designed program, that you are not admitting that it really shows that it takes intelligence to get information?

Does using a computer to model climate mean that climate is intelligently designed? After all, the model itself was intelligently designed.

Hint: the model is designed such that, for the aspects of the world that we are looking at, it mimics the natural world in ways that are informative (though certainly not in every way).

[delphi_ote]

That's all good and stuff, but why not do the same with actual biology instead?
It has been done. (http://forums.randi.org/showthread.php?postid=2094090#post2094090) The simulation is just a model of what we have already observed in the lab.

But please. By all means. Continue to ignore direct contradictory evidence to your belief.

[Cuddles]

I couldn’t get you link to work. I do not believe in perpetual motion machines. Dr Schneider believes his simulation represents the real world

Oops, the link was meant to be http://forums.randi.org/showthread.php?t=48951&page=8

To summarize it : AgingYoung has used a computer simulation, of part of the real world, that is only valid within it's design parameters of Newton's Laws, to design a machine that will run forever, thereby showing that Newton's Laws are not correct. Since he is attempting to do something which the simulation is not designed to do, any results he gets are completely meaningless, since they are not valid in the real world.

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

Given that you are both using exactly the same logic to make your points, do you now accept that perpetual motion is possible, or that your argument is incorrect?

[joobz]

Oops, the link was meant to be http://forums.randi.org/showthread.php?t=48951&page=8

To summarize it : AgingYoung has used a computer simulation, of part of the real world, that is only valid within it's design parameters of Newton's Laws, to design a machine that will run forever, thereby showing that Newton's Laws are not correct. Since he is attempting to do something which the simulation is not designed to do, any results he gets are completely meaningless, since they are not valid in the real world.

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

Given that you are both using exactly the same logic to make your points, do you now accept that perpetual motion is possible, or that your argument is incorrect?
Cuddles, nicely done.

[Tez]

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

Well in case anyone cares, this is untrue.

For a single system A in some state Q, the von-Neumann entropy of A is the same as (not the negative of!) the Shannon entropy of the "eigen-preparation" of Q (which is one special way of preparing the state Q, and not always the most desirable one).

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

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

[AmateurScientist]

Well in case anyone cares, this is untrue.

For a single system A in some state Q, the von-Neumann entropy of A is the same as (not the negative of!) the Shannon entropy of the "eigen-preparation" of Q (which is one special way of preparing the state Q, and not always the most desirable one).

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


Thanks, Tez, for that very good explanation. I even understood some of it. I recognize von Neumann from game theory and Eigen values from some branch of mathematics I studies eons ago but don't use much in my law practice.


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

Ah, but then you would be faced with a dilemma (ha, from my math studies --two horns). You would either have to hoard those cookies, or you would get fat. Anyway, I'm with you on the quantum abuse thing. It's one of life's little annoyances.

AS

[Paul C. Anagnostopoulos]

But what I'm really wondering is why, if you admit Ev shows information could evolve, and you admit that Ev is an intelligently designed program, that you are not admitting that it really shows that it takes intelligence to get information?
I just don't see where you get that from. The program starts with a random genome and information evolves through a simple set of rules. Why do you think that a set of human-designed rules is any different from an equivalent set of natural laws in this regard?

~~ Paul

[Paul C. Anagnostopoulos]

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

It is a rare foray into gobbledygook that does not begin
with a tribute to quantum mechanics. ---Jamie Whyte

[joobz]

Well in case anyone cares, this is untrue.

For a single system A in some state Q, the von-Neumann entropy of A is the same as (not the negative of!) the Shannon entropy of the "eigen-preparation" of Q (which is one special way of preparing the state Q, and not always the most desirable one).

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



I wish I got a cookie every time I spotted someone invoking quantum mechanical things they do not understand in the hopes of gaining cr ezedibility for their ideas....
Hi Tez,
I'm not certain he was claiming that the Shannon entropy was the negative of the von-neuman entropy. But rather that "Shannon's definition of information" is the negative of this entropy. Not having studied infromation theory, I don't know if such a view of information exists but at first blush doesn't seem too off.

In either case, thank you for your explanation. I'm one of the many engineers who will never design quantum devices, so I happily ignore those effects.

[Bronze Dog]

I just don't see where you get that from. The program starts with a random genome and information evolves through a simple set of rules. Why do you think that a set of human-designed rules is any different from an equivalent set of natural laws in this regard?

~~ Paul

Reminds me of some naturopaths who dismissed a well-designed negative study about the benefits of vitamin E in some area by simply stating that synthetic vitamin E is different from natural vitamin E.

[joobz]

Reminds me of some naturopaths who dismissed a well-designed negative study about the benefits of vitamin E in some area by simply stating that synthetic vitamin E is different from natural vitamin E.
Yeah, the synthetic is better absorbed and can be functional for longer durations due to the acetate group's slow cleavage. Lousy synthetic varieties that improve the natural stuff.:)

[delphi_ote]

Cookie!

It is a rare foray into gobbledygook that does not begin
with a tribute to quantum mechanics. ---Jamie Whyte
No doubt. If Tez got a cookie every time someone mentioned quantum mechanics, he'd end up with so many the Girl Scouts would come to him.

[Mr. Scott]

"Information" from nothing -- the snowflake (actual photo of one below).

The study of fractals shows that information and complexity can spontaneously arise from simplicity. A snowflake is a case in point. Nothing but water, air, wind, and a some temperature differences, and something that looks to us like it was intelligently designed emerges. I have a mathematical calculation in my hand from a Scientific American article which supports the claim that in the history of the earth, no two identical snowflake crystals have formed, even though 10^35 snowflake crystals have formed in that time. I have a book of hundreds of snowflake photos that all look unique and most look intelligently designed.

Now, imagine the world full of organic molecules before life emerged -- thrusting up and raining down and churning in the oceans down to the raging volcanic vents, forming together, like trillions of snowflakes, into all manner of complex organic molecules in fantastic patterns, and it just seems intuitively obvious that self replicating molecules -- the first life forms -- could emerge. And the process wouldn't stop when the first replicator started -- it kept happening to them and inside the bubbles that formed around them (the first cells).

Unless, of course, god just has an inordinate fondness for snowflakes as well as beetles and purple sea urchins. Can you imagine him hand-crafting each and every one? I can't.

Look into the crystal, creationists, and tell me if your gut says it was intelligently designed:
http://forums.randi.org/imagehosting/67364559fcf229ae5.jpg
Can you trust your gut?

PS: If I intelligently design a computer program that creates snowflake patterns, does that prove that snowflakes are intelligently designed?

Justin -- CHECK!

PPS: Watch the goal posts -- they are about to move.

[Beleth]

Beleth, it’s not an unfinished mansion, it’s a house of cards,We shall see.

and I’m not throwing rocks, I throwing mathematical data.Someone else had a sig once that described science as a solid wall and hypotheses as things thrown at the solid wall. A worthy hypothesis survived the impact unscathed and left the wall crumbling. Evolution is a pretty strong wall; I fear it will take more than a mathematical construct to crumble it.

But, as I said, we shall see.

And don’t make fun of my house, it happens to be a double door refrigerator box that came with built in ice-maker. I’m planning on adding a chest freezer box room addition as soon as cardboard prices drop a little.Riiiiight.

[Bronze Dog]

I find it funny that kleinman is doing exactly what woos accuse us of with that bumblebee thing. The oversimplified math model contradicts the observations, therefore it absolutely, positively must be the observations that are wrong.

[kleinman]

Paul, I didn’t say that ev doesn’t show that population helps, what I said was that huge populations don’t markedly reduce the number of generations for convergence sufficiently to allow macroevolution to occur. In addition large populations contradict Gould’s concept of punctuated equilibrium which he said occurs in small sub-populations. We don't know this, because we haven't modeled more than a measly million creatures. You won't let me extrapolate using that fitted curve, but if I did extrapolate to a lousy billion creatures, it would require 103 generations; to a trillion creatures, 21 generations. Of course, there is some asymptote it's approaching, although I haven't the slightest idea what that is. I think that is a sufficient reduction for macroevolution to take place. Wait, what was macroevolution, again? And how small is a small population of bacteria? Hang on, does punctuated equilibrium pertain to the evolution of an ancient mechanism such as genetic binding?
Why don’t you post the data you used for your curve fit and why don’t you use your equation to predict the generations for convergence with a population of two million and then run the case with ev and see how accurate your extrapolation is?
I really thought you had more to offer. I guess we know now.
I’m not offering anything, it is Dr Schneider’s ev program that is offering up the data. Have you run any cases yet?
Ev and the basics of information theory.The Shannon definition for information turns out to be mathematically equivalent to the negative of the quantum mechanical definition for entropy. If one considers that entropy is the measure of randomness this relationship becomes intuitively apparent. Increasing the information in a system reduces the randomness and thus reduces the entropy. So how does this relate to genetic evolution. One of the basic problems of Information theory is to take an initial ensemble with an initial probability distribution to a final ensemble with a final probability distribution by the input of information. In other words, you take a more random higher entropy ensemble to a less random lower entropy ensemble by the input of information. When information theorist talk about 1 bit of information, they are saying that based on a single yes or no question, the answer to that question allows them to decide which ensemble has a lower entropy. The answer to the binary question allows you to reduce the entropy and therefore the randomness by 1 bit. So you comment on the relationship between information theory and statistical mechanics. Your simply stating increased order(information) equals decreased entropy. So? Why does this matter to your kinetic arguement?
The kinetics of this model is strongly dependent on genome size and mutation rate. The smaller the genome the faster evolution by random point mutation and natural selection occur. Dr Schneider’s single published case from his model used a genome length of only 256 bases. This is 2000 times smaller than the smallest genome of any free living organism. The mutation rate also strongly affects the kinetics of this model. I have done series of cases investigating how mutation rate affects the kinetics of this model and Dr Schneider used a mutation rate of 1 mutation per 256 bases per generation which is near the optimum value for the most rapid kinetics. This mutation rate is about 4000 times higher than the average mutation rate seen in prokaryotes. He used the kinetics from his single published case to predict the evolution of a human genome in one billion years. If you simply change his mutation rate to the realistic value of 1 mutation per 1,000,000 bases per generations, his estimate for the evolution of a human genome in 1 billion years becomes 4 trillion years. If you use a larger genome than 256 bases, his estimate becomes even more preposterous. This would be equivalent to you using the rate constant for an imaginary chemical reaction that is millions of times faster than any realistic chemical reaction and applying that rate to the realistic chemical reaction. There is no scientific basis for this type of arithmetic.
Unlike many IDers who have criticized Dr Schneider’s simulation, I find his basic concept plausible. What I don’t find plausible is Dr Schneider’s use of unrealistic parameters. Dr Schneider used a genome length of only 256 bases (2000 times smaller than the smallest genome known in any free living organism) and a mutation rate of 1 mutation per 256 bases per generation (4000 times higher than the average mutation rate in prokaryotes) in his publication on ev. When more realistic parameters are used in the model, the rate of acquisition of information become profoundly slow as will unfold as the data from ev is presented. This rate of information acquisition becomes so slow that it shows that it takes hundreds of millions of generations to evolve less than 100 loci on a genome of only 100,000 bases. Point mutation and natural selection is a profoundly slow process. Far too slow to evolve a gene de novo. That's it? Um, again, Not enough time? THere are never situations where mutation rate changes? I'm sorry, the model is interesting in it's ability to show increased information with improvements in the binding site sequence. But you ignore, not all point mutations are created equal. Some loci are not as improtant as others (consider consensus sequences). You ignore insertion/deletion errors You ignore genetic exchange You ignore the ADMITTED limitations to the code presented
Dr Schneider said the following about his code from the following URL:
http://www.ccrnp.ncifcrf.gov/~toms/paper/ev/truman/ (http://www.ccrnp.ncifcrf.gov/~toms/paper/ev/truman/)
A good simulation does not attempt to simulate everything; only the essential components are modeled. For the issue at hand, the form of the genetic code is not relevant; information measured by Shannon's method is more general than that.
I do not ignore any of the other mechanisms that you mention. My contention has been from the beginning that ev show that macroevolution by random point mutations and natural selection is mathematically impossible when realistic parameters are used in the model. If you think that frame shift mutations, recombination, genetic exchanges or any other mechanism for altering a genome are more important than random point mutations, produce the evidence and a mathematical model that shows how these mechanisms can accomplish macroevolution. Or are you going to use your anything is possible scientific explanation? The theory of evolution remains without a mathematical foundation. The best model of evolution by random point mutations and natural selections shows that macroevolution is impossible by the mechanism it models.
I'm sorry, you claim an understanding of engineering, but haven't exercised any of the critical analysis required in the disipline. As an engineer, you MUST know what a math model is and what it can and can not do. I don't want to believe that you are being delibertly missleading, but you are leaving me little room to think otherwise.
And your idea of critical analysis is not to run any cases with ev and examine the behavior of the model and still jump to conclusions anyway. You don’t need much room to think when you don’t do any.
How do you get the original gene to cross-over or invert? You must still have some mechanism to create the original gene. Yes, and point mutation is one mechanism, but there are others (insertions, deletions, translocations, inversions, duplications...) in addition to genes from other organisms (intra- and inter-species).
If you think that frame shift mutations are the main mechanism for producing new genes, produce the evidence, make a mathematical model and show how it happens. Again, inversions, duplications and recombination require existing genes. Ev shows the rate acquisition of information is so profoundly slow for random point mutations and natural selection that creating a gene de novo by this mechanism is mathematically impossible. Intra and inter species transfers still require an existing gene. How do you make the original gene? At least Dr Schneider put his ideas into mathematical terms. Your arguments may convince naïve grade school students and devout evolutionarians but they don’t constitute a hard mathematical scientific proof.
But new genes are not created solely by random point mutations. I mention other mechanisms above. And yes, recombination does usually refer to resorting alleles, but recombination with errors can effectively create new genes. And this is in addition to horizontal transmission of genetic material.
Would you like to give some examples of errors in recombination that have created new genes? Then apply this mechanism in a mathematical model and show how macroevolution occurs by recombination errors. Of course this mechanism would not be very useful to prokaryotes.
What you appear to be doing is using a computer simulation, of part of the real world, that is only valid within it's design parameters of single point mutations, to show that life could not have evolved this way, thereby showing that the theory of evolution is not correct. Since you are extrapolating the results outside the design parameters (ie. there are more factors than just point mutation), any results you get are completely meaningless since they are not valid in the real world.
The following quotes were taken from Dr Schneider’s blog web page: http://www.lecb.ncifcrf.gov/~toms/paper/ev/blog-ev.html (http://www.lecb.ncifcrf.gov/~toms/paper/ev/blog-ev.html)

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

"Schneider's paper is misleadingly titled: "Evolution of biological information". But it is just a *computer* simulation. No actual *biological* materials (e.g. genomes of nucleic acids, proteins, etc) were used, nor does Schneider propose that his simulation be tested with *real* genomes or proteins Actual biological materials were used to determine the original hypothesis. Read the literature: Schneider1986 (http://www.lecb.ncifcrf.gov/~toms/paper/schneider1986)

It only becomes *real* biological information and random mutation and natural selection, when the simulation is tested in the *real* world, using *real* DNA, proteins, with *real* mutations and a *real* environment does the selecting. It is significant that Schneider does not propose this, presumably because he knows it wouldn't work.You are very bad at reading my mind, I have considered doing this experiment. Given the right conditions, it WILL WORK. Do you have th gumption to do the experiment yourself? That's the way real science works! FURTHERMORE, if you read the literature, you will recognize that related experiments have been repeatedly done for 20 years. Look up SELEX.

In the rest of the paper he uses the single word "selection". I take this as a tacit admission that his model is not a simulation of *real* biological natural selection. No. A rose is a rose by any other name. Selection is selection whether it be natural (generally meaning the environment of earth), breeding (by humans usually, though perhaps some ants select their fungi), SELEX or in a computer simulation. Of COURSE it is a simulation of natural selection! The paper would not be relevant to biology and would not have been published in a major scientific journal if it were not!

Schneider lets slip that there is another unrealistic element in his (and indeed all) computer simulations in that it (they) "does not correlate with time": So? Run the program slower if you want. Make one generation per 20 minutes to match rapid bacterial growth. THIS WILL NOT CHANGE THE FINIAL RESULT!

Well, when Schneider's simulation is actually tested with *real* "life" (e.g. a bacterium), and under *real* mutation and natural selection it gains information, then, and only then, would "creationists" be favourably impressed. But if they are like me, they would already be impressed (but unfavourably) that Schneider does not mention in his paper that his simulation should now be so tested in the *real* "biological" world. 1. The simulation was of phenomena in the "real" world.
2. Dr. Jones is invited yet again to do an experiment.

The following is a response Dr Schneider made to a statement made by David Berlinski (http://www.discovery.org/scripts/viewDB/index.php?command=view&id=51&isFellow=true).

Where attempts to replicate Darwinian evolution on the computer have been successful, they have not used classical Darwinian principles, and where they have used such principles, they have not been successful. The ev program disproves this statement since it uses classical Darwinian principles and was successful.

The previous statements are clear that Dr Schneider believes that ev simulates the real world. If the simulation is appropriate for small genomes then it is appropriate for large genomes. Macroevolution by mutation and natural selection is mathematically impossible.
Ev and the basics of information theory. The Shannon definition for information turns out to be mathematically equivalent to the negative of the quantum mechanical definition for entropy. Well in case anyone cares, this is untrue.
Blame that quote on Frank Andrews. I got it out of his text Equilibrium Statistical Mechanics. He has a chapter in that text where he derives Shannon’s definition for information and then relates this to the quantum mechanical definition of entropy.
There is a big difference when we consider both A and another system B, and the (possibly correlated) states - call them "QR" - between A and B (i.e. correlated probability distributions in the classical case). The Shannon entropy on Q is always less than or equal to that on QR, for the simple reason that in classical information theory you cannot be more uncertain about Q than you are about the joint variable QR. But in the quantum case, in certain cases the opposite is true - the von-Neumann entropy of the joint system can be 0 while that of the individual subsystems is >0!
Dr Schneider’s model consists only of a single system A that starts out with an initial ensemble and probability frequency distribution. Information is added by random mutations and natural selection to take system A to a final ensemble and probability frequency distribution. There is no other system B in Dr Schneider’s model. Tez, have you even looked at Dr Schneider’s model or are you like joozb and jump to conclusions without examining Dr Schneider’s model? Not only do evolutionists carry the thin skinned crybaby gene, it appears they carry the jump to conclusion without examining the facts gene as well.
I wish I got a cookie every time I spotted someone invoking quantum mechanical things they do not understand in the hopes of gaining credibility for their ideas....
Tez, how did you figure out Dr Schneider’s model, telekinesis?

