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Posted by: Fred Williams Apr 21 2005, 01:14 PM

From the ‘Does Dna Contain A Code?’ topic:

The Claim

Some time ago Dr Tom Schneider wrote the paper ‘http://www.lecb.ncifcrf.gov/~toms/paper/ev/ev.html', only to have it thoroughly refuted by Dr Royal Truman (http://www.trueorigin.org/schneider.asp). In Schnieder’s response, he offered very little in defense other than an article he wrote for the internet 'http://www.lecb.ncifcrf.gov/~toms/paper/ev/AND-multiplication-error.html' (Dr. Schnieder’s excuse for his scant rebuttal was “I have other things to work on”! (see http://www.lecb.ncifcrf.gov/~toms/paper/ev/truman/).

Several evolutionists have latched on to this defense, essentially parroting Schneider without realizing the speciousness of the article.

The illusion

It turns out the only defense Schneider offered is built on illusion. It is a strawman argument, followed by invalid assumptions on population genetics that have no support from even evolutionist journals!

Schneider writes “The multiplication rule does not apply to biological evolution”.

For starters, almost all of the protein chain calculations used by creationists are used to refute abiogenesis. Evolutionists love to point out time and time again how “evolution” is not abiogenesis! If we are to accept the evolutionists complaint and keep these two separate (IMO this an equivocation, but that’s another debate), then the evolutionist is forced to admit that Schnieder has erected a strawman!

He then writes: “We then find the card that has the most coins with heads up and we throw away all the other cards. So if even one card has an extra head, it will be found… That is what happens in nature.”

This is not true and easily disproved. This is called “truncation selection”, which doesn’t happen in nature! Aside from common sense, we can establish this using evolutionist’s own words from their journals [1] and from it’s absence from college textbooks. Truncation selection would be a powerful mechanism, but it only happens with man-made intervention like artificial selection (that’s the only time you’ll see it mentioned in the college biology books), or in programs like Dr. Schneider’s (thus one of many reasons his program is bogus). He tried to sneak it past us with the just-so statement “that is what happens in nature”, but there is not even the smallest shred of evidence this is true. It is an illusion masquerading as “science”.

To further enhance the illusion, he mentions the dandelion. The fact that a dandelion can maintain or increase it’s population rapidly due to huge numbers of progeny, has absolutely nothing to do with truncation selection! This was a remarkably short-sighted analogy by Schnieder, and I suspect evolutionists would have a hard time finding even one population geneticist to agree that this somehow supports truncation selection!

Conclusion

In summary, while it is true that the Multiplication Rule requires the events to be independent, Schnieder uses the argument as a strawman (if you accept the evolutionist terminology that differentiates between evolution and abiogenesis). He ends with amazingly naïve assumptions about population genetics that are not even remotely true, assumptions that have no support even from evolutionist literature.

Fred Williams

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[1] Schnieder applies extreme truncation selection. A less severe version of truncation selection is essentially called "synergistic epistasis", and even evidence for it is scant: “Although there is some theoretical support for synergistic epistasis (Szathmary 1993; Peck and Waxman 2000), there is little experimental support for this type of gene interaction (Willis 1993; Elena and Lenski 1997).” - Agrawal and Chasnov 2001. Also, “Current evidence is equivocal as to whether the required levels of epistasis exist.” - Siller 2001

Posted by: Modulous Apr 21 2005, 02:14 PM

I think the program is meant to show information increase when a selection method is used. Truncation selection (and his example), I'm sure, is a grossly simplified selection method. The program isn't bogus though since it clearly shows exactly what it porports to:-

With random mutations and a selection method, information content can increase.

Remove the selection, and information content decreases.

Now - I agree that implying that natural selection and truncation selection are synonymous may be stretching things a little, and I am not in a position of sufficient knowledge at this time to fully discuss this. However, I think it is a mistake to think that Schneider has attempted to fully model natural evolution with his program. I believe (though I haven't studied it fully yet so I could be wrong), it also shows (perhaps as side effect) how IC structures can evolve.

Anyway, back to reading.

Posted by: 92g Apr 21 2005, 02:35 PM

I need a little help with this. He seems to be trying to demonstrate the potential of taking a "randon" genome with a uniform disutribution of bases, and try to figure out the chances of getting a sequence that binds to another genome.

Its not hard to imagine that if I have a goal of getting to the binding sites, and arrange my program to do it, that eventually it will happen.