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

[joobz]

The kinetics of this model is strongly dependent on genome size and mutation rate. The smaller the genome the faster evolution by random point mutation and natural selection occur. Dr Schneider’s single published case from his model used a genome length of only 256 bases. This is 2000 times smaller than the smallest genome of any free living organism. The mutation rate also strongly affects the kinetics of this model. I have done series of cases investigating how mutation rate affects the kinetics of this model and Dr Schneider used a mutation rate of 1 mutation per 256 bases per generation which is near the optimum value for the most rapid kinetics. This mutation rate is about 4000 times higher than the average mutation rate seen in prokaryotes. He used the kinetics from his single published case to predict the evolution of a human genome in one billion years. If you simply change his mutation rate to the realistic value of 1 mutation per 1,000,000 bases per generations, his estimate for the evolution of a human genome in 1 billion years becomes 4 trillion years. If you use a larger genome than 256 bases, his estimate becomes even more preposterous. This would be equivalent to you using the rate constant for an imaginary chemical reaction that is millions of times faster than any realistic chemical reaction and applying that rate to the realistic chemical reaction. There is no scientific basis for this type of arithmetic.
You've repeated this, "I've changed the mutation rate..." statement several times. And I've stated several more that this point is moot. You don't know the actual mutation rate. Mutation rate can vary by the addition of any mutagenic compound. Multiple mutagenic pathways exists. And I'm sure there are more to be discovered. Also can you tell me HOW this program accounts for genetic exchange that occurs between cells?

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


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

I do not ignore any of the other mechanisms that you mention. My contention has been from the beginning that ev show that macroevolution by random point mutations and natural selection is mathematically impossible when realistic parameters are used in the model. If you think that frame shift mutations, recombination, genetic exchanges or any other mechanism for altering a genome are more important than random point mutations, produce the evidence and a mathematical model that shows how these mechanisms can accomplish macroevolution.
This may be the smartest thing you've said. I agree, that we need to verify this hypothesis. But the game that, "This model bad=evolution bad" wouldn't be acceptable for a freshman engineering course. It won't fly here. Sorry, try again.

Or are you going to use your anything is possible scientific explanation? The theory of evolution remains without a mathematical foundation. The best model of evolution by random point mutations and natural selections shows that macroevolution is impossible by the mechanism it models.
The fact that evolution can occur at all with JUST point mutations is a fairly substantial discovery. The fact that it alone doesn't explain evolution isn't unexpected. You can call it anything goes, but nothing have I said contridicts known scientific concepts. You can't state the same.

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

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

[fls]

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

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

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

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

Linda

[kleinman]

The kinetics of this model is strongly dependent on genome size and mutation rate. The smaller the genome the faster evolution by random point mutation and natural selection occur. Dr Schneider’s single published case from his model used a genome length of only 256 bases. This is 2000 times smaller than the smallest genome of any free living organism. The mutation rate also strongly affects the kinetics of this model. I have done series of cases investigating how mutation rate affects the kinetics of this model and Dr Schneider used a mutation rate of 1 mutation per 256 bases per generation which is near the optimum value for the most rapid kinetics. This mutation rate is about 4000 times higher than the average mutation rate seen in prokaryotes. He used the kinetics from his single published case to predict the evolution of a human genome in one billion years. If you simply change his mutation rate to the realistic value of 1 mutation per 1,000,000 bases per generations, his estimate for the evolution of a human genome in 1 billion years becomes 4 trillion years. If you use a larger genome than 256 bases, his estimate becomes even more preposterous. This would be equivalent to you using the rate constant for an imaginary chemical reaction that is millions of times faster than any realistic chemical reaction and applying that rate to the realistic chemical reaction. There is no scientific basis for this type of arithmetic.You've repeated this, "I've changed the mutation rate..." statement several times. And I've stated several more that this point is moot. You don't know the actual mutation rate. Mutation rate can vary by the addition of any mutagenic compound. Multiple mutagenic pathways exists. And I'm sure there are more to be discovered. Also can you tell me HOW this program accounts for genetic exchange that occurs between cells? You clearly are performing the model with blinders on. feel free to continue. Don't expect it to mean much to anyone.
I have run hundreds of cases with ev and you tell me I, the one with blinders on. You are correct that there are a wide variety of mutation rates. That is why I included mutation rates in the parametric studies I have done to see how mutation rate affects the rate of evolution. I understand that data doesn’t mean much to evolutionists especially when it contradicts their belief system.
I do not ignore any of the other mechanisms that you mention. My contention has been from the beginning that ev show that macroevolution by random point mutations and natural selection is mathematically impossible when realistic parameters are used in the model. If you think that frame shift mutations, recombination, genetic exchanges or any other mechanism for altering a genome are more important than random point mutations, produce the evidence and a mathematical model that shows how these mechanisms can accomplish macroevolution.
This may be the smartest thing you've said. I agree, that we need to verify this hypothesis. But the game that, "This model bad=evolution bad" wouldn't be acceptable for a freshman engineering course. It won't fly here. Sorry, try again.
See my discussion below on problems with mechanisms for evolution other than random point mutations and natural selection. I understand evolutionists are slow to get this but I will be patient with you until you are able to get off the ground.
And your idea of critical analysis is not to run any cases with ev and examine the behavior of the model and still jump to conclusions anyway. You don’t need much room to think when you don’t do any. I don't need to look at the blueprints to know that the Empire State Building can't be built with Laffy Taffy and I don't need to run the simulations because your ENTIRE PROPOSITION IS FLAWED.

Isn’t what you have just done what evolutionists like to call a strawman? The theory of evolution can’t be built on Laffy Taffy and it can’t be built on random point mutations and natural selection either.
If you think that frame shift mutations are the main mechanism for producing new genes, produce the evidence, make a mathematical model and show how it happens. Again, inversions, duplications and recombination require existing genes. Ev shows the rate acquisition of information is so profoundly slow for random point mutations and natural selection that creating a gene de novo by this mechanism is mathematically impossible. Intra and inter species transfers still require an existing gene. How do you make the original gene? At least Dr Schneider put his ideas into mathematical terms. Your arguments may convince naïve grade school students and devout evolutionarians but they don’t constitute a hard mathematical scientific proof. Would you like to give some examples of errors in recombination that have created new genes? Then apply this mechanism in a mathematical model and show how macroevolution occurs by recombination errors. Of course this mechanism would not be very useful to prokaryotes. I am not attempting a hard mathematical scientific proof (although I agree that that is a valuable endeavour). You are demonstrating that Ev cannot account for reality. You are claiming that Ev accurately models the proposed mechanism by which we arrived at the current state of affairs, therefore the flaw is in the proposed mechanism (point mutation and selection). I and others are pointing out that if your model doesn't account for reality, it is also possible that there is a flaw in the model. This especially becomes a consideration when the model lacks content validity. That you dismiss these concerns by insulting me does not change this. My point all along has been this - you have not excluded reasonable alternate explanations for your results, which makes all this effort meaningless; it cannot persuade.
I am not the only one who says that ev accurately models reality, Dr Schneider says this, Paul said this until he realized what ev showed when realistic parameters are used in the model. Paul is now doing the evolutionist twist to try and explain away his broad claims that he has made. See my paragraphs below on the problems for mechanisms other than random point mutations and natural selection. I think the more you consider the position you are taking, the less tenable it becomes. Point mutations and natural selection is the cornerstone for your theory, no other mechanism can replace it.

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

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

[Tez]

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

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


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

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

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


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

[delphi_ote]

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

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

[Paul C. Anagnostopoulos]

I am not the only one who says that ev accurately models reality, Dr Schneider says this, Paul said this until he realized what ev showed when realistic parameters are used in the model.
You really can't stop lying, can you?

~~ Paul

[kleinman]

Blame that quote on Frank Andrews. I got it out of his text Equilibrium Statistical Mechanics. You were the one that made the statement (unattributed to Andrews, whom I suspect you have misunderstood) - a statement which you followed by the equally trite "If one considers that entropy is the measure of randomness this relationship becomes intuitively apparent." I discussed the "two-systems" case because it shows this is nonsense - it is not intuitively apparent, because it is wrong! FWIW, I am hardly even following the particular discussion at hand (I have not the time nor patience of St. Paul A.), I was just pointing out that your statement clearly displayed ignorance of what the relationship between the Shannon and von-Neumann entropies is, and for that I need not know anything about the context in which you are trying to invoke the relationship. Of course that may or may not have a bearing on whether you know anything about the rest of what you're talking about - I'm not about to pass judgment because I haven't read the rest of it.
Sorry I didn’t put a reference section in that post, I have identified the source of the statement that Shannon information is mathematically equivalent to the negative of quantum mechanical definition for entropy on other threads. If you like believing increasing the information in a system increases the randomness in the system, spread your wisdom far and wide. I can tell you are an impatient type, you don’t even have the patience to spell Paul’s last name. I have the patience to do it, it is Anagnostopoulos. Sirens and red lights used to go off in my spell checker when I entered his name into a document but something has happened, my spell checker no longer responds to his name. The amount of information in my spell checker must have increased and therefore the randomness has increased.
He has a chapter in that text where he derives Shannon’s definition for information and then relates this to the quantum mechanical definition of
entropy. There is only one special circumstance (even for a single system) in which the relationship is one of equality. If you understood that circumstance, you could then make an argument about why it is the one relevant for this discussion (which, I repeat, I am hardly following). But you don't, so you can't.
Andrew’s derivation is for the general definition for Shannon’s information not a special case. The mathematical relationship that Andrew’s describes between Shannon’s information and the quantum mechanical definition of entropy is general as well, not for a specific case. Interestingly, Andrews does one numerical example in that chapter and it directly relates to Dr Schneider’s model. So, Tez if you want to believe that increasing the information in a system also increases the entropy, have at it.
Dr Schneider’s model consists only of a single system A that starts out with an initial ensemble and probability frequency distribution. Information is added by random mutations and natural selection to take system A to a final ensemble and probability frequency distribution. There is no other system B in Dr Schneider’s model. Tez, have you even looked at Dr Schneider’s model or are you like joozb and jump to conclusions without examining Dr Schneider’s model? I wasn't criticizing the model. I was criticizing you. I was pointing out that you don't understand von-Neumann entropy and are invoking quantum mechanics, presumably to try and sound more educated than you evidently are. Since I doubt there is any need for you to even think quantum-mechanically in the context of this argument, my friendly advice is to only talk about that which you do understand well. We can't all know everything.
Both you and Dr Schneider believe that increasing the information of a system increases the randomness in the system. Why you don’t have an intuitive problem with this makes me wonder. Get Andrew’s book, you can get it at Amazon. Andrew’s does a straightforward coherent derivation.

I know what you are, you’re a Tez dispenser, somebody pushes down on your head and something pops out of your mouth.
Increasing the information in a system reduces the randomness and thus reduces the entropy. Shannon information is a measure of randomness.
So is entropy. You need to get the Andrew’s text as well. Don’t let your head blow up, the theory of evolution is the only thing that is blowing up.
I am not the only one who says that ev accurately models reality, Dr Schneider says this, Paul said this until he realized what ev showed when realistic parameters are used in the model. You really can't stop lying, can you?
Be careful Paul, google is watching you.

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

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

[Paul C. Anagnostopoulos]

Be careful Paul, google is watching you.
Fine and dandy.


Are you ever going to post the data for your latest curve fit and then produce the next data point in that series to see how accurate your curve fit extrapolates the next point?
Well, let's see. I ran this experiment:

genome size 1024
binding sites 16
1 mutation / genome

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

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

~~ Paul

[fls]

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

Linda

[joobz]

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

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

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

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

[Apathia]

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

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

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

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

[kleinman]

Are you ever going to post the data for your latest curve fit and then produce the next data point in that series to see how accurate your curve fit extrapolates the next point? Well, let's see. I ran this experiment: genome size 1024, binding sites 16, 1 mutation / genome
Not just the input parameters, the population/generations for convergence data used to obtain your curve fit as well.
If you want to email me a Pascal Ev that runs on a PC along with the inputs, I can try to run a population of 2 million.
Dr Schneider’s posted version of ev pascal will run on a pc under the GNU version of the pascal compiler. You can download a version of that pascal compiler for your platform at:
http://www.gnu-pascal.de/binary/ (http://www.gnu-pascal.de/binary/)
The only thing I have had to change in Dr Schneider’s code to run larger cases are his variables maxgenomesize and maxbugs to get the larger cases to run. Be forewarned that the case with G=1000 and population of 1 meg took 300Mbytes of RAM. The population = 2 meg will take about 600Mbytes so if you don’t have 1 Gig of RAM on your computer, be prepared for a disk page file that will run so slow that RM&NS will seem speedy. This program also sucks up clock cycles so that any other applications running at the same time will go very slowly. The one advantage with the pascal version of ev is that you can break up the calculation into a series of small runs which you can do overnight while you aren’t using your computer.

You have the author of the program to consult with if you should have problems setting up the pascal version for your platform. If he won’t help, I’ll do what I can.
Alright. I'm ready to call it. I was willing to give you the benefit of the doubt and listen to what you had to say. But first I wanted to know why you had erected a strawman and were wasting your time disproving that. Your response so far has been, "you are too ignorant to realize that it is not a strawman". And I have given this possibility serious consideration because I realize that sometimes a statement can appear to be incorrect, but further explanation provides clarification and agreement. But in the end I cannot find that the evidence supports this supposition, despite a sincere effort (on my part) to try and make the evidence fit.
I have not said that quote you attribute to me.

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

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

[kleinman]

His repeated use of insults and jabs instead of substance highlights the fact that there is nothing to what he says. At best, he's found an interesting limitation in the ev model. At worst, he's an intentionally manipulative and deceiving individual who cares not for truth and discovery only that his faith is reaffirmed.
My best jabs are the mathematical data and your weak response to this is that I am manipulative and deceptive. Have you run any cases with ev yet or are you sticking with your anything is possible argument for the theory of evolution?
I've been following this thread with much interest but not posting, because back in college I dropped out of the Sciences and entered the Humanities when Calculus class gave me the final death blow.
Another evolutionist from the math is hard school of science. The theory of evolution must be true, it feels so good.

[Apathia]

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

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

[Beleth]

The theory of evolution must be true, it feels so good.
But that's the ironic thing, isn't it? Evolution doesn't feel good.

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

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

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

[joobz]

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

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

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

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

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

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

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

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

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

[Paul C. Anagnostopoulos]

Dr Schneider’s posted version of ev pascal will run on a pc under the GNU version of the pascal compiler. You can download a version of that pascal compiler for your platform at:
http://www.gnu-pascal.de/binary/
Snore. I'm not going to bother installing stuff just to compile the Pascal version. If you have one for the PC, send it. Otherwise never mind.


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

~~ Paul

[kleinman]

Another evolutionist from the math is hard school of science. The theory of evolution must be true, it feels so good. I admit being a doofus when it comes to math, and being a doofus in the way I worded my post, but that is irrelevant. How do you get from a flawed theory of how evolution occured to how it didn't occur at all?
If you understand the mathematics associated with balancing your checking account you will be able to get some understanding of what I am talking about in this debate.

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

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

My best jabs are the mathematical data and your weak response to this is that I am manipulative and deceptive. Have you run any cases with ev yet or are you sticking with your anything is possible argument for the theory of evolution?Why do I think you are being manipulative and deceptive? because your entire strategy has been a smoke screen.
Just pretend I’ve lit an incense candle.
For instance, Why bring in thermodynamics to your arguement?
Dr Schneider has used Information Theory to derive his model which is related to the 2nd law of thermodynamics. Read Dr Schneider’s paper http://www-lmmb.ncifcrf.gov/~toms/paper/ev/ev.pdf (http://www-lmmb.ncifcrf.gov/~toms/paper/ev/ev.pdf) where he makes it clear that his model is derived using principles of thermodynamics.
how does that affect the actual claim you make? I've asked this question several times.
This doesn’t affect my claims, I am only agreeing that Dr Schneider has employed the principles of thermodynamics properly in the formulation of his model. I agree that is application of the underlying theory is essentially correct.
thermodynamics is a study of equilibirium.
Professor!!!! Look at the word thermodynamics. The simplest examples in the study of thermodynamics are equilibrium cases, in general, thermodynamics studies as the word says dynamic or changing situations. You must really confuse your students.
Thermodynamics will tell you what the final result should be, but it WON'T tell you when it'll get there. UNLESS YOU KNOW THE ACTIVATION ENERGY.
Dr Schneider’s model is not simulating a chemical reaction with a rate constant associated with this chemical reaction, he is simulating information gain based on random point mutations and natural selection. If you start doing some examples with his model you might begin to understand the distinction.
I've asked for this info, but you fail to provide it. In fact, The model requries you to ENTER a rate. As such, you are simply using a kinetic analysis, not a thermodynamic one. The model shows that the system will tend to form a binding site thermodynamically. And you still claim that your arguements are based on mathematical principles, when you can't demonstrate a clear understanding of what those principles are.
There are several parameters that affect the rate of convergence of this model. The obvious one is the mutation rate, however, genome length, population, number of binding sites and other parameters affect the rate of evolution as well. You have locked your mind into thinking this is the simulation of a chemical reaction based on the 1st law of thermodynamics. This is not what Dr Schneider’s model simulates. Dr Schneider is simulating how random mutations and natural selection operate under the 2nd law of thermodynamics. The only way the 1st law of thermodynamics applies to Dr Schneider’s model is implicit in natural selection. The notion of natural selection is that the organism with more efficient use of the energy available to it will be able to put more of that energy toward reproduction. This is an implicit assumption in Dr Schneider’s model.
Do you really claim that running simulations is equivalent to "doing math".
No, because that is what Dr Schneider did with his single published case. What is required to understand the behavior of this model is to do a systematic parametric study. I have done this and if you did this, you would better understand my claims.
I again state your assumptions are wrong which makes the your view of the kinetic data meaningless. you can claim otherwise all you want, but you have not offered any proof.
You have made your decision without examining the data from ev.
You will have to forgive us for not ignoring the real world just because a simulation, with who-knows-how-many "reasonable sounding" assumptions, produces evidence that one or more of its assumptions is definitely wrong...
I don’t argue with evolutionists’ observations, I argue with the interpretation of these arguments.

[Paul C. Anagnostopoulos]

Dr Schneider is simulating how random mutations and natural selection operate under the 2nd law of thermodynamics.
He is? ... checks Java version code ... oops! I forgot the 2LoT module!

~~ Paul

[kleinman]

Dr Schneider’s posted version of ev pascal will run on a pc under the GNU version of the pascal compiler. You can download a version of that pascal compiler for your platform at: http://www.gnu-pascal.de/binary/ (http://www.gnu-pascal.de/binary/) Snore. I'm not going to bother installing stuff just to compile the Pascal version. If you have one for the PC, send it. Otherwise never mind.
You are so lazy, I will email the executable for the 2 meg population case. You do have intel processors on your computer?
What is the strawman you are talking about?The one where evolution proceeds by single-point mutation from large random genomes and has to evolve binding sites in some ill-specified short period of time. You know, the one trick straw pony.
Paul, haven’t you figured out that I am not affected by your crybaby complaints. You can continue to try to make the readers think that ev is the simulation of a large random genome but once this belly aching phase of this discussion ends we can start discussing what this model is simulating. That includes the assumption that there is a point where evolutionist stop belly aching.

[Paul C. Anagnostopoulos]

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

~~ Paul

P.S. Call me rude.

Edited to add: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1206269

http://www.pnas.org/cgi/content/full/102/25/8791

[joobz]

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


thank you for falling into the trap I set. :D :D
You've just proved what I knew all along, you really don't know the subject.

The origin of term "Thermodyanmics" is the translation of heat into mechanical engery. Hence, thermo and dynamic. But what it really is (especially when we use your beloved 2nd law) is a study of equilibirum systems.

So, again, thank you for proving to all, that you really don't know what you are doing.

[kleinman]

P.S. Call me rude.
I don’t need to, but I do appreciate you telling me that’s what you were trying to do.

I’ve sent you the ev pascal executable version to run the 2 meg population case along with the associated input files. Depending on the speed of your computer, that case will take 1-2 weeks of CPU time.

[kleinman]

Professor!!!! Look at the word thermodynamics. The simplest examples in the study of thermodynamics are equilibrium cases, in general, thermodynamics studies as the word says dynamic or changing situations. You must really confuse your students. thank you for falling into the trap I set.
You've just proved what I knew all along, you really don't know the subject.
Oh joozb, and you call me tricky and deceitful. How could you be so mean to me? What have I ever done to you?

Go back to your lower division classes and confuse your students.

[joobz]

Oh joozb, and you call me tricky and deceitful.
Yes, I know. I'm not proud of doing it, but it had to be done.
No scientist or rational person would presume to always be right. You've maintained a position of infallibility that I have no respect for.
How could you be so mean to me? What have I ever done to you?
You've simply missrepresented fact and truth. You continue to deny obvious evidence and respond with insults and personal attacks when your logic fails.

Go back to your lower division classes and confuse your students.
I do not know what you mean by "lower division". I can only assume it means "better education than Kleinman received.":)

[delphi_ote]

So is entropy. You need to get the Andrew’s text as well. Don’t let your head blow up, the theory of evolution is the only thing that is blowing up.
Earlier, you stated that Shannon information was the opposite of physical entropy. Now you state that they're the same thing. You've contradicted yourself on the most basic concept in all of information theory.

You need to pick up even the most basic text on information theory before you comment on the subject any further.

[Yahzi]

If I intelligently design a computer program that creates snowflake patterns, does that prove that snowflakes are intelligently designed?
What if you write a program that can beat you at chess?

Where did that information - the superior chess-playing ability - come from?

But of course, theology simply ignores facts it doesn't like.

(With apologies to Maxwell...) Yahzi's demon: it sits at the mouth of your proof, and only allows in facts that support your case, while effortlessly closing out facts that don't. Viola! truth from nothing!

[joobz]

(With apologies to Maxwell...) Yahzi's demon: it sits at the mouth of your proof, and only allows in facts that support your case, while effortlessly closing out facts that don't. Viola! truth from nothing!

Hey! The great part of Yahzi's demon is that you can ignore the facts that prove such a demon cannot exist, thereby proving it's existence!

[Almo]

Where I think we differ in this view point is that I think that natural selection will limit these microevolutionary changes and not allow an organism to diverge too far from its genetic optimum.

Evolution is not about "optimum". It is about "reproductive success," which may be far from optimum. The fit survive, yet the unfit may live. Read "Full House" by Stephen Jay Gould. He explains the common misconception of evolution as a ladder very well in that book.

[fls]

Okay. I'm fairly new here, so slap me if my timing is off.

This is my favourite melt-in-your-mouth shortbread cookie recipe:

1 c. unsifted flower
1/2 c. corn starch
1/2 c. confectioners sugar
3/4 c. butter
1 tsp. vanilla

In bowl, stir together first 3 ingredients. In large bowl with mixer at medium speed, beat butter until smooth. Beat in flour mixture and vanilla until well blended. Refrigerate 1 hour. Shape into 1-inch balls and place about 1-1/2 inches apart on ungreased cookie sheet. Flatten with lightly floured fork. Place half a candied cherry on top. Bake in 375 degree oven 10 to 12 minutes or until edges are lightly browned. Makes about 3 dozen cookies.

Linda

[Tez]

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

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

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

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

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

Be careful Paul, google is watching you.

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

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

Well, from what you say it seems that Andrews is a completely ignorant fool, who hasnt got a clue about entropy. He obviously throws about words he doesn't understand in order to look smart - I'm sure if he was reading my posts the moron would read into them things that werent there and then make drivelous and incorrect assertions about what I'd said in them.

Fortunately this term I am actually teaching graduate students (http://www3.imperial.ac.uk/theoreticalphysics/postgraduatestudy/mastersdegree/courses/quantuminformation ) about both quantum and classical entropy, and I am also actually exploiting differences between them in one of my current research projects. People who write textbooks clearly shouldn't be trusted for a deep understanding of anything - and so I for one am very secure in the fact that I know much more about the topic than him. I bet the twit is a chemist - that would explain it. Though even if thats the case he is a fellow scientist, and so I should apologize for him having led you so far astray - if you happen to be in london you are welcome to drop by my lectures next week to actually learn what that monkey-brain should have been saying in his derivation of the relationship(s) between the entropies.

Apologies from the scientific community on his behalf once again.

Tez

[kleinman]

Oh joozb, and you call me tricky and deceitful.Yes, I know. I'm not proud of doing it, but it had to be done.
No scientist or rational person would presume to always be right. You've maintained a position of infallibility that I have no respect for.
You haven’t run a single case with ev and you think you are prepared to offer a learned opinion. Save your drivel (Tez, I like that word too) for your evolutionist companions.
How could you be so mean to me? What have I ever done to you?You've simply missrepresented fact and truth. You continue to deny obvious evidence and respond with insults and personal attacks when your logic fails.
When will you stop your crying and run some cases with ev?
Go back to your lower division classes and confuse your students.I do not know what you mean by "lower division". I can only assume it means "better education than Kleinman received."
It doesn’t matter. Are you ever going to run any cases with ev?
So is entropy. You need to get the Andrew’s text as well. Don’t let your head blow up, the theory of evolution is the only thing that is blowing up.Earlier, you stated that Shannon information was the opposite of physical entropy. Now you state that they're the same thing. You've contradicted yourself on the most basic concept in all of information theory. You need to pick up even the most basic text on information theory before you comment on the subject any further.
You need to pay better attention to the details. What I said is that the Shannon definition of information is mathematically equal to the negative of the quantum mechanical definition of entropy.

When I saw that Paul had started this thread on “annoying creationists”, I told Paul I was going to join this discussion but I was going to bring my rain coat because I expected you crybaby evolutionists to throw your pabulum. Now I’ve got to wear my rain coat because evolutionist heads are blowing up.
Where I think we differ in this view point is that I think that natural selection will limit these microevolutionary changes and not allow an organism to diverge too far from its genetic optimum. Evolution is not about "optimum". It is about "reproductive success," which may be far from optimum. The fit survive, yet the unfit may live. Read "Full House" by Stephen Jay Gould. He explains the common misconception of evolution as a ladder very well in that book.
Is there a difference between less successful, more successful and most successful?
Okay. I'm fairly new here, so slap me if my timing is off. This is my favourite melt-in-your-mouth shortbread cookie recipe:
Linda, I think you timing is perfect, however, Tez has nuts in his cookies.
Well, from what you say it seems that Andrews is a completely ignorant fool, who hasnt got a clue about entropy. He obviously throws about words he doesn't understand in order to look smart - I'm sure if he was reading my posts the moron would read into them things that werent there and then make drivelous and incorrect assertions about what I'd said in them.
Did somebody push on your head again?

[Paul C. Anagnostopoulos]

Okay. I'm fairly new here, so slap me if my timing is off.
Nope, timing good.

~~ Paul

[delphi_ote]

You need to pay better attention to the details. What I said is that the Shannon definition of information is mathematically equal to the negative of the quantum mechanical definition of entropy.
Sorry, but that's not all you said. In the very next sentence (you know, the one I responded to in the first place) you make a patently false claim.
Increasing the information in a system reduces the randomness and thus reduces the entropy.
This statement is incorrect. I explained why in my first response. If that's not enough, check the Wikipedia entry on information theory. Shannon entropy and self information are one and the same, and they both increase as probability distributions approach uniformity. Please be intellectually honest and admit that this statement is incorrect.

[joobz]

Please be intellectually honest and admit that this statement is incorrect.
Honesty? You'll not get that from Kleinman. All you can hope fore is more insults. Maybe they'll be more clever.

[kleinman]

I did say both:
You need to pay better attention to the details. What I said is that the Shannon definition of information is mathematically equal to the negative of the quantum mechanical definition of entropy.
and
Increasing the information in a system reduces the randomness and thus reduces the entropy.
Both statements are mathematically and intuitively correct and represents what is occurring in Dr Schneider’s ev program. Remember that when we apply a coordinate system to a physical situation, plus and minus signs can be reversed depending on which way we decide to label the coordinate system. The coordinate system does not change the physical problem but in order to get proper result, you must maintain consistency throughout your calculation. When I set up a coordinate system for a physical problem, I try to set that coordinate system such that you match what intuitively happens in your calculations. Random point mutations and natural selection add information to the genome thus reducing the disorder of the genome and therefore the entropy of the genome. You are increasing the entropy and disorder of the universe in Dr Schneider’s model and thus reducing the information in the universe, however since entropy is not a conservative property, it won’t help trying to compute this value. I think if you study Dr Schneider’s model and run some cases you will start to get a sense of what I am saying.
Please be intellectually honest and admit that this statement is incorrect. Honesty? You'll not get that from Kleinman. All you can hope fore is more insults. Maybe they'll be more clever.
Joobz, run any cases from ev or you still able to come to conclusion without the data?

I wonder what annoys you evolutionists more, the fact that I say macroevolution is mathematically impossible based on the results of ev or that I am using a computer model written by an evolutionist to do it?

[delphi_ote]

Honesty? You'll not get that from Kleinman. All you can hope fore is more insults. Maybe they'll be more clever.
Well, we'll see what happens. This is a fairly simple thing that could be cleared up easily with no hard feelings. I study information theory, and I think it's important to get it right.

[joobz]

Well, we'll see what happens. This is a fairly simple thing that could be cleared up easily with no hard feelings. I study information theory, and I think it's important to get it right.

There are several points that are important to get right. This is just one of them, and I'm glad someone with knowledge of information theory is holding him to it. My complaint is that he still fails to address why he even invokes thermo. All of his arguements describe an issue of rate. Since the program requires the input of the mutation rate, this whole thermodynamic argument is a smoke screen.

the model shows that the model trends toward information. That's the power of it. that is the equilibrium point being reached. We don't know rate here and all we can do is make assumptions.

[kleinman]

Honesty? You'll not get that from Kleinman. All you can hope fore is more insults. Maybe they'll be more clever. Well, we'll see what happens. This is a fairly simple thing that could be cleared up easily with no hard feelings. I study information theory, and I think it's important to get it right.
If you evolutionarians are as smart as you think you are, you would go to the Evolutionisdead web site, in particular, study the following thread:
http://www.evolutionisdead.com/forum/viewtopic.php?t=348&sid=f42b17926a042f8bf08e0eb2cc13c212 (http://www.evolutionisdead.com/forum/viewtopic.php?t=348&sid=f42b17926a042f8bf08e0eb2cc13c212)
I have had extensive discussions with Paul and several other evolutionists. Doing this will help take you off the learning curve on this problem and you can avoid making a bunch of ignorant statements. If you examine that thread carefully you will find that I made several mistakes that I acknowledged but none affected my fundamental assertion that ev shows that macroevolution by random point mutations and natural selection is mathematically impossible. Delphi, I am not going to acknowledge that I have made a mistake in my interpretation of the application of information theory to Dr Schneider’s computer model. If you believe that information and entropy are equal, fine. I find that interpretation of these words illogical and find Frank Andrews’ (the writer of the textbook that I used in graduate school that discusses this issue) interpretation and mathematical derivation much too logical to ignore.
Well, we'll see what happens. This is a fairly simple thing that could be cleared up easily with no hard feelings. I study information theory, and I think it's important to get it right. There are several points that are important to get right. This is just one of them, and I'm glad someone with knowledge of information theory is holding him to it. My complaint is that he still fails to address why he even invokes thermo. All of his arguements describe an issue of rate. Since the program requires the input of the mutation rate, this whole thermodynamic argument is a smoke screen.
I don’t mind you holding me to it. In fact, turn up the heat. I want you to scrutinize every idea I present and parse every word because not only am I going to use Dr Schneider’s ev computer program to prove that macroevolution by random point mutation and natural selection is mathematically impossible, I am going to show how sloppy, superficial and hypocritical evolutionary pseudo-scientists are. If the peer reviewers at Nucleic Acids Research had done half as rigorous a review of Dr Schneider’s publication on ev as you are doing with my assertions here, we would not be having this discussion now. Once we get to a discussion of Dr Schneider’s work and you realize the preposterous way he extrapolated the data from his single published case in ev, I am going to throw these argument you are making with me right now, back into your tear stained faces. Of course you evolutionarians could never criticize a high priest of evolutionism, that would be rude. Well, this computer model was written by your high priest and you are stuck with it. Did you ever wonder why Dr Schneider is not engaging in this debate? He has always been a vigorous defender of his model in a very public way, just look at his web site. Now he is silent, leaving it to Paul and other evolutionists to try and defend your theory from this severe mathematical vise he has placed it in.
the model shows that the model trends toward information. That's the power of it. that is the equilibrium point being reached. We don't know rate here and all we can do is make assumptions.
There are measured values that enable the determination of the rates for Dr Schneider’s model. There are known measured mutation rates and known genome lengths. Dr Schneider has even proposed doing experiments to verify the results of his model.

You had better take a look at the Evolutionisdead link above so you don’t have to make so many assumptions. You also better write a keyboard macro for the words “strawman” and “irrelevant” because you won’t have any scientific arguments against what ev shows.

[joobz]

I have had extensive discussions with Paul and several other evolutionists. Doing this will help take you off the learning curve on this problem and you can avoid making a bunch of ignorant statements. If you examine that thread carefully you will find that I made several mistakes that I acknowledged but none affected my fundamental assertion that ev shows that macroevolution by random point mutations and natural selection is mathematically impossible.
Really?
Than, please show how it is. do you show that the simulation blows up? Do you show that the model under some conditions doesn't trend to order? These would be interesting and thought provoking. They would demonstrate a mathmatical impossibility.

or are you going to tell me, "it takes too long..." Unless you can show me the first two are happening and that this isn't a limitation of the simulation, you are just wrong.

I don't need to review another thread of your ramblings. You haven't made even the simple case of competence here. Why would you be any better elsewhere? No, the challenge is to you to explain why it is mathmatically flawed and WHY this is true for ALL of evolution and not just the model.

[kleinman]

I have had extensive discussions with Paul and several other evolutionists. Doing this will help take you off the learning curve on this problem and you can avoid making a bunch of ignorant statements. If you examine that thread carefully you will find that I made several mistakes that I acknowledged but none affected my fundamental assertion that ev shows that macroevolution by random point mutations and natural selection is mathematically impossible.Really? Than, please show how it is. do you show that the simulation blows up? Do you show that the model under some conditions doesn't trend to order? These would be interesting and thought provoking. They would demonstrate a mathmatical impossibility.
Let the ignorant evolutionist statements continue. I have never said that the ev simulation blows up. The only thing that appears to be blowing up in this discussion is Delphi ote’s head. Now, if you are talking about the failure of ev to converge for some input parameters, perhaps you should pose that question to Paul. He seems to have an explanation for this effect. His explanation supports my contention that ev shows that macroevolution by point mutations and natural selection is mathematically impossible.
or are you going to tell me, "it takes too long..." Unless you can show me the first two are happening and that this isn't a limitation of the simulation, you are just wrong.
According to Paul’s hypothesis, ev will fail to converge if the information capacity of the binding site exceeds Rfrequency. The simulation can not locate a binding site and therefore can not convergence. I am not convinced by his arguments however if he is saying that natural selection can not work when a particular mutation no matter whether beneficial or not doesn’t give enough information for natural selection to make the selection decision then I will see how his hypothesis plays out. For those cases that do converge, the number of generations required to accomplish the evolutionary process is so profoundly large when realistic parameters are used that it shows that macroevolution by random point mutations and natural selection is mathematically impossible.

Joozb, it is a fact of life that if you don’t have enough time for a certain process to occur, you have only two possible choices. Either speed up the process so you have time for it to occur or realize that the process is impossible. Dr Schneider has tried to speed up the process by using unrealistic input parameters in the model which doesn’t pass the scientific test. Maybe you ought to start thinking about increasing the age of the earth.
I don't need to review another thread of your ramblings. You haven't made even the simple case of competence here. Why would you be any better elsewhere? No, the challenge is to you to explain why it is mathmatically flawed and WHY this is true for ALL of evolution and not just the model.
With respects to your statement about my ramblings, I know where I am taking this discussion, do you know where you are going?
Now you get your information by telekinesis as well. Another sloppy evolutionarian who thinks that when he puts on a lab coat becomes a scientist. You still haven’t run any cases with ev, have you? You may think that ignorance is bliss but it isn’t science. Since you seem to be too lazy to run cases with ev, I will soon start posting results from this simulation and show why ev supports my assertions. You better warm up your keyboard macros for the words “strawman” and “irrelevant”. You are going to need them because they will be the only arguments available to you.

[Paul C. Anagnostopoulos]

According to Paul’s hypothesis, ev will fail to converge if the information capacity of the binding site exceeds Rfrequency. The simulation can not locate a binding site and therefore can not convergence. I am not convinced by his arguments however if he is saying that natural selection can not work when a particular mutation no matter whether beneficial or not doesn’t give enough information for natural selection to make the selection decision then I will see how his hypothesis plays out.
The Rcapacity issue is just an Ev issue; I don't think it would show up in real life. If you specify that binding sites are 5 bases wide, then you're limiting the code that can evolve there to about 10 bits. If that is lower than Rfrequency, more or less, then you simply can't evolve the code. So when you run large experiments in Ev, you have to make sure you don't run into Rcapacity problems.