How can this be an example of how the gentic code evolved? He's essentially starting with the letters, simply rearanging them until he finds the word he's looking for that he can attatch to a presumably existing sentence that makes sense to begin with.

He seems to have already assumed a genetic code, and he's just trying to imagine how the genome grew with more information.

This assumes a living being with a functioning code, and decoding mechanism. I don't see how it could be any evidence for how the code came into exisitance.



http://www.lecb.ncifcrf.gov/~toms/paper/ev/latex/node5.html

I think its more of an attempt to answer Spetner's charges than Gitt's.

How does selection pressure work in a simulation?

Terry

Posted by: Modulous Apr 21 2005, 02:42 PM

I think the 'goal' is to make least 'mistakes'. So in the end the goal is to survive.





He's not trying to demonstrate how the code came about in the first place, but how random mutations combined with selection can result in an increase in information.

Posted by: chance Apr 21 2005, 02:54 PM

I am just researching into this, so I don’t have much to add, but I will make one observation.
The ‘ev’ program is somewhat falsifiable, because it could have (but did not) demonstrate that you could not get from A to B, and there was no way of knowing that in advance of running the program. The arguments now focus on who is using the ‘correct’ assumptions in the ev program.

Posted by: 92g Apr 21 2005, 03:53 PM

Maybe you need to have a discussion with Mr. Anagnostopoulos.....



Terry

Posted by: Paul C. Anagnostopoulos Apr 21 2005, 05:13 PM

Ev starts with a population of creatures with random chromosomes. Part of the chromosome contains a "gene" with a weighting matrix and a threshold. The other portion of the chromosome has certain positions chosen to be the binding sites.

On each cycle, *every* position on the chromosome is evaluated with the gene to see if it binds there. Mistakes are counted when the selected positions are not bound, and when other positions are bound by mistake. The half of the creatures with the most mistakes are killed off and replaced by clones of the better half. Mutations are performed each cycle.

The goal of Ev is to show that the Shannon information content of the chromosome can increase from zero to a (turns out) predictable number of bits over time. It does so. Ev has nothing to do with abiogenesis or the evolution of the modern protein synthesis mechanism.

Ev does demonstrate the evolution of a code, however.

~~ Paul

Posted by: 92g Apr 21 2005, 05:30 PM

It attempts to show the change in the information contained in the genetic code. The "code" is not evolving. It still uses the same symbols and syntax.

Terry

Posted by: Paul C. Anagnostopoulos Apr 21 2005, 06:12 PM

The chromosome is a sequence of 2-bit numbers that just happen to be displayed as A, C, G, and T. These "bases" are taken in groups to form weights, thresholds, and binding sites.

The weights form a code (not the "genetic code") as the creatures evolve. In particular, the code could be used to correct binding site sequence mutations.

Hey look, we're famous:

http://www.lecb.ncifcrf.gov/~toms/paper/ev/blog-ev.html#fairytale2005Apr21

~~ Paul

Posted by: 92g Apr 21 2005, 07:46 PM

One can only believe that if he has time to pay attention to this wonderful web site, then he has time to answer Royal Truman's critique.

Terry

Posted by: Modulous Apr 22 2005, 02:07 AM

Somebody might have sent him an email. I doubt he spends all day monitoring the entire internet for mentions of his program.

Posted by: Paul C. Anagnostopoulos Apr 22 2005, 05:57 AM

I sent him an email.

~~ Paul

Posted by: Fred Williams Apr 24 2005, 08:57 PM

It’s been some time since I looked at Tom's program, but I recall that it is not falsifiable at all because it will essentially work every time. I was not surprised at all his program did what he predicted it would, given the input parameters. I would have been surprised it did *not* work! It's rigged for success, and does not emulate naturalistic accumulation. Too many unrealistic assumptions (i.e. truncation selection, high favorable mutation rate, etc).

Fred

Posted by: Fred Williams Apr 24 2005, 09:07 PM

No, it doesn't. I would be surprised if he stated as much in his email to you. As I believe Terry mentioned, a code is properly defined as symbols, syntax, and semantics. IMO this is sufficient to define a code, though Gitt attaches "prgamatics" (action) and "apobetics" (purpose or intent). I think the last two are obvious once you get to the semantics level.

So how in the world did his program evolve a new "code"?