$R_{\mathrm{frequency}}=\log_2(\mathit{genomesize}/\mathit{bindingsites})$

~~ Paul

[Yahzi]

my fundamental assertion that ev shows that macroevolution by random point mutations and natural selection is mathematically impossible.
I keep asking this, and you keep ignoring it.

What makes you think the EV program is an accurate model of reality? What makes you think someone was able to simulate the entire history of evolution, especially given that we can't even simulate weather to more than a week in advance?

The answer, of course, is that you're just bonkers. The program was created to show that information can evolve from simple beginnings. It accomplished that. The fact that this model does not evolve information fast enough is irrelevant, because that is not what the model was intended to do.

Voodoo.

[delphi_ote]

Delphi, I am not going to acknowledge that I have made a mistake in my interpretation of the application of information theory to Dr Schneider’s computer model. If you believe that information and entropy are equal, fine. I find that interpretation of these words illogical and find Frank Andrews’ (the writer of the textbook that I used in graduate school that discusses this issue) interpretation and mathematical derivation much too logical to ignore.
There's nothing to interpret or argue about here. The equation for Shannon entropy is the sum of -p*log(p). The equation for self information is the sum of -p*log(p). Shannon entropy is a measure of the uncertainty per symbol. The self information per symbol is a measure of how much you learn on average when you receive a symbol. The less even a probability distribution, the more certain I am what the outcome of the event will be before it happens. This means the entropy is lower. It also means I don't learn very much on average, so the average self information is low.

Simple example. If I'm certain of the outcome (p=1,) then the entropy is zero. I also don't learn anything at all when I learn the outcome, so the self information is zero.

This statement is incorrect.
Increasing the information in a system reduces the randomness and thus reduces the entropy.
If you have a problem with that, you should've taken it up with Claude Shannon. But please don't misrepresent his work now that he's gone.

[Foster Zygote]

I've read enough to confirm my earlier assessment that Kleinman is, in fact, working backward from his conclusion. I'd be interested in seeing the scientific community's response to his work after being published in an appropriate peer-reviewed journal. Until then there's little more to do here but to start posting pictures of cats.

[joobz]

Let the ignorant evolutionist statements continue. I have never said that the ev simulation blows up. The only thing that appears to be blowing up in this discussion is Delphi ote’s head. Now, if you are talking about the failure of ev to converge for some input parameters, perhaps you should pose that question to Paul. He seems to have an explanation for this effect. His explanation supports my contention that ev shows that macroevolution by point mutations and natural selection is mathematically impossible.
Paul has demonstrated quite well, with well reasoned responses why his view is reliable. He even admits error and mistakes when he performs them. As such, I have all reason to trust Paul's view.

You have demonstrated several times, beyond reasonable doubt, that you have little to know clue what you are talking about. The fact that you can be so wrong about such fundamental facts and not even admit them proves that you have no credibility what so ever.


According to Paul’s hypothesis, ev will fail to converge if the information capacity of the binding site exceeds Rfrequency. The simulation can not locate a binding site and therefore can not convergence. I am not convinced by his arguments however if he is saying that natural selection can not work when a particular mutation no matter whether beneficial or not doesn’t give enough information for natural selection to make the selection decision then I will see how his hypothesis plays out. For those cases that do converge, the number of generations required to accomplish the evolutionary process is so profoundly large when realistic parameters are used that it shows that macroevolution by random point mutations and natural selection is mathematically impossible.

your time arguement has been reported and dissmissed. please try another approach.


Joozb, it is a fact of life that if you don’t have enough time for a certain process to occur, you have only two possible choices. Either speed up the process so you have time for it to occur or realize that the process is impossible. Dr Schneider has tried to speed up the process by using unrealistic input parameters in the model which doesn’t pass the scientific test. Maybe you ought to start thinking about increasing the age of the earth.
Pardon me if I don't consider your view as "realistic". I've already stated as everyone else had, that your assestions are wrong. there is more to life than what's in the model. Anyway, mistakes Schneider may have made have no bearing on you being right or wrong. You are wrong despite him.


With respects to your statement about my ramblings, I know where I am taking this discussion, do you know where you are going?
Instead of "taking the discussion" somewhere. Get there! did I not ask for your reasons up front? Did I not ask for your data? No respectable scientist leads the witness. Present your facts, and let them hold on thier own. If they can't, then you are wrong. Simple.

You present your view as if it was some gambit that requires careful plotting. That's the action of a con artist, not a scientist.


Now you get your information by telekinesis as well. Another sloppy evolutionarian who thinks that when he puts on a lab coat becomes a scientist. You still haven’t run any cases with ev, have you? You may think that ignorance is bliss but it isn’t science. Since you seem to be too lazy to run cases with ev, I will soon start posting results from this simulation and show why ev supports my assertions.

I've asked you to do this all along. You haven't. I'm sure though that you'll respond with some, "it takes too long." argument again.



You better warm up your keyboard macros for the words “strawman” and “irrelevant”. You are going to need them because they will be the only arguments available to you.
Let's try it now.

You have become the "strawman" that is easy to tear apart. You are "irrelevant". Yup, seems to fit quite nicely, thank you.

[joobz]

I've read enough to confirm my earlier assessment that Kleinman is, in fact, working backward from his conclusion. I'd be interested in seeing the scientific community's response to his work after being published in an appropriate peer-reviewed journal. Until then there's little more to do here but to start posting pictures of cats.


Peer reviewed journals would require him to address questions with actual proof and logic. I don't see that happening any time soon.

[joobz]

There's nothing to interpret or argue about here. The equation for Shannon entropy is the sum of -p*log(p). The equation for self information is the sum of -p*log(p). Shannon entropy is a measure of the uncertainty per symbol. The self information per symbol is a measure of how much you learn on average when you receive a symbol. The less even a probability distribution, the more certain I am what the outcome of the event will be before it happens. This means the entropy is lower. It also means I don't learn very much on average, so the average self information is low.

Simple example. If I'm certain of the outcome (p=1,) then the entropy is zero. I also don't learn anything at all when I learn the outcome, so the self information is zero.

This statement is incorrect.

If you have a problem with that, you should've taken it up with Claude Shannon. But please don't misrepresent his work now that he's gone.

Why should he admit error? He's infallible. Must be the second coming.

[kleinman]

I've read enough to confirm my earlier assessment that Kleinman is, in fact, working backward from his conclusion. I'd be interested in seeing the scientific community's response to his work after being published in an appropriate peer-reviewed journal. Until then there's little more to do here but to start posting pictures of cats.
So we have another evolutionist who figures things out with telekinesis. I was invited by Dr Schneider to examine his ev program. This problem wasn’t addressed with reversed engineering. I addressed this problem by doing a parametric study of ev.

Foster Zygote’s idea of a peer reviewed journal is one in which all the peers are indoctrinated in evolutionary dogma for example Nucleic Acid Research. The peer review they performed on Dr Schneider’s paper was sloppy. If they had simply question Dr Schneider about genome lengths and mutation rates in his model, they would have not allowed Dr Schneider’s unscientific extrapolations to be published.

Since none of you evolutionists have posted results from ev, I thought I would get the ball rolling. This initial series is based on Dr Schneider’s single published case. In that case, he used a genome length of G=256 bases, a mutation rate of 1 per genome per generation, the number of binding sites gamma=16, a site width of 6 bases and a population of 64. Below are the results of a series of runs based on Dr Schneider’s baseline case with the exception that the genome length G is doubled for each case in the series. The first column gives the genome length G, the second column gives the generations required to obtain a perfect creature (all binding sites identified where they should be and no binding sites identified where they shouldn’t be).
G \ generations for PC
256 \ 662
512 \ 2412
1024 \ 18030
2048 \ 35468
4096 \ 163722
8192 \ 710152
16384 \ stopped at 400,000 generations, no selection occurring
The first thing you should note is that in order to get a realistic mutation rate when using a mutation rate of 1/G per generation, you must have a genome length of G~=1,000,000. This series stopped converging at G=16,384. Up to that point, this series is showing a convergence rate proportional to ~G^2. If that rate of increase of generations could be maintained, the table would look like this:
G \ Generations for convergence
8192 \ 700,000
16,384 \ 2,800,000
32,768 \ 11,200,000
65,536 \ 44,800,000
131,072 \ 179,200,000
262,144 \ 716,800,000
524,288 \ 2,867,200,000
1,048,576 \ 11,468,800,000
2,097,152 \ 45,875,200,000
4,194,304 \ 183,500,800,000
8,388,608 \ 734,003,200,000
This data does not represent the evolution of an entire genome of the length G, it represents the evolution of 16 binding sites each 6 bases wide on that genome. Only 96 of the total G number of loci are evolving. The rest of the genome is still a random sequence of bases. Note that for a genome the size of e coli, it would take around 200 billion generations to evolve only 96 loci on a genome of that length. Dr Schneider’s case of these 16 binding sites on a 256 base genome accumulates information at 1 bit per 11 generations. Model these same 16 binding sites on a realistic genome length with a realistic mutation rate and accumulation of information slows to 1 bit per 2 billion generations, far too slow to explain how macroevolution occurs.

Evolutionarians will complain, how can you extrapolate the data when you don’t have convergence for the 16,384 base case? I give evolutionarians the benefit of the doubt. Paul has an explanation for why these cases do not converge once you exceed a certain genome length but this explanation doesn’t rescue the theory of evolution, it makes the theory of evolution less likely. It is not only increasing genome lengths that makes ev converge more slowly, there are other mathematical factors the argue against the theory of evolution.

[kleinman]

Why should he admit error? He's infallible. Must be the second coming.
And joozb said this on the “A Simple Argument against Intelligent Design” thread:
I thank you for your defense. Although, I don't doubt that my English teachers wished I had tried harder at learning spelling and grammar. I was always to busy reading my science books, encyclopedias, playing math games...
Now you crybabies have complained that I was rude to you because I told you to write an intelligible sentence. I spoke to you truthfully with some force behind it because you are supposed to be an educated person and should have a better command of the English language. Instead you and your whimpering cohorts cried about this for several days so don’t start lecturing me about admitting errors you hypocrite.

Why is it that so many of those posting lack the courage to put their real name to their words?

Why don’t you play some math games with Dr Schneider’s ev program and see whether what I am saying is true, or is that to threatening to your belief system?

[joobz]

Since none of you evolutionists have posted results from ev, I thought I would get the ball rolling. This initial series is based on Dr Schneider’s single published case. In that case, he used a genome length of G=256 bases, a mutation rate of 1 per genome per generation, the number of binding sites gamma=16, a site width of 6 bases and a population of 64. Below are the results of a series of runs based on Dr Schneider’s baseline case with the exception that the genome length G is doubled for each case in the series. The first column gives the genome length G, the second column gives the generations required to obtain a perfect creature (all binding sites identified where they should be and no binding sites identified where they shouldn’t be).

G \ generations for PC
256 \ 662
512 \ 2412
1024 \ 18030
2048 \ 35468
4096 \ 163722
8192 \ 710152
16384 \ stopped at 400,000 generations, no selection occurring
WOW! you are right. It's a perfect proof. We'll never evolve into the perfect creature. that makes sense.

The first thing you should note is that in order to get a realistic mutation rate when using a mutation rate of 1/G per generation, you must have a genome length of G~=1,000,000.
why? explain this assumption.
This series stopped converging at G=16,384. Up to that point, this series is showing a convergence rate proportional to ~G^2. If that rate of increase of generations could be maintained, the table would look like this:
G \ Generations for convergence
8192 \ 700,000
16,384 \ 2,800,000
32,768 \ 11,200,000
65,536 \ 44,800,000
131,072 \ 179,200,000
262,144 \ 716,800,000
524,288 \ 2,867,200,000
1,048,576 \ 11,468,800,000
2,097,152 \ 45,875,200,000
4,194,304 \ 183,500,800,000
8,388,608 \ 734,003,200,000
This data does not represent the evolution of an entire genome of the length G, it represents the evolution of 16 binding sites each 6 bases wide on that genome. Only 96 of the total G number of loci are evolving. The rest of the genome is still a random sequence of bases.
So does this model prove that our genome is entirely a random sequence of bases? That's a new one to me.

Note that for a genome the size of e coli, it would take around 200 billion generations to evolve only 96 loci on a genome of that length. Dr Schneider’s case of these 16 binding sites on a 256 base genome accumulates information at 1 bit per 11 generations. Model these same 16 binding sites on a realistic genome length with a realistic mutation rate and accumulation of information slows to 1 bit per 2 billion generations, far too slow to explain how macroevolution occurs.
I knew rate had to be here somewhere. I should remember this next time. ALL e-Coli mutate identically simultaneously. There is no variation between the E-coli species. that's an important thing to know.

Evolutionarians will complain, how can you extrapolate the data when you don’t have convergence for the 16,384 base case? I give evolutionarians the benefit of the doubt. Paul has an explanation for why these cases do not converge once you exceed a certain genome length but this explanation doesn’t rescue the theory of evolution, it makes the theory of evolution less likely.

Ah Paul, looks like we lost. He proven that extrapolation is flawless. You can always extend the data BEYOND the values measured/reported without any concern for error. man, who would have known.

It is not only increasing genome lengths that makes ev converge more slowly, there are other mathematical factors the argue against the theory of evolution.really? like?
You've again only presented rate and I've bashed that one into the ground. So tell me. Really? Other reasons? feel free to post them.

[Foster Zygote]

Peer reviewed journals would require him to address questions with actual proof and logic. I don't see that happening any time soon.

Yeah, that was pretty much my point. :)

[Foster Zygote]

My cat's breath smells like cat food.

[joobz]

And joozb said this on the “A Simple Argument against Intelligent Design” thread:

Now you crybabies have complained that I was rude to you because I told you to write an intelligible sentence. I spoke to you truthfully with some force behind it because you are supposed to be an educated person and should have a better command of the English language. Instead you and your whimpering cohorts cried about this for several days so don’t start lecturing me about admitting errors you hypocrite.


Really?
Here was my reply to your insult laden post:

Originally Posted by kleinman http://forums.randi.org/helloworld/buttons/viewpost.gif (http://forums.randi.org/showthread.php?p=2090296#post2090296)
I have had evolutionists correct my grammar, but Professor joobz, your English instructors should have never let you get past 1st grade. Why don’t you rephrase that collection of words into something intelligible and I’ll try to respond to it.

You are correct, i had written this rapidly and late, here is the corrected form.

Originally Posted by joobz
and this matters? I deny the notion that a full human genome would poof into existence and then mutate to form binding sites.

Can you honestly call me a hypocrite? you know what that word means, right? However, why should I be suprized that you'd ignore the facts of our exchanges when you so readily ignore facts of the case you are trying to make.

[kleinman]

According to Paul’s hypothesis, ev will fail to converge if the information capacity of the binding site exceeds Rfrequency. The simulation can not locate a binding site and therefore can not convergence. I am not convinced by his arguments however if he is saying that natural selection can not work when a particular mutation no matter whether beneficial or not doesn’t give enough information for natural selection to make the selection decision then I will see how his hypothesis plays out.The Rcapacity issue is just an Ev issue; I don't think it would show up in real life. If you specify that binding sites are 5 bases wide, then you're limiting the code that can evolve there to about 10 bits. If that is lower than Rfrequency, more or less, then you simply can't evolve the code. So when you run large experiments in Ev, you have to make sure you don't run into Rcapacity problems.
I am not sure whether you can say this is only a mathematical peculiarity of the ev model and not representative of a real problem for RM&NS.. Ultimately, natural selection must determine whether a mutation offers a selective advantage or not. This may be attributing a precision to natural selection that does not exist in reality. Natural selection may be able to identify a single harmful mutation easily but a single mutation that doesn’t offer an immediate selective advantage but if combined with future mutations that would confer an advantage, how would natural selection select for the early bases in gene formation that does not confer an advantage? Dr Schneider’s selection process allows for this with his weight matrix. When you are talking about the de novo formation of a large gene, how would natural selection start the process?
my fundamental assertion that ev shows that macroevolution by random point mutations and natural selection is mathematically impossible.I keep asking this, and you keep ignoring it. What makes you think the EV program is an accurate model of reality? What makes you think someone was able to simulate the entire history of evolution, especially given that we can't even simulate weather to more than a week in advance?
Sorry, I thought I already answered this. I believe that Dr Schneider properly included all the critical variables and mathematically related them in a plausible manner. In addition, I include quotes from the author of the model:
The following quotes were taken from Dr Schneider’s blog web page: http://www.lecb.ncifcrf.gov/~toms/paper/ev/blog-ev.html (http://www.lecb.ncifcrf.gov/~toms/paper/ev/blog-ev.html)

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

"Schneider's paper is misleadingly titled: "Evolution of biological information". But it is just a *computer* simulation. No actual *biological* materials (e.g. genomes of nucleic acids, proteins, etc) were used, nor does Schneider propose that his simulation be tested with *real* genomes or proteins Actual biological materials were used to determine the original hypothesis. Read the literature: Schneider1986 (http://www.lecb.ncifcrf.gov/~toms/paper/schneider1986)

It only becomes *real* biological information and random mutation and natural selection, when the simulation is tested in the *real* world, using *real* DNA, proteins, with *real* mutations and a *real* environment does the selecting. It is significant that Schneider does not propose this, presumably because he knows it wouldn't work.You are very bad at reading my mind, I have considered doing this experiment. Given the right conditions, it WILL WORK. Do you have th gumption to do the experiment yourself? That's the way real science works! FURTHERMORE, if you read the literature, you will recognize that related experiments have been repeatedly done for 20 years. Look up SELEX.

In the rest of the paper he uses the single word "selection". I take this as a tacit admission that his model is not a simulation of *real* biological natural selection. No. A rose is a rose by any other name. Selection is selection whether it be natural (generally meaning the environment of earth), breeding (by humans usually, though perhaps some ants select their fungi), SELEX or in a computer simulation. Of COURSE it is a simulation of natural selection! The paper would not be relevant to biology and would not have been published in a major scientific journal if it were not!

Schneider lets slip that there is another unrealistic element in his (and indeed all) computer simulations in that it (they) "does not correlate with time": So? Run the program slower if you want. Make one generation per 20 minutes to match rapid bacterial growth. THIS WILL NOT CHANGE THE FINIAL RESULT!

Well, when Schneider's simulation is actually tested with *real* "life" (e.g. a bacterium), and under *real* mutation and natural selection it gains information, then, and only then, would "creationists" be favourably impressed. But if they are like me, they would already be impressed (but unfavourably) that Schneider does not mention in his paper that his simulation should now be so tested in the *real* "biological" world. 1. The simulation was of phenomena in the "real" world.
2. Dr. Jones is invited yet again to do an experiment.

The following is a response Dr Schneider made to a statement made by David Berlinski (http://www.discovery.org/scripts/viewDB/index.php?command=view&id=51&isFellow=true).

Where attempts to replicate Darwinian evolution on the computer have been successful, they have not used classical Darwinian principles, and where they have used such principles, they have not been successful. The ev program disproves this statement since it uses classical Darwinian principles and was successful.

http://www.lecb.ncifcrf.gov/~toms/paper/ev/blog-ev.html (http://www.lecb.ncifcrf.gov/~toms/paper/ev/blog-ev.html)
Dr Schneider made the following comments in response to statements made by Fred Williams about ev.
Fred Williams complains that the "program is not real-world, not even close. New information was not created naturalistically." It is not clear what he means by 'real-world' or 'naturalistically'. If you read the Ev paper (http://www.lecb.ncifcrf.gov/~toms/papers/ev/) carefully you will note that the model parallels the natural situation.

Dr Schneider said the following on his FAQ page at:
http://www.lecb.ncifcrf.gov/~toms/paper/ev/faq-for-ev.html (http://www.lecb.ncifcrf.gov/~toms/paper/ev/faq-for-ev.html)
Why don't you do a real biological experiment instead of just a computer model?The primary reason is that we don't have infinite resources and time. If you have the resources (a molecular biology lab), are interested in doing an experiment, and would like to discuss it please contact me.

The previous statements are clear that Dr Schneider believes that ev simulates the real world. If the simulation is appropriate for small genomes then it is appropriate for large genomes. Macroevolution by mutation and natural selection is mathematically impossible.
The answer, of course, is that you're just bonkers.
I may be bonkers but I do know how to do arithmetic. Dr Schneider believes the ev simulates reality. The only thing preventing him from running real laboratory experiments is he doesn’t have the laboratory to do it.
The first thing you should note is that in order to get a realistic mutation rate when using a mutation rate of 1/G per generation, you must have a genome length of G~=1,000,000. why? explain this assumption.
It’s not an assumption, this is a measured rate. Mutation rates for prokaryotes vary between 10^-4 to 10^-12 with an average of 10^-6 to 10^-8. You can confirm this in any introductory biochemistry text, or google and confirm the information. Don’t be lazy, check this out yourself.
So does this model prove that our genome is entirely a random sequence of bases? That's a new one to me.
Actually the whole model is new to you. I’ve been discussing this model with Dr Schneider, Paul and other evolutionists for about 6 months, if you don’t want to look stupid, you probably should not jump to conclusions on what the model is simulating until you become familiar with the model. You still don’t understand the model yet but I’ll be patient with you. The model does not simulate the evolution of an entire genome, it only simulates the evolution of a small portion of the genome where the binding sites are. The entire genome is random initially and only the portion with the binding site evolves the rest of the genome remains random.
Note that for a genome the size of e coli, it would take around 200 billion generations to evolve only 96 loci on a genome of that length. Dr Schneider’s case of these 16 binding sites on a 256 base genome accumulates information at 1 bit per 11 generations. Model these same 16 binding sites on a realistic genome length with a realistic mutation rate and accumulation of information slows to 1 bit per 2 billion generations, far too slow to explain how macroevolution occurs.I knew rate had to be here somewhere. I should remember this next time. ALL e-Coli mutate identically simultaneously. There is no variation between the E-coli species. that's an important thing to know.
Actually the mutation rate is generally slower than 10^-6. If you think you are ready, I’ll start posting the references with measured mutation rates for different e coli strains but I think you are putting the cart before the horse.
Evolutionarians will complain, how can you extrapolate the data when you don’t have convergence for the 16,384 base case? I give evolutionarians the benefit of the doubt. Paul has an explanation for why these cases do not converge once you exceed a certain genome length but this explanation doesn’t rescue the theory of evolution, it makes the theory of evolution less likely. Ah Paul, looks like we lost. He proven that extrapolation is flawless. You can always extend the data BEYOND the values measured/reported without any concern for error. man, who would have known.
I don’t believe it, I think I have found a point we can agree on. Engineers know that extrapolation outside the range of your data based on a curve fit can give very inaccurate predictions, particularly with a highly nonlinear model like ev. Dr Schneider and Paul have done this and gotten very inaccurate predictions. I think you will find that my extrapolations are very conservative and underestimate the number of generations for convergence. I have more data from ev that verifies this. As you become more familiar with ev this will become more apparent.
It is not only increasing genome lengths that makes ev converge more slowly, there are other mathematical factors the argue against the theory of evolution. really? like? You've again only presented rate and I've bashed that one into the ground. So tell me. Really? Other reasons? feel free to post them.
Again, you are putting the cart before the horse but I’ll give you an example. Dr Schneider’s selection process is based on a weight matrix that traverses the genome that looks for a mathematical match between the matrix and base sequence. If the weight matrix does not find a match where it should it is counted as an error or if the weight matrix finds a match on the genome where there should not be a binding site, it is considered an error as well. The creatures in the population with the least number of errors are allowed to reproduce while those with the most errors are selected out. A problem with this type of selection process is that binding sites recognized in the nonbinding site region early in the evolutionary process have a smaller selective effect than later in the evolutionary process. Because of this effect, evolution proceeds more rapidly early in the process and slows down as the evolutionary process proceeds. I don’t think this accurately models the real situation.
Peer reviewed journals would require him to address questions with actual proof and logic. I don't see that happening any time soon. Yeah, that was pretty much my point.
Of course that doesn’t apply to anything that you evolutionists post in this blog. Joozb, your anything is possible argument for proof of abiogenesis is worthy scientific proof that would pass any evolutionist peer reviewed journal. And Foster Zygote, your qualifications as master poster and defender of thin skinned evolutionist crybabies puts anything you would write on this blog above the need for peer review. James Randi might as well close down this site because unless if it isn’t published in a peer reviewed journal it can’t be true. Can’t you evolutionist mount a better case than this?
Can you honestly call me a hypocrite? you know what that word means, right? However, why should I be suprized that you'd ignore the facts of our exchanges when you so readily ignore facts of the case you are trying to make.
Yes, because you let this issue linger on and when you finally posted a second time you did it on a different thread. You are doing the same with the question about the relationship of Shannon information and entropy. You understand my description of the model but would rather engage in this debate about the minus sign. If this is the best argument you can raise to my assertions about what ev shows, don’t be surprised when those who don’t have your evolutionary indoctrination don’t believe you.

[Foster Zygote]

Of course that doesn’t apply to anything that you evolutionists post in this blog. Joozb, your anything is possible argument for proof of abiogenesis is worthy scientific proof that would pass any evolutionist peer reviewed journal. And Foster Zygote, your qualifications as master poster and defender of thin skinned evolutionist crybabies puts anything you would write on this blog above the need for peer review. James Randi might as well close down this site because unless if it isn’t published in a peer reviewed journal it can’t be true. Can’t you evolutionist mount a better case than this?

There's only one person involved in this exchange who is behaving like a thin skinned crybaby. Perhaps you could include some of your colorful language in your paper when you submit it for journal publication, I'm sure it would help you get your point across. When is that going to be, by the way? Certainly a discovery of such import needs to be presented to the world of science, not hidden away on an informal 'blog' (it's actually a forum). After all, what you are claiming to have uncovered is by far the greatest discovery in the last century of biological science.

[kleinman]

Of course that doesn’t apply to anything that you evolutionists post in this blog. Joozb, your anything is possible argument for proof of abiogenesis is worthy scientific proof that would pass any evolutionist peer reviewed journal. And Foster Zygote, your qualifications as master poster and defender of thin skinned evolutionist crybabies puts anything you would write on this blog above the need for peer review. James Randi might as well close down this site because unless if it isn’t published in a peer reviewed journal it can’t be true. Can’t you evolutionist mount a better case than this? There's only one person involved in this exchange who is behaving like a thin skinned crybaby. Perhaps you could include some of your colorful language in your paper when you submit it for journal publication, I'm sure it would help you get your point across. When is that going to be, by the way? Certainly a discovery of such import needs to be presented to the world of science, not hidden away on an informal 'blog' (it's actually a forum). After all, what you are claiming to have uncovered is by far the greatest discovery in the last century of biological science.
So Foster Zygote, you asked me what my credentials were and I told you what they were. When I asked you what your credentials are, you didn’t answer.

I don’t mind that I’m presenting this information on the net. I actually was content to discuss this on the Evolutionisdead forum until the evolutionists who were willing to discuss it were running short of counter arguments. Paul had asked me to raise the issue on this forum a while back and when I saw his “Annoying Creationist” thread, I took him up on the offer. I guess the evolutionists on this forum were not prepared for the claims that I am making based on the results from ev. I’ll give you time for this to soak in and then I’ll show you why I believe these claims to be true. I did try to write a letter to the editors at Nucleic Acids Research since they published the ev paper but they don’t accept letters to the editor. I don’t consider what I have done as being the greatest discovery in the last century of biological science. Many scientists have said that it is mathematically impossible for life to have evolved. You can start with Francis Crick. I am only addressing Dr Schneider’s model because of his superficial analysis of his model and the inaccurate extrapolations that he drew based on this superficial analysis. Many IDers have criticized Dr Schneider’s conclusions because of his use of an unrealistically small genome and an unrealistically high mutation rate in his single published case but Dr Schneider shrugged off these criticisms. Because of my engineering background and training with the development and application of large scale computer simulations, I simply put those skills to use on Dr Schneider’s model. I did a systematic parametric study with ev. So here we are. I don’t expect there are many readers of this site who willing to put in the effort to understand Dr Schneider’s model but there may be a few. As long as this discussion is not interrupted too much by bloggers posting about cats (don’t get me wrong, I like cats, I have two of them) then maybe a coherent discussion can be started.

[Paul C. Anagnostopoulos]

G \ generations for PC
256 \ 662
512 \ 2412
1024 \ 18030
2048 \ 35468
4096 \ 163722
8192 \ 710152
16384 \ stopped at 400,000 generations, no selection occurring
In the last case, Rfrequency is 10 bits, while Rcapacity is about 11--12 bits. Tough for the binding site code to evolve, maybe even impossible.

I'd expect that it might get somewhere after sufficient generations. From that trend, you'd expect it to take 3.5 million generations or more, so no progress after 400K generations isn't suprising.

~~ Paul

[Paul C. Anagnostopoulos]

I am not sure whether you can say this is only a mathematical peculiarity of the ev model and not representative of a real problem for RM&NS.. Ultimately, natural selection must determine whether a mutation offers a selective advantage or not. This may be attributing a precision to natural selection that does not exist in reality. Natural selection may be able to identify a single harmful mutation easily but a single mutation that doesn’t offer an immediate selective advantage but if combined with future mutations that would confer an advantage, how would natural selection select for the early bases in gene formation that does not confer an advantage? Dr Schneider’s selection process allows for this with his weight matrix. When you are talking about the de novo formation of a large gene, how would natural selection start the process?
The beginning of your paragraph has nothing to do with the end. Unless there is some sort of mechanism to artificially constrain the width of binding sites, real evolution does not have the Rcapacity problem. That said, I'm sure it's harder to evolve wide binding sites than narrow ones. I think typical widths are 6--12 bases, but I might be dreaming that.

Meanwhile, there probably never was any whole-cloth formation of a large gene. Same reason you've never seen an empty lot on Tuesday and a completed palace on Wednesday.

~~ Paul

[delphi_ote]

I expected someone interested in this subject enough to talk about it so much would at least have some interest in getting it right. Instead, he's ignoring the error.

Re-reading my posts, I noticed something. To be completely correct, I should've been careful to distinguish between self information and average self information. Self information is about a single outcome. Average self information is averaged over a distribution, and is identical to Shannon information.

[joobz]

It’s not an assumption, this is a measured rate. Mutation rates for prokaryotes vary between 10^-4 to 10^-12 with an average of 10^-6 to 10^-8. You can confirm this in any introductory biochemistry text, or google and confirm the information. Don’t be lazy, check this out yourself.
Again, this value is constant throughout all populations, throughout all of time and represents the only way dna continues. My comment on "random sequences

Actually the whole model is new to you. I’ve been discussing this model with Dr Schneider, Paul and other evolutionists for about 6 months, if you don’t want to look stupid, you probably should not jump to conclusions on what the model is simulating until you become familiar with the model. You still don’t understand the model yet but I’ll be patient with you.
I understand the model well enough to see the power of it and the limitations.

The model does not simulate the evolution of an entire genome, it only simulates the evolution of a small portion of the genome where the binding sites are. Ahh, and this is how evolution occured? Only certain sections evolving at a time? Hmm? This is your gotcha? You really are a silly little man.

The entire genome is random initially and only the portion with the binding site evolves the rest of the genome remains random.There's no reason to believe this. You are just kidding yourself. I know, reality is hard to take, but once you accept it, you can move on.


Actually the mutation rate is generally slower than 10^-6. If you think you are ready, I’ll start posting the references with measured mutation rates for different e coli strains but I think you are putting the cart before the horse. That's nice. Average mutation rates of a entire population with out any mutagenic stressors.... Again, you are simply wrong...

I don’t believe it, I think I have found a point we can agree on. Engineers know that extrapolation outside the range of your data based on a curve fit can give very inaccurate predictions, particularly with a highly nonlinear model like ev. Dr Schneider and Paul have done this and gotten very inaccurate predictions. I think you will find that my extrapolations are very conservative and underestimate the number of generations for convergence. I have more data from ev that verifies this. As you become more familiar with ev this will become more apparent. Well, that's reasonable. But again I fail to see the connection to reality. there's a model that looks at one small part of the whole picture and you claim it does it all. That's delusional.

Again, you are putting the cart before the horse but I’ll give you an example. Dr Schneider’s selection process is based on a weight matrix that traverses the genome that looks for a mathematical match between the matrix and base sequence. If the weight matrix does not find a match where it should it is counted as an error or if the weight matrix finds a match on the genome where there should not be a binding site, it is considered an error as well. The creatures in the population with the least number of errors are allowed to reproduce while those with the most errors are selected out. A problem with this type of selection process is that binding sites recognized in the nonbinding site region early in the evolutionary process have a smaller selective effect than later in the evolutionary process. Because of this effect, evolution proceeds more rapidly early in the process and slows down as the evolutionary process proceeds. I don’t think this accurately models the real situation.and I'd agree. I think there are deviations from reality. EVEN MORE of a reason why a flaw here doesn't equal a flaw in the theory.

Of course that doesn’t apply to anything that you evolutionists post in this blog. Joozb, your anything is possible argument for proof of abiogenesis is worthy scientific proof that would pass any evolutionist peer reviewed journal. And Foster Zygote, your qualifications as master poster and defender of thin skinned evolutionist crybabies puts anything you would write on this blog above the need for peer review. James Randi might as well close down this site because unless if it isn’t published in a peer reviewed journal it can’t be true. Can’t you evolutionist mount a better case than this?Better than 50+ years of genetics? We've given you the facts. You've given us half truths and foolishness.

Yes, because you let this issue linger on and when you finally posted a second time you did it on a different thread.
? what? Do you know what hypocrite means?

In any case, look back over the thread and look to see who was polite and who wasn't. I stopped being polite when I realized you were meaningless.
You are doing the same with the question about the relationship of Shannon information and entropy. You understand my description of the model but would rather engage in this debate about the minus sign.
I never claimed to know shannon entropy. I deferred to Tez and delphi_ote for that. If you check, I was even willing to give you the benefit of the doubt on that one.
I demonstrated that you didn't understand thermodynamics and had no real clue of it's applications. Again, that's your problem, not mine.
If this is the best argument you can raise to my assertions about what ev shows, don’t be surprised when those who don’t have your evolutionary indoctrination don’t believe you.
again, you claim an 'indoctrination'. i've asked for evidence. You haven't given it. There's no indoctrination, just your inability.

[Foster Zygote]

So Foster Zygote, you asked me what my credentials were and I told you what they were. When I asked you what your credentials are, you didn’t answer.
Sorry, missed that. I have no credentials in the fields of biology or chemistry, but then I haven't made any major claims regarding either. I simply wanted to know who was making the claim that he was about to overturn a century and a half of biological science.
I don’t mind that I’m presenting this information on the net. I actually was content to discuss this on the Evolutionisdead forum until the evolutionists who were willing to discuss it were running short of counter arguments. Paul had asked me to raise the issue on this forum a while back and when I saw his “Annoying Creationist” thread, I took him up on the offer. I guess the evolutionists on this forum were not prepared for the claims that I am making based on the results from ev.
I'd still like to see what other scientists have to say about your work in a peer reviewed journal. Is that ever going to happen? Far from being unprepared for your claims, the evolutionists on this forum seem to have heard much of this sort of thing before. And they've shown that you've made many fundamental errors which you have not fully addressed.
I’ll give you time for this to soak in and then I’ll show you why I believe these claims to be true.
You promised to do this a few days ago.
I did try to write a letter to the editors at Nucleic Acids Research since they published the ev paper but they don’t accept letters to the editor.
Really? You didn't quote the Bible did you?
I don’t consider what I have done as being the greatest discovery in the last century of biological science.
Well that's just what you'd be doing if you were to show that all of evolutionary theory has been a huge mistake.
Many scientists have said that it is mathematically impossible for life to have evolved. You can start with Francis Crick.
You mean this (http://www.positiveatheism.org/india/s1990a01.htm) Francis Crick? Where did he say that?
I am only addressing Dr Schneider’s model because of his superficial analysis of his model and the inaccurate extrapolations that he drew based on this superficial analysis. Many IDers have criticized Dr Schneider’s conclusions because of his use of an unrealistically small genome and an unrealistically high mutation rate in his single published case but Dr Schneider shrugged off these criticisms. Because of my engineering background and training with the development and application of large scale computer simulations, I simply put those skills to use on Dr Schneider’s model. I did a systematic parametric study with ev. So here we are. I don’t expect there are many readers of this site who willing to put in the effort to understand Dr Schneider’s model but there may be a few.
If you prove that evolution could not happen in the model you haven't shown it to be impossible in reality because the model doesn't perfectly model reality. Far from it.

[Paul C. Anagnostopoulos]

In the last case, Rfrequency is 10 bits, while Rcapacity is about 11--12 bits. Tough for the binding site code to evolve, maybe even impossible.

I'd expect that it might get somewhere after sufficient generations. From that trend, you'd expect it to take 3.5 million generations or more, so no progress after 400K generations isn't suprising.
I ran this model overnight. After 2.5 million generations it's gotten nowhere. I'd say we've run into the Rcapacity problem.

Just for a check, I'll run it with somewhat smaller genome sizes and see what happens.