Hmm, I see in the link you provided that Tom makes it clear his program does not evolve a genetic code. I guess this particular claim of yours is now defunct since the very author of it doesn’t think it evolves a code.

Fred

Posted by: Paul C. Anagnostopoulos Apr 25 2005, 08:33 AM

I did not say it evolved a/the genetic code. No one is claiming that code is synonymous with genetic code, are they?

Here is Terry's list of requirements. Are we still agreed on these?

So let's see how this pertains to Ev:
1) The set of symbols are the four values ("bases") 0--3.

2) The sequence of values is irregular.

3) The values appear in the regular structures making up the weighting matrix, the threshold value, and the binding site sequences.

4) The values occur repeatedly.


~~ Paul

Posted by: Fred Williams Apr 25 2005, 10:46 AM

What is the syntax? What is the meaning attached to the syntax? (example: codon = syntax, codon encodes amino acid = meaning).

Here is another example:

Symbols: English alphabet
Syntax: words comprised of symbols, ie "evolution"
Meaning attached to syntax (words): ie "evolution" = fairytale.

Why don't you ask Tom if he thinks his program evolved a new "code"?

Fred

Posted by: Paul C. Anagnostopoulos Apr 25 2005, 04:44 PM

A codon is not syntax. It's just a "word" composed of three "letters." I suppose a sequence of codons followed by a stop codon might be considered a "sentence," but the sum total of the syntax is the period at the end of the sentence. There are no other characteristics that we associate with syntax.

As far as meaning is concerned, if any sequence of letters or numbers or molecules performs a function, then it has meaning. That is, if what we mean by meaning is "An interpretation of the message over and above the sequence itself."

~~ Paul

Posted by: Paul C. Anagnostopoulos Apr 25 2005, 05:19 PM

Schneider thinks a code evolves, albeit a very simple one. The set of all possible site-length sequences are coded into two subsets: those that are recognized by the weight matrix and those that are not.

~~ Paul

Posted by: Fred Williams Apr 28 2005, 08:59 AM

Yes, there is. In programming, while syntax encompasses the set of instructions and their required order (similar to the traditional definition you gave above), it can also refer to individual opcodes.

Fred

Posted by: Fred Williams Apr 28 2005, 09:07 AM

I'd love to see Tom put that in writing somewhere on his site. So don't get me wrong, I'd have to see him say this in writing before I believe he would make such a blatantly erroneous statement.

BTW, let's clarify something. I asked you if Tom said his program can evolve a new code. You responded that Tom "thinks a code evolves". Of course he would say this, every atheist is required to say this or else he is admitting he is not an atheist. But that is not what I asked. It sounds like you are dodging my question. Does Tom think his program evolved a new code, yes or no.

Fred

Posted by: Calipithecus Apr 28 2005, 12:12 PM

I don't see how you figure that. Can you provide an example?

Posted by: Modulous Apr 29 2005, 05:32 AM

I think there is a little bit of confusing terms here. But its not a big issue. The code isn't evolving anymore than the DNA code is evolving. DNA uses the same 'symbols' to represent the same protiens universally. The point of the program is to show information increase due to random mutations and selection. Which it does.

Posted by: Fred Williams Apr 29 2005, 04:35 PM

No, it doesn't, it's an illusion. The illusion is built around two things: 1) low-level statistical informaton (Shannon) masquarading as real, tangible information (ie a code) and, IMO more importanty, 2) the word "selection". The selection in Tom's program is not real-world, not even close. New information was not created naturalistically. Artificial Shannon information, perhaps, random with natural selection, no.

So in short Tom's program did not even create new Shannon information naturalistically. At best it did so artificially. It's a bogus attempt to deal with the information problem.

Fred

Posted by: Modulous Apr 30 2005, 04:16 AM

Its not masquerading. If you look at the paper its quite clear that its Shannon information it discusses.



Its not Artificial Shannon information, it IS Shannon Information. The selection method used wasn't 'natural selection', but that doesn't mean it isn't Shannon Information. I think Tom dealt with this in his single paragraph about this thread. Don't like the selection method? Change it and see what happens. Shannon Information doesn't rely on a selection method, its just a measure of information. I don't even know what a definition of Artificial Shannon information would be.

Its not meant to be 'real world'. Its meant to show that random mutation coupled with selection increases the Shannon Information content. It does this.