~~ Paul

[kleinman]

I am not sure whether you can say this is only a mathematical peculiarity of the ev model and not representative of a real problem for RM&NS.. Ultimately, natural selection must determine whether a mutation offers a selective advantage or not. This may be attributing a precision to natural selection that does not exist in reality. Natural selection may be able to identify a single harmful mutation easily but a single mutation that doesn’t offer an immediate selective advantage but if combined with future mutations that would confer an advantage, how would natural selection select for the early bases in gene formation that does not confer an advantage? Dr Schneider’s selection process allows for this with his weight matrix. When you are talking about the de novo formation of a large gene, how would natural selection start the process? The beginning of your paragraph has nothing to do with the end. Unless there is some sort of mechanism to artificially constrain the width of binding sites, real evolution does not have the Rcapacity problem. That said, I'm sure it's harder to evolve wide binding sites than narrow ones. I think typical widths are 6--12 bases, but I might be dreaming that.
I added the bold face to your quote. Your theory about Rcapacity says the exact opposite. I will summarize your hypothesis:
If Rcapacity = 2 * binding site width is less than Rfrequency then ev will not converge. The mathematics of ev is saying that it is more difficult to evolve narrow binding sites on larger genomes.
I expected someone interested in this subject enough to talk about it so much would at least have some interest in getting it right. Instead, he's ignoring the error. Re-reading my posts, I noticed something. To be completely correct, I should've been careful to distinguish between self information and average self information. Self information is about a single outcome. Average self information is averaged over a distribution, and is identical to Shannon information.
If you want to understand where my view on the relationship between Shannon Information and entropy comes from, you and Tez can make a field trip to the college library where Tez teaches quantum mechanics and get the text Equilibrium Statistical Mechanics by Frank Andrews. Not only does Andrews derive Shannon’s equation and relate it to information theory, he gives a numerical example very similar to Dr Schneider’s problem. I hope the library still exists and wasn’t burned down by evolutionarians in their zeal to burn Bibles.
It’s not an assumption, this is a measured rate. Mutation rates for prokaryotes vary between 10^-4 to 10^-12 with an average of 10^-6 to 10^-8. You can confirm this in any introductory biochemistry text, or google and confirm the information. Don’t be lazy, check this out yourself. Again, this value is constant throughout all populations, throughout all of time and represents the only way dna continues. My comment on "random sequences
Joozb, do you believe that the mutation rate for living things were much higher for primitive life forms than the values measures now? I’m not sure what you mean by “dna continures”. I will try to make my comment on your last phrase as gently as possible, you are grammatically challenged.
The model does not simulate the evolution of an entire genome, it only simulates the evolution of a small portion of the genome where the binding sites are.Ahh, and this is how evolution occured? Only certain sections evolving at a time? Hmm? This is your gotcha? You really are a silly little man.
Hey, don’t get mad at me, this is Dr Schneider’s model, he’s the one who uses the data from this model to predict the evolution of a human genome.
The entire genome is random initially and only the portion with the binding site evolves the rest of the genome remains random.There's no reason to believe this. You are just kidding yourself. I know, reality is hard to take, but once you accept it, you can move on.
I thought you said you understood this model. Paul, you need to help joozb on a few details on the ev model.
Actually the mutation rate is generally slower than 10^-6. If you think you are ready, I’ll start posting the references with measured mutation rates for different e coli strains but I think you are putting the cart before the horse.That's nice. Average mutation rates of a entire population with out any mutagenic stressors.... Again, you are simply wrong...
Again, you are going to the wrong complaint window. Dr Schneider wrote the model and used average values to predict the evolution of a human genome. The only problem with his average values is they have no basis in reality.
I don’t believe it, I think I have found a point we can agree on. Engineers know that extrapolation outside the range of your data based on a curve fit can give very inaccurate predictions, particularly with a highly nonlinear model like ev. Dr Schneider and Paul have done this and gotten very inaccurate predictions. I think you will find that my extrapolations are very conservative and underestimate the number of generations for convergence. I have more data from ev that verifies this. As you become more familiar with ev this will become more apparent. Well, that's reasonable. But again I fail to see the connection to reality. there's a model that looks at one small part of the whole picture and you claim it does it all. That's delusional.
The reason why you fail to see the connection to reality that ev has is because you think you understand the model when you don’t. You call me delusional when you believe in a theory that says the most complex molecules known came into existence by random process and your miracle worker natural selection. Sorry, but natural selection can not do miracles.
So Foster Zygote, you asked me what my credentials were and I told you what they were. When I asked you what your credentials are, you didn’t answer.Sorry, missed that. I have no credentials in the fields of biology or chemistry, but then I haven't made any major claims regarding either. I simply wanted to know who was making the claim that he was about to overturn a century and a half of biological science.
All that I am doing is taking an evolutionist’s mathematical model of random point mutations and natural selection and looking at the behavior of the model with realistic parameters. If you have a problem with the data from the model take it to Dr Schneider, he wrote the model. I notice that no evolutionist has ever question Dr Schneider’s claims based on his use of unrealistic parameters in his model, but when I use realistic parameters in his model, I now am overturning a century and a half of biological science. If the theory of evolution is true, it can withstand my puny efforts. Since you don’t have any scientific credentials should I immediately use the Page Down key as soon as I see your posts? I won’t do this, if you have a valid point to make, I will try to address it.
I don’t mind that I’m presenting this information on the net. I actually was content to discuss this on the Evolutionisdead forum until the evolutionists who were willing to discuss it were running short of counter arguments. Paul had asked me to raise the issue on this forum a while back and when I saw his “Annoying Creationist” thread, I took him up on the offer. I guess the evolutionists on this forum were not prepared for the claims that I am making based on the results from ev.I'd still like to see what other scientists have to say about your work in a peer reviewed journal. Is that ever going to happen? Far from being unprepared for your claims, the evolutionists on this forum seem to have heard much of this sort of thing before. And they've shown that you've made many fundamental errors which you have not fully addressed.
You have a PhD chemical engineer and an instructor in quantum mechanic examining my claims. You have Dr Schneider’s coworker who wrote the online version of the computer model. I don’t think the evolutionists on this forum have seen what Dr Schneider’s model shows when realistic parameters are used unless they have been following the Evolutionisdead forum on this topic. Don’t confuse evolutionist misunderstanding of ev as my making fundamental errors. The problem you have is that you think the ev model can be explained with a sound bite. It is not a trivial calculation and requires some study to understand the model. When you do understand the model, you will understand my claims.
I’ll give you time for this to soak in and then I’ll show you why I believe these claims to be true. You promised to do this a few days ago.
Evolutionist ground has been drying for a century and a half, it will take gentle rains for a while for this to soak in. Unfortunately, the only thing I have done so far is cause a flash flood, I’ll slow it down for you.
I did try to write a letter to the editors at Nucleic Acids Research since they published the ev paper but they don’t accept letters to the editor.Really? You didn't quote the Bible did you?
I didn’t quote the Bible to the editors at Nucleic Acids Research but if I thought it was appropriate, I would have. Do you have a problem with the Bible? Is that why you object to my mathematical arguments against the theory of evolution?
I don’t consider what I have done as being the greatest discovery in the last century of biological science. Well that's just what you'd be doing if you were to show that all of evolutionary theory has been a huge mistake.
I don’t believe all aspects of the theory of evolution are wrong, only the aspects associated with macroevolution are wrong.
Many scientists have said that it is mathematically impossible for life to have evolved. You can start with Francis Crick. You mean this (http://www.positiveatheism.org/india/s1990a01.htm) Francis Crick? Where did he say that?
Check what wikipedia has to say:
http://en.wikipedia.org/wiki/Francis_Crick#Directed_Panspermia (http://en.wikipedia.org/wiki/Francis_Crick#Directed_Panspermia)
Crick did modify his views when the RNA world hypothesis was raised, perhaps he would have modified his views again if he had seen the results of Dr Schneider’s ev model. If I had an opportunity to ask Crick a question, I would ask him how would an intelligent life form obtain the initial life to spread?
I am only addressing Dr Schneider’s model because of his superficial analysis of his model and the inaccurate extrapolations that he drew based on this superficial analysis. Many IDers have criticized Dr Schneider’s conclusions because of his use of an unrealistically small genome and an unrealistically high mutation rate in his single published case but Dr Schneider shrugged off these criticisms. Because of my engineering background and training with the development and application of large scale computer simulations, I simply put those skills to use on Dr Schneider’s model. I did a systematic parametric study with ev. So here we are. I don’t expect there are many readers of this site who willing to put in the effort to understand Dr Schneider’s model but there may be a few. If you prove that evolution could not happen in the model you haven't shown it to be impossible in reality because the model doesn't perfectly model reality. Far from it.
Dr Schneider gives a good answer to this which he posted on his site:
http://www.ccrnp.ncifcrf.gov/~toms/paper/ev/truman/ (http://www.ccrnp.ncifcrf.gov/~toms/paper/ev/truman/)
A good simulation does not attempt to simulate everything; only the essential components are modeled. For the issue at hand, the form of the genetic code is not relevant; information measured by Shannon's method is more general than that.
Dr Schneider believes his ev model simulates random point mutations and natural selection realistically and so do I.
You also ignore what evolutionist Dr Schneider, peer review author of the published ev computer model has said about his model:
The following quotes were taken from Dr Schneider’s blog web page: http://www.lecb.ncifcrf.gov/~toms/paper/ev/blog-ev.html (http://www.lecb.ncifcrf.gov/~toms/paper/ev/blog-ev.html)

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

"Schneider's paper is misleadingly titled: "Evolution of biological information". But it is just a *computer* simulation. No actual *biological* materials (e.g. genomes of nucleic acids, proteins, etc) were used, nor does Schneider propose that his simulation be tested with *real* genomes or proteins Actual biological materials were used to determine the original hypothesis. Read the literature: Schneider1986 (http://www.lecb.ncifcrf.gov/~toms/paper/schneider1986)

It only becomes *real* biological information and random mutation and natural selection, when the simulation is tested in the *real* world, using *real* DNA, proteins, with *real* mutations and a *real* environment does the selecting. It is significant that Schneider does not propose this, presumably because he knows it wouldn't work.You are very bad at reading my mind, I have considered doing this experiment. Given the right conditions, it WILL WORK. Do you have th gumption to do the experiment yourself? That's the way real science works! FURTHERMORE, if you read the literature, you will recognize that related experiments have been repeatedly done for 20 years. Look up SELEX.

In the rest of the paper he uses the single word "selection". I take this as a tacit admission that his model is not a simulation of *real* biological natural selection. No. A rose is a rose by any other name. Selection is selection whether it be natural (generally meaning the environment of earth), breeding (by humans usually, though perhaps some ants select their fungi), SELEX or in a computer simulation. Of COURSE it is a simulation of natural selection! The paper would not be relevant to biology and would not have been published in a major scientific journal if it were not!

Schneider lets slip that there is another unrealistic element in his (and indeed all) computer simulations in that it (they) "does not correlate with time": So? Run the program slower if you want. Make one generation per 20 minutes to match rapid bacterial growth. THIS WILL NOT CHANGE THE FINIAL RESULT!

Well, when Schneider's simulation is actually tested with *real* "life" (e.g. a bacterium), and under *real* mutation and natural selection it gains information, then, and only then, would "creationists" be favourably impressed. But if they are like me, they would already be impressed (but unfavourably) that Schneider does not mention in his paper that his simulation should now be so tested in the *real* "biological" world. 1. The simulation was of phenomena in the "real" world.
2. Dr. Jones is invited yet again to do an experiment.

The following is a response Dr Schneider made to a statement made by David Berlinski (http://www.discovery.org/scripts/viewDB/index.php?command=view&id=51&isFellow=true).

Where attempts to replicate Darwinian evolution on the computer have been successful, they have not used classical Darwinian principles, and where they have used such principles, they have not been successful. The ev program disproves this statement since it uses classical Darwinian principles and was successful.

http://www.lecb.ncifcrf.gov/~toms/paper/ev/blog-ev.html (http://www.lecb.ncifcrf.gov/~toms/paper/ev/blog-ev.html)
Dr Schneider made the following comments in response to statements made by Fred Williams about ev.
Fred Williams complains that the "program is not real-world, not even close. New information was not created naturalistically." It is not clear what he means by 'real-world' or 'naturalistically'. If you read the Ev paper (http://www.lecb.ncifcrf.gov/~toms/papers/ev/) carefully you will note that the model parallels the natural situation.

Dr Schneider said the following on his FAQ page at:
http://www.lecb.ncifcrf.gov/~toms/paper/ev/faq-for-ev.html (http://www.lecb.ncifcrf.gov/~toms/paper/ev/faq-for-ev.html)
Why don't you do a real biological experiment instead of just a computer model?The primary reason is that we don't have infinite resources and time. If you have the resources (a molecular biology lab), are interested in doing an experiment, and would like to discuss it please contact me.

The previous statements are clear that Dr Schneider believes that ev simulates the real world. If the simulation is appropriate for small genomes then it is appropriate for large genomes. Macroevolution by mutation and natural selection is mathematically impossible.
In the last case, Rfrequency is 10 bits, while Rcapacity is about 11--12 bits. Tough for the binding site code to evolve, maybe even impossible. I'd expect that it might get somewhere after sufficient generations. From that trend, you'd expect it to take 3.5 million generations or more, so no progress after 400K generations isn't suprising. I ran this model overnight. After 2.5 million generations it's gotten nowhere. I'd say we've run into the Rcapacity problem. Just for a check, I'll run it with somewhat smaller genome sizes and see what happens.
I appreciate you confirming what I said about this case. What might be of interest to you is comparing the extrapolation I made with this series and the extrapolation you made with the 100k genome, mutation rate of 10^-6 and population of 1meg and how close our extrapolated values are becoming.

[delphi_ote]

I hope the library still exists and wasn’t burned down by evolutionarians in their zeal to burn Bibles.
Not only do you refuse to retract your mistake, now you're accusing me of being an anti-intellectual arsonist when you know next to nothing about me. Even if you don't respect those who point out your errors, I would hope you'd have enough respect for your religion to be courteous and honest. I guess being right in this argument is more important to you than the precepts of the religion you're trying to protect.

But don't let me interrupt. I beleve you were bearing false witness against people in Jesus' name. Please continue your hypocracy. Nothing I could say could possibly undermine your argument more thoroughly.

[joobz]

Joozb, do you believe that the mutation rate for living things were much higher for primitive life forms than the values measures now? I’m not sure what you mean by “dna continures”. I will try to make my comment on your last phrase as gently as possible, you are grammatically challenged.

I don't "believe" that mutation rates were higher. I KNOW that there are stressors (we call them mutagens) that exist that enhance this rate. you can ignore their involvement in a simulation, but real life doesn't. So, again, you are wrong.

BTW, you are right. I'm guilty of typing fast and not proofing. But that has no bearing on the truth of all other points made. models can simply life to help understand it. But reality does what it does. We observe and develop theories. Our observations of reality support evolution. You're observation that the model has errors doesn't change that. Please try again.

Hey, don’t get mad at me, this is Dr Schneider’s model, he’s the one who uses the data from this model to predict the evolution of a human genome.

I thought you said you understood this model. Paul, you need to help joozb on a few details on the ev model.

Again, you are going to the wrong complaint window. Dr Schneider wrote the model and used average values to predict the evolution of a human genome. The only problem with his average values is they have no basis in reality.
again, I see the limitations in the theory. You are just wrong.

The reason why you fail to see the connection to reality that ev has is because you think you understand the model when you don’t. You call me delusional when you believe in a theory that says the most complex molecules known came into existence by random process and your miracle worker natural selection. Sorry, but natural selection can not do miracles.
The fact you state "random Process" shows you are foolish. There's a random driving force, but a non random selection. just in the same way that the Canyons are carved by a water running down to the sea; elegant, complex structures commonly occur in the wake of an energy potential. Your desire to pretend otherwise is not my problem.



All that I am doing is taking an evolutionist’s mathematical model of random point mutations and natural selection and looking at the behavior of the model with realistic parameters. If you have a problem with the data from the model take it to Dr Schneider, he wrote the model. I notice that no evolutionist has ever question Dr Schneider’s claims based on his use of unrealistic parameters in his model, but when I use realistic parameters in his model, I now am overturning a century and a half of biological science.
Because his expectations of the model and what he is trying to learn from it is not the same as your expectations. As long as he acknowledges the limitations of the model, he is making sound observations. Don't play the game that, "he did it." It doesn't work. Stand up for your own ideas.

If the theory of evolution is true, it can withstand my puny efforts.
And it has. your efforts are missled and wrong.

[kleinman]

But don't let me interrupt. I beleve you were bearing false witness against people in Jesus' name. Please continue your hypocracy. Nothing I could say could possibly undermine your argument more thoroughly.
Hey, an evolutionarian who knows the Bible, how did you get past GEN 1:1 before you decided it was all hogwash?
Joozb, do you believe that the mutation rate for living things were much higher for primitive life forms than the values measures now? I’m not sure what you mean by “dna continures”. I will try to make my comment on your last phrase as gently as possible, you are grammatically challenged.I don't "believe" that mutation rates were higher. I KNOW that there are stressors (we call them mutagens) that exist that enhance this rate. you can ignore their involvement in a simulation, but real life doesn't. So, again, you are wrong.
We don’t have to ignore the effects of mutagens, how high of a mutation rate to you think can be maintained in a living organism?
All that I am doing is taking an evolutionist’s mathematical model of random point mutations and natural selection and looking at the behavior of the model with realistic parameters. If you have a problem with the data from the model take it to Dr Schneider, he wrote the model. I notice that no evolutionist has ever question Dr Schneider’s claims based on his use of unrealistic parameters in his model, but when I use realistic parameters in his model, I now am overturning a century and a half of biological science. Because his expectations of the model and what he is trying to learn from it is not the same as your expectations. As long as he acknowledges the limitations of the model, he is making sound observations. Don't play the game that, "he did it." It doesn't work. Stand up for your own ideas.
You need to read what Dr Schneider’s “expectations” of his model are, I have posted what he has said several times already on this thread, go read his web site if you want to know what his “expectations” are. Why do you get so angry when I agree with an evolutionist’s view of his computer program that it models reality?
If the theory of evolution is true, it can withstand my puny efforts. And it has. your efforts are missled and wrong.
Hey joobz, maybe I’m right, you already have said anything is possible.

[joobz]

You need to read what Dr Schneider’s “expectations” of his model are, I have posted what he has said several times already on this thread, go read his web site if you want to know what his “expectations” are. Why do you get so angry when I agree with an evolutionist’s view of his computer program that it models reality?
You completely don't understand, do you? Whether or not Dr. Schneider is right or wrong has no bearing on evolution being real or not. His model works well to describe that information can occur from only point mutations and natural selection. There are boundries where this works, but that it can happen means something. Feel free to play the kinetics game again. but you'll still be wrong. The model doesn't account for everything.
Hey joobz, maybe I’m right, you already have said anything is possible.
Nice use of delibertly misquoting and missinterpreting my statements. you can't use fact, so you must use intellectual gambits. it doesn't work. Science moves on without you.

[kleinman]

Nice use of delibertly misquoting and missinterpreting my statements. you can't use fact, so you must use intellectual gambits. it doesn't work. Science moves on without you.
There is a reason why Paul calls me the “Annoying Creationist”, however I don’t look at my quoting of evolutionists as twisting their words, I look at it as illuminating your twisted words. So remember google is watching you.

Where is science going anyway?

[fishbob]

There is a reason why Paul calls me the “Annoying Creationist”, however I don’t look at my quoting of evolutionists as twisting their words, I look at it as illuminating your twisted words. So remember google is watching you.

Where is science going anyway?

Doesn't matter.
You can't get there from where you are.

[kleinman]

Doesn't matter. You can't get there from where you are.
I beg to differ, I got my AAA tour guide (which happens to be a peer reviewed journal) and they clearly marked the map with an orange marker. They asked me if I wanted to visit fantasyland and I said no, there are enough evolutionists on the James Randi Educational Foundation forum for me.

[Yahzi]

So we have another evolutionist who figures things out with telekinesis.
Dude... you can't get anything right.

Telekinesis (http://en.wikipedia.org/wiki/Psychokinesis)

[delphi_ote]

Hey, an evolutionarian who knows the Bible, how did you get past GEN 1:1 before you decided it was all hogwash?
That statement is almost incomprehensible, but it seems as though you're placing a few details about history above being honest and moral. If you represent Christianity, then I'll happily call it all hogwash.

[delphi_ote]

Where is science going anyway?
Toward the truth. Join us, won't you? It's great.

[Beleth]

I don’t mind that I’m presenting this information on the net. I actually was content to discuss this on the Evolutionisdead forum until the evolutionists who were willing to discuss it were running short of counter arguments. Paul had asked me to raise the issue on this forum a while back and when I saw his “Annoying Creationist” thread, I took him up on the offer.
You could have started a new thread, you know. Did you choose to respond in the "Annoying Creationists" thread because you are a Creationist?

[Apathia]

You could have started a new thread, you know. Did you choose to respond in the "Annoying Creationists" thread because you are a Creationist?

He is, and he's volunteered to play the role of annoying. I don't agree with his conclusion (That Evolution is impossible and therefore never happened) but the more I read of him, my opinion is he is making an important contribution to evolutionary research and theory by these criticisms. I'm afraid he won't be taken seriously, and it will yet be some years before these issues will get addressed in scientific journals.

[delphi_ote]

I'm afraid he won't be taken seriously, and it will yet be some years before these issues will get addressed in scientific journals.
Can you summarize what issues you think are being raised that aren't being addressed by the scientific community?

[kleinman]

You could have started a new thread, you know. Did you choose to respond in the "Annoying Creationists" thread because you are a Creationist?
I’m the “Annoying Creationist” Paul Anagnostopoulos is pissed off at. How could I ignore such an honor bestowed by a moderator on this forum? The following data was in part developed by the ev program Paul ported over to the java language.

Dr. Schneider in his paper, “Evolution of biological information” published in Nucleic Acid Research and available online at http://www.ccrnp.ncifcrf.gov/~toms/paper/ev/ev.html (http://www.ccrnp.ncifcrf.gov/~toms/paper/ev/ev.html), states that the transition from a random to fully evolved system is “rapid, demonstrating that information gain can occur by punctuated equilibrium.”

This rapid gain of information only occurs with unrealistically small genomes and unrealistically large mutation rates. As the genome length is increased, the number of generations necessary to complete the evolutionary process increases at an exponential rate. The mutation rate has a more linear effect on the rate of evolution but still reducing the unrealistically high mutation rate to a more realistic value reduces the rate of information gain in a more linearly proportional manner.

The significance of this mathematical behavior in the ev program demonstrates the huge number of generations necessary for any real genome to theoretically evolve by a random mutation/natural selection process. The number of generations needed to complete a single evolutionary step for a bacterium reproducing every 20 minutes with genome length of 5,000,000 base pairs exceeds the age of the earth. For a genome the length of a human, approximately 3,000,000,000 base pairs in length, his program demonstrates that the 1,000,000 generations which evolutionists propose separate us from our closest related primate relative could not occur by a random mutation point mutations and natural selection.

In addition, ev shows that huge populations do not have the needed effect to accelerate evolution by RM&NS sufficiently to make this a possible mechanism for macroevolution. As an example of this mathematical behavior of ev with increasing population, the following series were run with genome length G=256, mutation rate of 1 mutation per 256 bases per generation, gamma=16, site width=6. Cases marked with evpascal required the pascal version of ev due to memory limitations in the java version of the program.
Population \ Generations for Rs >= Rf
64 \ 675
128 \ 807
256 \ 481
512 \ 646
1024 \ 452
2048 \ 268
4096 \ 178
8192 \ 247
16384 \ 166
32768 \ 186
65536 \ 189 evpascal
The following series used all the same parameters except G=512.
64 \ 2925
128 \ 1858
256 \ 1508
512 \ 1157
1024 \ 1027
2048 \ 953
4096 \ 694
8192 \ 610
16384 \ 534
32768 \ 369 evpascal
65536 \ 297 evpascal
131072 \ 387 evpascal
The following series used all the same parameters except G=1024
64 \ 10108
128 \ 4446
256 \ 4095
512 \ 3896
1024 \ 2710
2048 \ 1684
4096 \ 1445
8192 \ 1702
16384 \ 1931 evpascal
32768 \ 1548 evpascal
65536 \ 1124 evpascal
131072 \ 847 evpascal
262144 \ 868 evpascal

Each one of these series show that increasing population only shows a marked effect on the rate of convergence with small populations. As the population size increases, further increases in population have a decreasing effect on the rate of convergence.

This population effect is in direct contradiction to Stephen Gould’s hypothesis of punctuated equilibrium in which evolution occurs rapidly in small sub-populations. The smaller the population, the greater the number of generations required to acquire the information to evolve the genome by random point mutations and natural selection as shown by Dr Schneider’s ev computer model.

You all have a nice weekend.

[Apathia]

Can you summarize what issues you think are being raised that aren't being addressed by the scientific community?

That's bit broader than I meant. It's in regards to this model that was hailed as being an, if not complete and certainly simple, faithful simulation of the process of the Darwinian Theory of Evolution. There seems to be a snag. Perhaps there isn't one after all. It's just it seems that way to me now, and I'm not a scientist, so I'm open to be corrected. I've never thought that Darwin was the last word on evolution. So it seems to me that disputes of this sort can encourage progress. If there is a real snag in the classic theory, I look forward to exciting developments. Dr. Kleinmann may be annoying in this context, but I hope he's not superficially dismissed. A pain, right? But pain often serves a purpose that that should be addressed, even if you chase it away with an advil.

I'm being a bit of a Devil's advocate here, as a "satan" as the the Book of Job put it. I'm naive enough to think that we might back away from the name calling to, if not agreeing on anything, valuing the process.

[delphi_ote]

That's bit broader than I meant.
I was just hoping you saw something interesting I had missed.
It's in regards to this model that was hailed as being an, if not complete and certainly simple, faithful simulation of the process of the Darwinian Theory of Evolution.
If we're going for an entirely accurate model, that's going to be extremely difficult, maybe even impossible. But people are definitely working on these problems in bioinformatics and evolutionary computation. If our friend has something interesting to say, I'm certain people in those fields would listen.
I'm being a bit of a Devil's advocate here, as "satan" as the the Book of Job put it. I'm naive enough to think that we might back away from the name calling to, if not agreeing on anything, valuing the process.
I was more than willing to hear the man out until he proved he couldn't retract a very simple error.

[joobz]

That's bit broader than I meant. It's in regards to this model that was hailed as being an, if not complete and certainly simple, faithful simulation of the process of the Darwinian Theory of Evolution. There seems to be a snag. Perhaps there isn't one after all. It's just it seems that way to me now, and I'm not a scientist, so I'm open to be corrected. I've never thought that Darwin was the last word on evolution. So it seems to me that disputes of this sort can encourage progress. If there is a real snag in the classic theory, I look forward to exciting developments. Dr. Kleinmann may be annoying in this context, but I hope he's not superficially dismissed. A pain, right? But pain often serves a purpose that that should be addressed, even if you chase it away with an advil.

I'm being a bit of a Devil's advocate here, as "satan" as the the Book of Job put it. I'm naive enough to think that we might back away from the name calling to, if not agreeing on anything, valuing the process.

If you double back over the thread, you'll notice that I've given kleinman ample time to present his case and I have acknowledged that his critique of the model is valid. He found a problem with the model. Paul acknowledged where the limitations to the model are. However, The conclusion that kleinman generalizes it to real life is the problem. No person on this thread has ever claimed that darwin was the end all of evolutionary theory. Far from it in fact. But to state that the entire concept is wrong because some computer program doesn't work is just juvinile.

I've been willing to discuss with kleinman and listen to him when many have ignored him. I invite you to go back a check the transcripts. As he says, "google is watching." Between us, he was the first to throw verbal stones. He is the one who refuses to acknowledge when he was blatantly wrong about entropy and thermodynamics. His whole concept of 'time too long' in the model is a poor arguement. There is no new knowledge he has provided.

No, kleinman is just a noisy gong. loud and clangy but devoid of substance. He is of no use to anyone.

As I said. Science moves on without him. We don't know where it's going. It's the nature of discovery, but we don't hide what we discover. We don't change observations to fit our theories. We fit our theories to observations. As we learn more, we will change and improve.

this is completely opposite of kleinman's desire. He offers nothing worthwhile. I am done with him.

[Beleth]

I’m the “Annoying Creationist” Paul Anagnostopoulos is pissed off at.
I'll take that as a Yes.

How did you arrive at the Creationist conclusion?

[Paul C. Anagnostopoulos]

I added the bold face to your quote. Your theory about Rcapacity says the exact opposite. I will summarize your hypothesis:
If Rcapacity = 2 * binding site width is less than Rfrequency then ev will not converge. The mathematics of ev is saying that it is more difficult to evolve narrow binding sites on larger genomes.
I wish you'd stop calling it a theory. If I need a 12-bit code and I've only got 8 bits, it just won't work, period.

However, in real life, there are two issues. On the one hand, a narrow binding site wouldn't have sufficient bases to contain a code unique enough* to be useful in genetic binding. On the other hand, a wider site can contain a unique code, but is it harder to evolve the ligand? Actually, I really don't know. Point taken.

~~ Paul

* Yes, yes, I know.

[Paul C. Anagnostopoulos]

We don’t have to ignore the effects of mutagens, how high of a mutation rate to you think can be maintained in a living organism?
I don't know, but perhaps we have sex to show for it:

http://news.nationalgeographic.com/news/2001/07/0709_sexorigin.html

~~ Paul

[Paul C. Anagnostopoulos]

That's bit broader than I meant. It's in regards to this model that was hailed as being an, if not complete and certainly simple, faithful simulation of the process of the Darwinian Theory of Evolution. There seems to be a snag. Perhaps there isn't one after all. It's just it seems that way to me now, and I'm not a scientist, so I'm open to be corrected. I've never thought that Darwin was the last word on evolution. So it seems to me that disputes of this sort can encourage progress. If there is a real snag in the classic theory, I look forward to exciting developments. Dr. Kleinmann may be annoying in this context, but I hope he's not superficially dismissed. A pain, right? But pain often serves a purpose that that should be addressed, even if you chase it away with an advil.
What snag? The one where we agree that the diversity of life cannot arise solely from point mutations on random gigabase genomes in a few million years?

What classic theory? The one where we agree that Darwin didn't have the whole story 150 years ago?

By all means, Kleinman should make his case. I've been talking to him since June and I'm still waiting for the case.

~~ Paul

[delphi_ote]

The one where we agree that the diversity of life cannot arise solely from point mutations on random gigabase genomes in a few million years?
That's just the thing. Recent research has shown point mutation isn't the the only way genes get shifted around in natural evolution. There are a lot of different types of mutations that change the genome of an organism; especially those that sexually reproduce. Full chromosomal duplication events seem to be very important (http://www.sciencemag.org/cgi/content/abstract/313/5793/1596) in plant evolution.* There also seems to be a lot of gene evolution caused by tandem duplication events. Really weird things happen in genomes, too. Mitochondrial DNA or Chloroplast DNA can end up in the nuclear genome. Something like 8% of the human genome consists of retroviral DNA. Lots of junk collects in genomes over time. Most of it does nothing, but some of it seems to be important for evolution and biology. How did life begin? How are genes formed? What is the importance of various types of mutation?

These are questions at the the cutting edge of molecular biology and evolutionary biology. Scientists in these fields are trying to answer them by performing experiments and working in the lab. What is kleinman's answer? What does he think the underlying mechanisms are which produced the "endless forms most beautiful"? "Godddidit" is just an excuse for ignorance. How exactly did it happen?

* I'm R. Cunningham. :D

[Yahzi]

You completely don't understand, do you? ...The model doesn't account for everything.
Son, you're trying to tell a witchdoctor that his voodoo doll ain't got no mojo.

You might as well spit into a hurricane.

:D

[Myriad]

Likewise, at this rate, roughly an entire human genome of ~4 * 10^9 bits (assuming an average of 1 bit/base, which is clearly an overestimate) could evolve in a billion years, even without the advantages of large environmentally diverse worldwide populations, sexual recombination and interspecies genetic transfer. However, since this rate is unlikely to be maintained for eukaryotes, these factors are undoubtedly important in accounting for human evolution.(emphasis added)

"This rate" refers to the rate of information increase per generation shown by the ev model with the low-valued parameters that Kleinman is complaining about.

I just wanted to point out that not only did Dr. Schneider not claim that the ev model simulates all important factors in evolution, he explicitly stated the contrary. Kleinman usually leaves out the boldfaced sentence when he quotes this passage.

Respectfully,
Myriad

P.S. I've been playing around with the model. The curve of generations to convergence depends on the details of the selection mechanism. Change it so that ties are won by the bug whose worst mistake (greatest absolute value of the difference between the binding strength value from the weight matrix and the threshold) is less than the other bug's worst mistake, and the convergence time becomes (at least approximately) linear with respect to the genome length.

[Paul C. Anagnostopoulos]

P.S. I've been playing around with the model. The curve of generations to convergence depends on the details of the selection mechanism. Change it so that ties are won by the bug whose worst mistake (greatest absolute value of the difference between the binding strength value from the weight matrix and the threshold) is less than the other bug's worst mistake, and the convergence time becomes (at least approximately) linear with respect to the genome length.
Welcome, Myriad! That's an interesting result. Do you include both mistakes at binding sites and spurious bindings in the determination of the worst mistake?

~~ Paul

[Myriad]

Welcome, Myriad!

Thanks, Paul! As a long-time lurker, I know this is a great forum.

That's an interesting result. Do you include both mistakes at binding sites and spurious bindings in the determination of the worst mistake?

Yes. For binding sites it's how far below the threshold, for nonbinding sites it's how far above the threshold.

For the tests I've done with that selection model so far, I also pegged the threshold at zero. I doubt that makes a difference (it makes little or no difference with ev's normal selection rules), but I'd better mention it in case I'm wrong about that.

Respectfully,
Myriad

[Paul C. Anagnostopoulos]

Yes. For binding sites it's how far below the threshold, for nonbinding sites it's how far above the threshold.
That makes sense.


For the tests I've done with that selection model so far, I also pegged the threshold at zero. I doubt that makes a difference (it makes little or no difference with ev's normal selection rules), but I'd better mention it in case I'm wrong about that.
We're considering a parameter that allows the user to specify a constant threshold value. If you have the time, could you run your modified Evj with a genome size of about 1K, in the normal mode and the threshold=0 mode, about ten times each with different seeds, so we can see if there is a significant difference in generations to perfect creature?

~~ Paul

[Myriad]

No problem, except that it will have to wait until next week. I'm leaving on a Thanksgiving holiday trip in the morning. While away I'll have access to the Internet but not to the system I'm running the model on.

Respectfully,
Myriad

[Paul C. Anagnostopoulos]

Thanks, Myriad. No hurry on running those experiments.

I mentioned your tie-breaking method to Schneider and he said to congratulate you on introducing this new method. He asked what you do when two tied bugs have the same worst mistake difference; how do you break ties when breaking ties?

~~ Paul

[Dr Adequate]

We don't know this, because we haven't modeled more than a measly million creatures. You won't let me extrapolate using that fitted curve, but if I did extrapolate to a lousy billion creatures, it would require 103 generations; to a trillion creatures, 21 generations. Of course, there is some asymptote it's approaching, although I haven't the slightest idea what that is. No?

1 generation, obviously.

It is sometimes said that an infinite number of monkeys with typewriters would eventually produce Hamlet. This is an understatement. Actually, if you had an infinite number of monkeys, one of them would type Hamlet straight off.

---

The mistake Kleinman has made, or one of them, is to take a realistic value for p (the probability of a point mutation for a given base) but not for n (the population). This gives a totally unrealistic value for the probability that a given substition will occur in the gene pool per generation, which is given by:

q = 1 - (1 - p/3)n

If, for example, we take a realistic value for p of 10-8, then for a measly million organisms, q is 0.3%. For a lousy billion, it's 96.4%.

If we use a more realistic order of magnitude for the bacteria, say something like the 1014 present in a single human gut, then my calculator isn't accurate enough to tell us the difference between q and 1.

Schneider is forced by practical constraints to take n to be small, and has compensated for this by using an unrealistic value for p to give himself a realistic value for q. This is eminently sensible, since it is the amount of variation within the gene pool, rather than the variation between individuals per generation, that determines the rate of evolution.

Kleinman, on the other hand, has chosen his numbers so that the value for q is wildly unrealistic; this is why his estimate of the time the process would take is also wildly unrealistic.

[Kopji]

By definition, no apparent, perceived or claimed evidence in any field, including history and chronology, can be valid if it contradicts the Scriptural record.

http://www.answersingenesis.org/home/area/about/faith.asp


I think you guys are great but at the end of the day you are talking to yourselves. Creationists are not arguing from a position of intellectual integrity where they might ever be wrong if you provided evidence.

[Paul C. Anagnostopoulos]

No?

1 generation, obviously.
Yes, that's the obvious asymptote. Somehow it doesn't seem fair to use that as the practical asymptote, however. Wait a moment, what is a "practical asymptote"? I have no idea. :D

~~ Paul

[joobz]

Yes, that's the obvious asymptote. Somehow it doesn't seem fair to use that as the practical asymptote, however. Wait a moment, what is a "practical asymptote"? I have no idea. :D

~~ Paul
How does this agree with Hardy-Weinberg Equilibirum? Or is that only for sexually reproducing species?