The information problem being what? That information content can't increase through mutation and selection? Well, I think the program certainly shows that Shannon Information does increase with mutation and selection, and that is all it sets out to do. If you want to develop new definitions of Information and explain how that cannot increase with mutation and selection and how your model is closer to the DNA issue than Shannon Information then go right ahead. Write a program, submit it for peer review and win a Nobel prize (or at least a phd :-D)

Posted by: Paul C. Anagnostopoulos May 2 2005, 06:36 AM

More comments from Tom Schneider:

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

~~ Paul

Posted by: George R May 6 2005, 05:22 PM

As a courtesy I can add that the very long list of notes on the cited page are chronolological. You will see that notes from April 21 2005 & on are relevant to this forum as they directly reference this thread.

I shamelessly copy them here to save the thread from unintelligiblity as readers are focred to follow a line of debate splattered across other web sites.

Posted by: 92g May 6 2005, 05:39 PM

I don't think he understands the complaint. I wont pretend to speak for Fred, but for me, the question at the fundamental level does not center around the information stored by means of the genetic code, and I think that what Mr. Schneider is attempting to manipulate with his program, but the origin of the genetic code itself.

Terry

Posted by: George R May 6 2005, 05:41 PM

This is a telling comment from any designer of a model.

If I tell you that my model of the real world contains the minimum number of steps and variables to produce an intended result, I am saying that it is irreducibly complex.

If true, the irony is that ev is self-refuting: It will not achieve the results if parts are removed. So if it does generate information, but also demonstrates that this achievement can be the product of a irreducibly complex algorithm.

It may indeed be ideally the product of an irrreducible complex algorithm once the cost of reproducing "life" that contains any reproductive algiorithm as part of its own replication.

Before all the hand-waving starts about redundant computer steps and components that would in fact make the mechanism "better", bear in mind that (1) there is a real "cost" of buying theoretical add-ons in algorithms and in nature, and (2) the edxistence of a spare limb will not necessarily prepare or place that limb to take on the task of a specialized limb eg a broken right leg... nor does an extra add instruction nmake for a "takover" of a missing one in an algorithm (3) that a hit on one of the irreducible parts would terminate replication.

Granting FTSA that ev does perform the task that the author set out for it to achieve, the maintenance of the algorithm by a similar process as part of replication would seem not to be possible, and yet a looser "spare parts" algorithm would come at a higher cost and not necessarily achive any positive results.

Posted by: 92g May 6 2005, 05:45 PM

Excellent points...

Terry

Posted by: Modulous May 6 2005, 11:24 PM

That's fine, really. The program isn't there to demonstrate the origins of the genetic code, I think we can agree here. It was orginally brought up by Paul C when he said "Information can arise from random sequences of DNA, as Tom Schneider has shown with Ev.", but then mistakenly said "Tom Schneider's Ev program creates a code from random DNA.". Obviously this is an error. Creating a code from a random code doesn't really make any sense, right?

But we are essentially agreed, the origin of codes isn't the issue with the Ev program. That side of the debate seems to have stemmed from an overlooked mistake.



Ironic, given that the program actually evolves irreducibly complex structures isn't it? I think we can agree that Schneider hasn't programmed artificial intelligence Unfortunately, your argument rests on the idea that irreducibly complex things must have been designed and you neglected to actually demonstrate this to be true. If you want to start up a thread about ID and irreducibly complex structures, I'm more than happy to join in.

Posted by: Paul C. Anagnostopoulos May 7 2005, 08:12 AM

So you're saying that Behe's idea was that every object and process has a fundamental core of components that, when reduced, will render the object or process "broken"? That's not what he said, but let's assume it.

Such a statement is vacuous. It renders every object and process irreducibly complex at some point. Consider the process of snowflake formation. If we remove water vapor, temperature, gravity, or various other components, we can't obtain snowflakes. Are they irreducibly complex?

I thought the idea was that things are potentially irreducibly complex only if they are contingent.

~~ Paul

Posted by: Paul C. Anagnostopoulos May 7 2005, 08:16 AM

Schneider thinks that Ev creates a code, and I agree. It is not the genetic code; no one ever said that. It is a simple code that distinguishes binding sites from all other sites. If someone disagrees, then he needs to try harder to define what a code is, ensuring that the definition doesn't rule out everything but the extant genetic code.


And the entire idea is only interesting if the definition of irreducible complexity isn't a tautology.

Posted by: Modulous May 7 2005, 08:40 AM

Then maybe I missed a major part of his paper. Where does he say anything about the code being created by the program?

Posted by: Paul C. Anagnostopoulos May 7 2005, 04:11 PM

He says nothing about it in the paper. He said it to me personally, and has now mentioned it in his blog.

If we could just define code carefully, we could decide for ourselves whether Ev creates a code.

~~ Paul

Posted by: 92g May 7 2005, 06:57 PM

From Schneider's quotes above:



Terry

Posted by: Paul C. Anagnostopoulos May 8 2005, 06:06 AM

Correct, it does not evolve something like the extant genetic code. It does evolve a code, however. There is more than one possible code!

Let me see if I can get him to clarify, or state that I am wrong.

This is an awful lot of argument over a topic we could clarify if we would just define code.

~~ Paul

Posted by: Fred Williams May 8 2005, 05:59 PM

Before I critique the latest comments, I want to qualify a few things, comments I have made in the past but probably not yet on this forum. Dr. Schneider’s work with sequence logos is both interesting and IMO a good approach at identifying binding sites. I think this aspect of his work is good science. I also find his description of Shannon information as a “reduction in uncertainty” to be correct, it is the same way I interpreted Shannon’s paper. Both evolutionists and creationists have stumbled on this, often thinking uncertainty is information, which it is not, nor did Shannon intend it to be taken that way. Where we quickly diverge though stems from our worldviews, Schneider’s being that all life arose naturalistically. Whenever you start from a flawed assumption, you will ultimately produce bad science, and I believe Schneider’s Ev program has been overwhelmingly proven to be bad science and I think it would serve him best to abandon it and remain focused on his sequence logo work.

Now back to the latest comments put forth …

I think there is a good reason Tom told you this personally and did not mention it in his paper. Even through a biased evolutionary journal, this claim would have been tough for any reviewer to swallow because it is blatantly incorrect.

As I pointed out in this http://www.evolutionfairytale.com/forum/index.php?showtopic=122&view=findpost&p=1147 back in April, specifically item #1:

“Easily the most common tactic used by evolutionists is to equivocate on what a code is. ”

On several occasions on this board we have provided a definition for a code. I know Terry has, and speaking for myself I have offered this straightforward definition to work with:

Code:

A formal communication system consisting of symbols, syntax, and semantics. Examples: English language, Morse code, Fortran, ‘C’, Swahili, genetic code.

This is what we mean when we say “code!” It is essentially synonymous with “language”. Gitt takes it a step further and adds “apobetics” and “pragmatics”, which I believe are fine and good, but in my opinion are really extensions of “semantics” and already implied. So the definition above keeps it simple and straightforward.

Schneider’s definition of a code is an equivocation because it is too encompassing. He first starts out equating a code to a “message”, which essentially is correct, but then goes too far by calling parts of the message a code. Even a standard definition out of Webster’s shows Schneider is reaching:

Code: “a system of signals or symbols for communication”

A part of a message, say a single symbol, is not a system itself of symbols! He then uses the worst possible example, a “parity bit”. No one I know would ever call a parity bit a code. While it is true a parity bit protects a message against error (albeit partially), it is not part of the coded message. Instead it is a hang-on symbol, it does not have semantics in the true sense of any language (i.e. there is not a single human or computer language that defines syntax or semantics to a parity bit). The parity bit is in fact wasteful in message transmission - the little good it adds in partially protecting the message is easily outweighed by the waste of using the bit in the transmission. It has been completely obsoleted by more robust methods, such as checksums and CRCs[1].

As I mentioned in a prior post, the word syntax has been used interchangeably for both individual symbols, and their defined order. But I have never once heard code used interchangeably with its parts, until I read it on Schneider’s web site.

So going forward on this forum we will use the above definition I gave for a code, that way we can put an end to the endless repetition of equivocating over this. I’ll put a topic together and pin it, or perhaps come up with some sort of FAQ or glossary to handle these types of issues. I will grant that due to the “de-evolution” of our language, we do need to be clear in our definitions, and code is one of those words that has kind of taken a life of its own and why we need to clearly define it here (the word information and evolution are other obvious examples that need to be clearly defined).