[Dr Adequate]

How does this agree with Hardy-Weinberg Equilibirum? Or is that only for sexually reproducing species? I don't see how H-W E comes into it. The point is simply that if you have an infinite number of organisms, then one of them (or, to be precise, an infinite number of them) will, on reproducing, hit on exactly the right set of mutations to produce whatever it is you want. Long odds mean nothing to an infinite population.

Hence, as the population size tends to infinity, the number of generations to get any particular result tends to 1.

[joobz]

I don't see how H-W E comes into it. The point is simply that if you have an infinite number of organisms, then one of them (or, to be precise, an infinite number of them) will, on reproducing, hit on exactly the right set of mutations to produce whatever it is you want. Long odds mean nothing to an infinite population.

Hence, as the population size tends to infinity, the number of generations to get any particular result tends to 1.
That i get, but H-E states that with large population (along with 4 other criteria) you can suppress evolutionary changes from natural selection.

I see what you state and completely agree, but for that organism which hits the right combination, it would have to be the only surviving organism. For sexually reproducing systems, the formation of that binding site has to be dramatically beneficial for it's effect to be felt in the entire species. Otherwise, it gets diluted throughout the population.

[kleinman]

I hope you all had a nice weekend.

It's in regards to this model that was hailed as being an, if not complete and certainly simple, faithful simulation of the process of the Darwinian Theory of Evolution. If we're going for an entirely accurate model, that's going to be extremely difficult, maybe even impossible. But people are definitely working on these problems in bioinformatics and evolutionary computation. If our friend has something interesting to say, I'm certain people in those fields would listen.
Delphi, I have tried to be clear about my claims and I will repeat them again so you won’t be confused about what I am saying. I assert that Dr Schneider’s ev computer model of evolution by random point mutations and natural selection shows that when realistic parameters are used in the model that this mechanism is profoundly slow, too slow to explain macroevolution. This model also refutes key points of Gould’s hypothesis of punctuated equilibrium and also that huge populations such as those seen with bacterial colonies do not appear to have large impact in accelerating the evolutionary process.

I have acknowledged many times that ev does not include other possible mechanisms to explain genetic evolution such as recombinations, inversions, frame shift mutations and so on. However, the mathematical fact that ev removes random point mutations and natural selection as the key mechanism for macroevolution will undermine all other possible mechanisms. It is not impossible to mathematically model these other mechanisms. The most difficult part would be measuring accurate parametric data for use in such models such as numbers of frame shifts which are helpful and harmful and number of inversions which are helpful and harmful and so on and defining plausible selection mechanisms.
I'm being a bit of a Devil's advocate here, as "satan" as the the Book of Job put it. I'm naive enough to think that we might back away from the name calling to, if not agreeing on anything, valuing the process. I was more than willing to hear the man out until he proved he couldn't retract a very simple error.
Delphi, there is a difference between you and me. When Dr Schneider made his claims about ev, I went ahead and did analysis of what he said and specifically point out the flaws in his analysis. Now you want to harp on this issue with Shannon information is mathematically equivalent to entropy or the negative of entropy. I told you to get the text Equilibrium Statistical Mechanics by Frank Andrews which is the source of my view. In that text, Andrews does an example very similar to Dr Schneider’s problem. If you study what Andrews is saying, you might have a better understanding of what I am saying. Delphi, you are getting close to understanding this point when you said:
To be completely correct, I should've been careful to distinguish between self information and average self information. Self information is about a single outcome. Average self information is averaged over a distribution, and is identical to Shannon information.
The conclusion that kleinman generalizes it to real life is the problem.
Dr Schneider believes his model simulates real life, so do the peer review editors at Nucleic Acids Research who published Dr Schneider’s extrapolation of the ev model to the evolution of a human genome. Are you trying to say that ev only simulates reality when unrealistic parameters are used in the model and should not be applied to reality when realistic parameters are used in the model?
No, kleinman is just a noisy gong. loud and clangy but devoid of substance. He is of no use to anyone.
Don’t forget, I’m annoying as well.
I’m the “Annoying Creationist” Paul Anagnostopoulos is pissed off at.I'll take that as a Yes. How did you arrive at the Creationist conclusion?
I believe the Bible is a totally believable and trustworthy book, but forget about me proving this to you mathematically. I will prove to you that macroevolution is mathematically impossible (at least my random point mutations and natural selection) using an evolutionist’s model.
We don’t have to ignore the effects of mutagens, how high of a mutation rate to you think can be maintained in a living organism?I don't know, but perhaps we have sex to show for it:
http://news.nationalgeographic.com/n...sexorigin.html (http://news.nationalgeographic.com/news/2001/07/0709_sexorigin.html)
People on this forum have accused me of going about my proof backwards but this link you have posted has it sdrawkcab. They realize that it requires a high mutation rate in order to get sufficient numbers of genetic changes to explain the theory of evolution so they postulate this occurrence. There are a couple of obvious problems, the first is how do you get prokaryotic evolution and the second is that high mutation rates kill living things. But don’t let my arguments stop you, produce the laboratory data, add this affect to your mathematical model and show how macroevolution occurs mathematically.
What snag? The one where we agree that the diversity of life cannot arise solely from point mutations on random gigabase genomes in a few million years?
Now Paul, you know that ev does not simulate the evolution of a random gigabase genome. Why don’t you start ev with the genome from e coli except allow for 96 loci with a random distribution and then evolve your 16 binding sites using that initial condition and see whether ev converges more quickly.

I think that you will find that point mutations and natural selection is the cornerstone of your theory. You have no other mechanism to explain the de novo evolution of a gene.
What classic theory? The one where we agree that Darwin didn't have the whole story 150 years ago?
Darwin had no idea how complex living things are. He didn’t know they were irreducibly complex. If he had, I don’t think he would have extrapolated his observations the way he did.
By all means, Kleinman should make his case. I've been talking to him since June and I'm still waiting for the case.
I believe Dr Schneider understands my case, this is why he won’t discuss this issue publicly. To the rest of you devout evolutionarians, this mathematical science that I am presenting to you will soak in over time.
The one where we agree that the diversity of life cannot arise solely from point mutations on random gigabase genomes in a few million years? That's just the thing. Recent research has shown point mutation isn't the the only way genes get shifted around in natural evolution.
I look forward to you proving the theory of evolution mathematically. Perhaps you will be the one to change the theory of evolution from a soft science of show and tell into a hard mathematical science. Dr Schneider came close but no prize, only refutation of the theory when realistic parameters are used in his model.
What is kleinman's answer? What does he think the underlying mechanisms are which produced the "endless forms most beautiful"? "Godddidit" is just an excuse for ignorance. How exactly did it happen?
Delphi, I’m the “Annoying creationist” so use your skills in deductive logic to figure out what I believe is the mechanism which produced the "endless forms most beautiful". You have put your faith in mutation and natural selection as the explanation for this yet your view has huge mathematical scientific gaps.
I'm R. Cunningham.
Don’t worry, I won’t tell anyone. By the way, having a drink won’t help you deal with reality.
Likewise, at this rate, roughly an entire human genome of ~4 * 10^9 bits (assuming an average of 1 bit/base, which is clearly an overestimate) could evolve in a billion years, even without the advantages of large environmentally diverse worldwide populations, sexual recombination and interspecies genetic transfer. However, since this rate is unlikely to be maintained for eukaryotes, these factors are undoubtedly important in accounting for human evolution."This rate" refers to the rate of information increase per generation shown by the ev model with the low-valued parameters that Kleinman is complaining about.

I just wanted to point out that not only did Dr. Schneider not claim that the ev model simulates all important factors in evolution, he explicitly stated the contrary. Kleinman usually leaves out the boldfaced sentence when he quotes this passage.
Welcome Myriad. It should be pointed out to the readers that Myriad is one of the few evolutionists who post on the Evolutionisdead forum who had the curiosity and intellectual courage to investigate what Dr Schneider model shows.

I have never claimed that random point mutations and natural selection is the only mechanism that can be used to explain macroevolution. I have only asserted that this mechanism is the cornerstone for the theory and that this mechanism is far too slow to explain macroevolution as shown by the results from this model when realistic parameters are used. I have also asserted that Dr Schneider’s claim of the evolution of the human genome in one billion years by the rate of information acquisition from his single published case of the evolution of 16 binding sites on a 256 base genome with a mutation rate of 1 mutation per 256 bases per generation is a preposterous extrapolation that does not warrant publication in any serious scientific journal.
P.S. I've been playing around with the model. The curve of generations to convergence depends on the details of the selection mechanism. Change it so that ties are won by the bug whose worst mistake (greatest absolute value of the difference between the binding strength value from the weight matrix and the threshold) is less than the other bug's worst mistake, and the convergence time becomes (at least approximately) linear with respect to the genome length.
How long are you going to talk about do this before you actually do it? Is our friendly wager about jiggling the threshold and increasing the rate of convergence still on?
Kleinman usually leaves out the boldfaced sentence when he quotes this passage.
Myriad, I went back and looked at where I have quoted the above text written by Dr Schneider. I have quoted this text 11 times on the Evolutionisdead forum and 2 times on this forum and in all cases I have included the boldfaced sentence. So stop being a jackass. If you are going to attribute something to me, post the quote.
We don't know this, because we haven't modeled more than a measly million creatures. You won't let me extrapolate using that fitted curve, but if I did extrapolate to a lousy billion creatures, it would require 103 generations; to a trillion creatures, 21 generations. Of course, there is some asymptote it's approaching, although I haven't the slightest idea what that is. The mistake Kleinman has made, or one of them, is to take a realistic value for p (the probability of a point mutation for a given base) but not for n (the population). This gives a totally unrealistic value for the probability that a given substition will occur in the gene pool per generation, which is given by:
I’m not sure what probabilities you are trying to compute. If you are trying to get an idea of what Dr Schneider ev model is simulating by looking at his model as a simplified probabilistic model, then you will find population has less than an additive affect on the probabilities of a mutation occurring at the proper locus. Genome length has a multiplicative effect on the probabilities involved in this problem and mutation rate has at best an additive affect. Genome length is the dominant parameter in this probability problem.

Paul, the only problem I have with your extrapolations is that they are extremely inaccurate. Your extrapolations have improved but I have had to drag you kicking and screaming the whole way. That’s ok though, I have promised to be patient with you.
By definition, no apparent, perceived or claimed evidence in any field, including history and chronology, can be valid if it contradicts the Scriptural record.I think you guys are great but at the end of the day you are talking to yourselves. Creationists are not arguing from a position of intellectual integrity where they might ever be wrong if you provided evidence.
I happen to agree with the above quote but I also know that there are many different ways people interpret the Scriptures. Even evolutionists who believe very little in the Bible think that when they quote it, they got it right.

I am using Biblical arguments against the theory of evolution. I am using the many Biblical admonitions to measure and weigh to determine what is true. The mathematical arguments I raise here is measuring and weighing your theory. The measurements shown from ev show that the theory of evolution is lacking when placed on the mathematical scale.

[gopi]

I think you guys are great but at the end of the day you are talking to yourselves. Creationists are not arguing from a position of intellectual integrity where they might ever be wrong if you provided evidence.

Not all people who believe in the Bible believe that it is perfect and correct in a literal sense throughout. Also, not all people who have questions about possible holes in the theory of evolution are definitively creationists.

Personally, I don't have much biology knowledge. I've found the discussion here to be reasonably enlightening, and I think that it will help me if I get into a discussion of the scientific basis for evolution.

Back on the topic of Ev vs. kleinmann, I'm still waiting for kleinmann's justification of Ev's accuracy _for_his_purposes_. So far, it sounds like he's doing the equivalent of using a Newtonian physics simulator, and showing how it doesn't accurately match high speed particle movement observations - and then claiming this disproves relativity.

[gopi]

[FONT=Times New Roman]
However, the mathematical fact that ev removes random point mutations and natural selection as the key mechanism for macroevolution will undermine all other possible mechanisms.


Excellent. This is clear and concise. Since your entire argument depends on this statement, can you elaborate as to why you argue that the other possible mechanisms don't have a significant enough impact?

[joobz]

Back on the topic of Ev vs. kleinmann, I'm still waiting for kleinmann's justification of Ev's accuracy _for_his_purposes_. So far, it sounds like he's doing the equivalent of using a Newtonian physics simulator, and showing how it doesn't accurately match high speed particle movement observations - and then claiming this disproves relativity.
While not knowing the modeling you describe, it sounds like an accurate comparison.

The issue here is model vs. reality. many models that simulate reality don't have logical features built into them but are there to make approximate views. For instance, many of the models that describe the binding of white blood cells onto inflammed blood vessels in circulation actually use gravity as a driving force. But considering that hardly any of our vessels are perpendicular to gravity, this parameter is just wrong. What the gravity term really is is just a driving force to vessel walls that isn't clearly identified. But this didn't destroy the models ability to provide some insights into scaling issues.

The problem is that when ever you have a model vs. observation problem, you have to go with the observed phenomenon. It's what's actually happening. You have to bow to reality when doing the math. If Paul was to defend the model as a perfect representation of evolution, I'd attack him as well. But He has stated well the limitations to what the model shows.

Kleinman has a wish to see fullfilled and he'll do any intellecutally dishonest act to see that his wish is granted.

[Beleth]

I believe the Bible is a totally believable and trustworthy book, but forget about me proving this to you mathematically.Don't worry, I will not ask you to prove it mathematically. I just want to know what convinced you of the believability and trustworthiness of the Bible.

I will prove to you that macroevolution is mathematically impossible (at least my random point mutations and natural selection) using an evolutionist’s model.You certainly do seem earnest about that. And yet you mention that there are other methods that would lead to macroevolution besides random point mutations. I'm wondering if those, or perhaps an as-yet-unimagined mechanism, could be the cause of macroevolution. It just seems premature to me, frankly, to jump straight to Creationism at this point.

[kleinman]

However, the mathematical fact that ev removes random point mutations and natural selection as the key mechanism for macroevolution will undermine all other possible mechanisms. Excellent. This is clear and concise. Since your entire argument depends on this statement, can you elaborate as to why you argue that the other possible mechanisms don't have a significant enough impact?
My pleasure, I enjoy bringing clarity to the muddled concepts associated with theory of evolution. Let’s start with sexual recombination. This mechanism when it occurs without errors can not create a new gene. This mechanism can only cause a rearrangement of existing genes in the gene pool. When you combine the concept of recombination with the concept of natural selection, you can actually lose alleles from the gene pool. You can actually lose information in the gene pool by this mechanism. Gene duplication and chromosomal duplication has been proposed as an important mechanism of evolution. However, in order to duplicate a gene or chromosome, you must initially have a gene or chromosome to duplicate, you need the initial gene(s). You must have some mechanism to created the initial gene(s) to duplicate. You are dependent on random point mutations and natural selection in order to create the new gene. In addition, you need random point mutations in order to convert the duplicated gene to a new gene. Interspecies gene transfers requires the existence of the original gene and is therefore subject to the same type of argument as gene duplication, you still need the original gene. In addition, you have the difficulty of explaining how an interspecies gene transfer finds its way to the gametes. Gene inversions also require an existing gene to be inverted. Insertion and deletions require an existing gene. Choose your mechanism, I believe if you consider each mechanism, you will find that point mutations must be the cornerstone to the theory of evolution.

One particularly difficult issue when using mechanisms other than random point mutations as the mechanism for evolution is that these other mechanisms lead to large number of base changes in a single generation. If any one of these base changes is fatal to the organism, it doesn’t matter how many helpful mutations may have occurred. Every base change must either be beneficial or at a minimum neutral. If any of these base changes are harmful, this organism will be selected against.

Joozb has chosen to quote gopi, what’s happening joozb, you running out of ideas already?
Back on the topic of Ev vs. kleinmann, I'm still waiting for kleinmann's justification of Ev's accuracy _for_his_purposes_. So far, it sounds like he's doing the equivalent of using a Newtonian physics simulator, and showing how it doesn't accurately match high speed particle movement observations - and then claiming this disproves relativity.
Gopi, if you are going to make this type of analogy, it is not I who ignores the speed of light in a physics simulator. It is Dr Schneider who ignores realistic parameters in his model. Dr Schneider has used unrealistic parameters in his model, this is equivalent to Dr Schneider putting in a particle speed greater than the speed of light in his mathematical model and then extrapolating that behavior to the real situation. I believe that Dr Schneider has essentially related the parameters in his model correctly but that is only half the story. In order to predict behavior with his model, it requires the use of realistic, known, measured parameter values.
While not knowing the modeling you describe, it sounds like an accurate comparison.
Joozb, your analysis of gopi’s model shows as much scientific rigor as your analysis of Dr Schneider’s ev model. How could anyone deny such impressive analysis?
I believe the Bible is a totally believable and trustworthy book, but forget about me proving this to you mathematically.Don't worry, I will not ask you to prove it mathematically. I just want to know what convinced you of the believability and trustworthiness of the Bible.
My suggestion to you is read the Bible (more than once) and you might understand.

[Beleth]

My suggestion to you is read the Bible (more than once) and you might understand.Is reading the Bible more than once what convinced you?

[Yahzi]

Is reading the Bible more than once what convinced you?
:D

It never ceases to amaze me. These fundies will harangue all day long with "logic" and "reason." Then you ask them, "Did that convince you?"

And when they say no, they always seem surprised that you get upset.

"Why do you think I would be convinced by something that didn't convince you?"

[kleinman]

My suggestion to you is read the Bible (more than once) and you might understand.Is reading the Bible more than once what convinced you?
The more I read the Bible, the more I am convinced it is true. I recommend you read it more than once because it is difficult to read the Bible like a novel. Until you understand that part of the book is Biblical law, part of the book is historical, part of the book is a song book, part of the book is prophetical, part of the book is instructional. These different parts are woven into a tapestry that can be difficult to understand until you read this book several times. Many people if they have any knowledge of the Bible, it is limited to a couple small segments of the book, for example the Noah flood story or the story of David and Goliath or maybe the Christmas story.

I am not sure this is the answer you or looking for so I will put it this way. The Bible is God’s love letter to us. It is filled with God’s promises of His lovingkindness, mercy and forgiveness that He has for us. But the Bible also tells of God’s requirement of justice and what is due us. When that day of judgment comes, you will not be able to choose the terms of your defense. So you better have a really good lawyer when you face that Judge.

[Timble]

I am not sure this is the answer you or looking for so I will put it this way. The Bible is God’s love letter to us. It is filled with God’s promises of His lovingkindness, mercy and forgiveness that He has for us. But the Bible also tells of God’s requirement of justice and what is due us. When that day of judgment comes, you will not be able to choose the terms of your defense. So you better have a really good lawyer when you face that Judge.


A Moslem would say the same about the Koran, a Jew about the Torah, and so on....you can't all be right, or possibly you can't all be all right - they might all be partly true, and then again they may all be wrong.