But all of the above aside, Schneider still has not addressed the many serious problems that have been brought forth against his program. He mentioned that he cannot answer every challenge, and while I sympathize with that, he should of at least seriously tackled the holes that Dr Royal Truman pointed out, holes that I re-emphasized in my OP and are simply fatal to his claim of naturally evolving information. He continues to ignore the fact that his program uses severe truncation selection, something that does not occur in nature yet he continues to claim his program simulates nature! His mutation rate is also too high. Schneider replied to this by saying “Obviously if the rate were made lower (only 10 fold lower to reach HIV rates) the evolution would take longer, but the essential result should be the same.” The reason the result is the same, is because his program does not take into account the negative effects of an accumulating genetic load - he doesn’t let it happen by using severe truncation! As Truman pointed out “Error catastrophe would be inevitable.” [2] This alone refutes his program completely and convincingly as nothing more than an illusion. For icing on the cake, perhaps arguably the most untenable parameter in his program is the high rate of positive selection, essentially 50%! Some GA programs use 1 in 1000, and even many evolutionists will acknowledge that is a reach!

There is another way to look at this. Consider the fact that Schneider’s program, at least on my inspection of it, appears to be set up to work every time. It’s odds of success are unity! This illustrates the absurdity of the claim that his program shows information is added naturalistically (random change plus natural selection). Whenever a program has a guaranteed outcome, we know the information is already present from the beginning. Consider the following analogy: two engineers are given the task of writing a program that prints “hello world”. One engineer uses the easy way and his program simply prints the message. A less competent engineer uses random mutation with truncation selection to achieve the same result over many iterations. They both achieve the same programmed outcome, and hence have the same amount of Shannon information (we could rightly argue the less efficient version has less information, but we won’t here for the sake of argument). Both programs, before they run, have the same amount of information – they already have encoded the phrase “hello world” within their program. Schneider’s program already has the information Rsequence ~= Rfrequency. In the end, his program is no different than Dawkin’s “METHINKS IT IS LIKE A WEASEL” program that has long since been refuted. It is no wonder Schneider can’t see the obvious given that Dawkins was one of the reviewers of his paper.

I understand that it would be very hard to come to grips that something you wrote and have pushed for such a long time is seriously flawed, after putting so much work and effort into it. I hope Dr Schneider remains focused on his sequence logo work with the working genome, and eventually comes to realize he is not making productive use of his time defending his fatally flawed Ev program. As the noted physicist Richard P. Feynman once said,

“The first principle is that you must not fool yourself, and you are the easiest person to fool.”

---
1. http://www.cnet.com/Resources/Info/Glossary/Terms/parity.html
2. http://www.trueorigin.org/schneider.asp

Posted by: Paul C. Anagnostopoulos May 8 2005, 06:25 PM

The chromosomes in the Ev creatures do not have Rsequence = Rfrequency when the simulation starts. Yet they do after sufficient generations are simulated. Where does the information "come from"? Obviously from the design of the program: Information is "imparted" to the chromosomes by the cyclical application of evaluation, selection, and mutation. We might say that information is transfered from the environment to the organisms. And that is exactly what we can say about real organisms, too.

Regarding the code that Ev evolves: It has symbols, syntax, and semantics. Your definition is fine, but you appear to have an additional unstated requirement that the code look like something you think of as a "language."

~~ Paul

Posted by: Paul C. Anagnostopoulos May 8 2005, 06:41 PM

What would be a more realistic selection process?

~~ Paul

Posted by: Fred Williams May 13 2005, 09:31 PM

My two examples also do not have the target before the code runs! You have to run the code (or simulation) first, then you will have your target. Just like Schneider’s program, the information is there from the start, this is simply indisputable! I cannot stress enough just how erroneous the conclusions are that Schneider draws from his program. It’s really no different than Dawkins long since debunked “Weasel” program. Given all the other problems mentioned, the fact that the program already has the information encoded within it is mere icing on the cake in proving this illusion.



Here you unwittingly make my point for me. Thanks!



You can say all you want, you can say the moon is made of cheese. But that does not make it true. There is no evidence anywhere to support Schneider’s parameters, none. Zippo. Show me a study on truncation selection in nature (do a google search of this and my name and website comes up more than studies do!). Show me a study where the beneficial mutation rate is 50%.



You are trying to do an end run around my point. Please respond with evidence and/or an explanation of how his program produced a new code (symbols, syntax, and semantics). Just don’t say it is so, that is a waste of everyone’s time.

Fred

Posted by: Fred Williams May 13 2005, 09:33 PM

That’s a fair question. First, the process should account for the various costs in moving a mutation. For example, even if a mutant receives a beneficial mutation, there is no guarantee it will survive to the next generation. Genetic deaths can occur due to random death, i.e. a rock falling on your head, being a prude, suffering a lethal mutation, being a homozygote when the trait is heterozygote advantage, and other costs (Haldane estimated there was probably only a 10% reproductive excess available to move favorable traits.).

So after a “beneficial” mutation is added, go through and account for the genetic deaths. Keep track of the genetic load while you go. Keep track of each organism’s fitness, so when you apply “selection” you do proper probability calculations and not automatically eliminate the most unfit. For example, if organism A is 51% fit compared to the rest of the population, and organism B is 49 % fit, there still is at least a 49% chance organism B could survive when selection is applied across the population to meet some the pre-programmed goal for that generation (i.e. the goal may be to keep the population at a constant size every generation; or the program can be set to allow the population to grow at 1% per generation, etc. The point is, organism B could easily survive to the next generation, unless you apply truncation selection and remove him just because he was on the wrong side of the curve, albeit barely).

You’ll be hard-pressed to see an evolutionist ever program a model like this, because they know it is doomed to fail, unless they use fantasyland assumptions like Schneider did and crank up the beneficial mutation rate to 50% and apply truncation selection.

Fred

Posted by: Modulous May 13 2005, 10:24 PM

What information is there from the start?



The program design acts like the laws of nature. Since the program was not designed to simulate the creation of rules it doesn't need to account for how the rules get there, just that there are rules. I am not suggesting that the programs rules simulate nature, but that laws of nature exist before life does. The program shows us that random mutation, coupled with a selection method can increase information content without any information theory violations or thermodynamic violations or any other violations of known physical laws.

The program wasn't designed to tackle Haldane's dilemma or reproductive load. They are all fair arguments, that the program was not intended to tackle. The program was not intended to show everything. It was only designed to show that random mutation coupled with a selection method can lead to an increase in Shannon information. I assume you don't dispute this?

Posted by: Fred Williams May 14 2005, 06:56 AM

As I said a few posts ago (Post #37), “Schneider’s program already has the information Rsequence ~= Rfrequency. In the end, his program is no different than Dawkin’s “METHINKS IT IS LIKE A WEASEL” program that has long since been refuted.”



No, it doesn’t. Nature does not use truncation selection, nor does nature produce a 50% beneficial mutation rate, nor does nature prevent error catastrophe (extinction).



I never said it had to tackle “Haldane’s Dilemma”. Paul asked how it could use more realistic selection, and I explained how. Just because the terminology is the same that Haldane used, it is also the same terminology any population geneticist should use and itself is not “Haldane’s Dilemma” per se.



You assume incorrectly. I submit that since his program guarantees Rsequence ~= Rfrequency every time, that no new information is created since Rsequence ~= Rfrequency is encoded in the program before you run it. Now does this mean that “random mutation coupled with a selection” cannot produce new information? Of course not! That is, provided the selection method is intelligent, you can certainly produce new information. For example, a Genetic Algorithm can be given a target or a range of solutions to look for, and run ad infinitum until something useful is detected. This requires intelligence to determine when that useful thing has occurred. The aerospace industry, for example, has occasionally used programs similar to Genetic algorithms to search for various solutions. These are really no more than trial&error experiments, and the only reason any new information is ever culled is because intelligence is present (an engineer) to harness the information and put it to use. The point is this: an increase in information is impossible outside the presence of already-existing intelligence (i.e. an intelligent sender).

This thread is now going in circles. Unless there are any novel ideas that are added to this thread, I see no reason to not close it. For example, if Paul could explain the “code” (a communication system comprised of symbols, syntax, semantics) that Schneider’s program produced, we could discuss that. Or if someone provided evidence or any citation on truncation selection occurring in nature, etc. Otherwise we have reached the point where we are just repeating ourselves.

Fred

Posted by: Modulous May 14 2005, 07:35 AM

Rsequence (information in binding sites) starts off as approximately 0 am I right? Does that not imply that it has no information?





You missed a part of my quote there: . I am not suggesting that the programs rules simulate nature, but that laws of nature exist before life does. I never implied that nature uses truncation selection. I have frequently agreed with you on this matter. The program has to have physical laws in order to do anything. So, yes, these laws are designed, these laws aren't what the program addresses.




As above really. What is the information content of Rsequence at the beginning of the program?



So nature itself cannot dictate what is useful then? I was under the impression that the ability to acquire resources and mating partners was considered by nature to be inherently useful.


Is your objection to the program the fact that Rfrequency is a pre-selected constant?

Posted by: Paul C. Anagnostopoulos May 14 2005, 07:38 AM

It wasn't unwittingly. I agree that the information has to be somewhere, in some form, in order for it to find its way into the genome. This is also true in nature. Don't you agree?


Are you saying that the information does not find its way into the genome by repeated application of evaluation, selection, and mutation?

Ev does not simulate a beneficial mutation rate of 50%. It applies random mutations to each creature on each cycle, the number of mutations specified by a parameter (usually 1).

I modified Ev so it does not do truncation selection. Instead, it replicates the second-, third-, and fourth-best creatures, replacing the second-, third-, and fourth-worst ones. The best and worst creatures were left alone for good measure. Instead of taking about 800 generations to evolve a perfect creature, it took about 10,000.


You mean don't make just-so statements like "There is no evidence anywhere to support Schneider's parameters"?

The code evolved in Ev is very simple, nowhere near as interesting as the genetic code. The symbols and syntax are wired in already. What evolves is the semantics: The code selects the binding sites and does not select any other sites.

~~ Paul

Posted by: Paul C. Anagnostopoulos May 14 2005, 07:43 AM

The interesting issue here is that of the information source. Evolution is a process of transferring information from the environment to the genome. The genome "learns" to survive in the environment by encoding information that complements the information in the environment, so the organism can survive in the environment.

There is never going to be a simulation, or a real organism, that "makes up information" out of whole cloth without that information having already been somewhere else. An exception is that a genome could evolve useful information by accident, but we all agree that accident does not explain the wealth of life around us.

~~ Paul

Posted by: Paul C. Anagnostopoulos May 14 2005, 07:50 AM

The objection I hear most often is that the evolution of binding site recognition was built into the program. The program does not somehow evolve a genome that does "something useful" without any presumption about what that useful thing will be beforehand.

This is an interesting remark and is worth discussing. To make it have teeth, one would have to show that actual organisms evolve useful mechanisms without any influence from the environment concerning what those mechanisms should do. I can't conceive how one would demonstrate such a thing, except to show that it occasionally happens by chance.

Note that nothing stops us from changing Ev so that the number of binding sites is chosen randomly rather than prespecified.

~~ Paul

Posted by: Fred Williams Jun 1 2005, 04:27 PM

It was brought to my attention that Dr Schnieder responded to my comments:

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

Specifically:

Tom is apparently unaware that sorting is also truncation selection! The definition he provided is not a complete definition. For example, from this evolutionist web site:

“In truncation selection individuals are sorted according to their fitness. Only the best individuals are selected for parents.” [http://www.geatbx.com/docu/algindex-02.html#P424_21435]

This is precisely what Tom’s program is doing! Tom, your program is using severe truncation selection, you simply cannot claim otherwise.

It should be noted that Paul’s adjustments still amounted to truncation selection, just not 100% truncation selection such as is implemented in Tom’s program. But it is still radical truncation selection because virtually all members are being ranked and truncated, except the worst. So it is more like 99% severe truncation! Note what happened after Paul’s adjustment:

“Instead of taking about 800 generations to evolve a perfect creature, it took about 10,000.”

It took 10x more generations, just after a minor modification where the truncation selection was still radically severe!

As far as Tom’s “gauntlet” I provided a reasonable starting point to remove truncation selection from his program in http://www.evolutionfairytale.com/forum/index.php?showtopic=165&view=findpost&p=1876. As I mentioned in this post, evolutionists must know such simulations are doomed to fail if they even approach realistic selection and mutation methods.

It is not my responsibility, or any of the other scientists, to write a new program or adjust Tom’s to prove his program is flawed. It is Tom’s program that is being critiqued, and it is up to him to address the errors. I consider this case closed until realistic selection and mutation are used in his program, plus an explanation of how his program can have a 100% guarantee of success and not have Rsequence~=Rfrequency already encoded within the program, albeit very inefficiently (see penultimate paragraph in this http://www.evolutionfairytale.com/forum/index.php?showtopic=165&view=findpost&p=1774)

This thread is hereby closed, except for any further comments by Dr Schnieder. I will email him that I have responded to his truncation blog rebuttal to this forum.

Fred