Information and Genetics

Truncation selection is selection by a fitness algorithm. Natural selection is random, relative to fitness. For example, if you had a bunch of goats in the wild on a mountain, having good eyesight will help them survive, but it won't guarantee survival - there's a random component. On the other hand, if you're breeding goats and do an eyesight test before determining to mate them or not, you're employing truncation selection.Avida and tierra, as well as my example that I linked to, use natural selection by default (they do contain options that make them partially use truncation selection). Many commercial algorithms use truncation selection.------------------
"Illuminant light,
illuminate me."

Hi, Fred! What a surprise!Perhaps you'll return more ready to discuss than declare. If evolution is wrong it will be shown wrong through evidence and reason, not through extended personal incredulity.Have a great time away!--Percy

In genetics, truncation selection can be a form that natural selection takes, but it's such an extreme form that it's unlikely to occur in practice. Truncation selection occurs when there is a threshold in a quantitative trait (height, for example); all individuals that fall above the threshold survive and reproduce, while none of those below the threshold do. Natural selection is much more likely be partly random: more fit individuals have a higher probability of reproducing, but the probability is always less than 1.0. (On the other hand, the converse is not true: there are genotypes that give the individual zero chance of reproducing.)------------------

I just unzipped a fresh copy of avida. Here's the genesis file (configuration), just so you can see what is default for yourself.http://www.daughtersoftiresias.org/progs/genesisTo Fred:
Fred, you might want to take a look at it, since you've apparently never run the program:Fred, if you have any questions as to what a variable does: ASK. Don't just assert. ASK. You've been wrong on about everything you've asserted about Avida so far, so let's not do it again, OK?------------------
"Illuminant light,
illuminate me."[This message has been edited by Rei, 09-30-2003]

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Two comments to Mammuthus: Most creation scientists I know used to be evolutionist scientists. Two authored college evolutionary textbooks (Kenyon, Parker). Regarding transposons, I did not misspell it. I mistyped it. I’m sorry you can’t see the difference. This type of trivial attack is not productive, don’t you agree?

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You name a grand total of 2? And 99% of biologists named Steve accept the theory of evolution. The vast majority of creationists are not scientists and those that are usually have degrees in fields completely unrelated to genetics or evolution. For example, your two examples of evolutionists that became creationists, Kenyon studies biophysics, not evolution, and Gary Parker was always a creationist and apparently fabricated the story of his "conversion" from evolution to creationsm http://www.theistic-evolution.com/parkerdebate.htmlRegarding transposons, I am not particularly on your case because of your misspelling of the word, that can happen to anyone. But the entire argument you presented was extremely sloppy for someone on a high horse about how erudite and scholarly creationists are. You claimed that you read something you could not specify on transposons that somehow presented a problem for evolution. I rebutted the argument and presented a heap of citations (no mine was not among them) that you duly ignored. I did not claim all creationists are stupid. I claim that the vast majority are so poorly informed about the subject of evolution that they by default have to rely on their religious dogma or the regurgitation of fallacies posted by organizations like ARN or your own website in order to debate...that is why there is such a mind numblingy consistent pattern to the questions and comments from new creationists that log on here and on other sites. If you want to be anti-evolution, by all means, but be that way because you actually know what it is and disagree with it for intellectual reasons (like some of the IDists..at least semi intellectual reasons)...but not because of a knowledge deficit and fear of pissing off your religious communities values.[This message has been edited by Mammuthus, 10-01-2003]

I hope those answers about truncation selection were okay. The more important point is that the type of selection is irrelevant to this thread's topic. It won't be possible to tell why Fred rejects this until he responds to the rebutals. So far he's only been repeating his initial assertion (while casting ad hominems at Rei), which doesn't tell us much.--Percy

Yes, thank you. I understand better now. But let me try to phrase it in my own words to see if I understand.In real life, individual organisms have different phenotypes and there may be some of those that are an advantages or disadvantages that natural selection may act on.When a GA is set up it employess evolutionary mechanisms to allow novel outputs to evolve. These include some way of generating different "organisism" and some way of selecting them.In real life, organisms may die by purely random events that have nothing directly to do with there phenotype. (e.g., an asteroid landing on you). In the GA this fact of life may or may not be used. If only the criteria that define "better" are used to select then we have truncation selection. If instead a mix of randomness is used to kill of "organisms" we do not have truncation selection.It seems to me that this isn't either or. There is some parameter that specifies the amount of influence that random death will have or there should be such a parameter to allow one to use the GA in a variety of ways.If I'm in a hurry I turn the randomness down and get truncation selection, if I'm more interested in simulating "real life" I turn it to some other value. E.g, "real life" at the end of the cretaceous had a very suddenly large random component.(as an aside, in real life, is there ever a really random component. The creteaceous extinction appears to be random relative to long term evolutionary pressures, but isn't it really a sudden change in the nature of selective pressures? After it being small and a scavenger may have been a great survival advantage. Isn't it always "truncation selection"? That is selecting for what is desired? But nature keeps changing (slowly or quickly) what is "desired"? )

I agree. Isn't the point that complexity can arise from things which model the evolutionary process? It seems to me that creationists insist that no such compleity can arise from any "random", unguided process. GA's show that this statement is false.Creationists also specifically insist that life 'as we know it', could not arise from such a process. The GA's do not precisely show that this statement is false. They do not perfectly model the unfolding of life on earth.However, given the degree to which GAs do produce novel results of some complexity they do strongly "suggest" that evolutionary process might be capable of producing life as we know it. And we are left with no good argument as to why we shouldn't go with that suggestion.Darwin said that processes of this kind would produce diversity and complexity. He could not test that directly in the lab. We can now and his prediction has been fulfilled.To rebut this wouldn't someone have to say exactly what the process is and why a particular model of it isn't close enough?Fred seems to have attempted to rebut this without being clear on what he thinks a "real" evolutionary" process is like and why, in particular, it has not been modeled.He has, to me, made statments about one use of a GA as if it applied to all uses of all GAs. This doesn't, to me, rebut the point being made.

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(as an aside, in real life, is there ever a really random component. The creteaceous extinction appears to be random relative to long term evolutionary pressures, but isn't it really a sudden change in the nature of selective pressures? After it being small and a scavenger may have been a great survival advantage. Isn't it always "truncation selection"? That is selecting for what is desired? But nature keeps changing (slowly or quickly) what is "desired"? )

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Being small and a scavanger would be considered a selective advantage in the new environment that follows an asteroid impact. Standing in the wrong place when the asteroid hits would be considered a random component.------------------

Just a notice... I'm going on a business trip this week (late monday -> late friday), and will only have limited net access... so, in short, I'll be doing a "Fred" impersonation and disappearing. Of course, I'll be back as soon as possible so that I can respond to the posts that Fred won't make in reply to my posts to him.------------------
"Illuminant light,
illuminate me."[This message has been edited by Rei, 10-06-2003]

OK, where were we? Following is a synopsis of what has transpired in this thread and where I think we are.* I claimed GAs generally do not emulate evolution nor offer evidence that information can arise naturalistically. I gave several reasons, in no specific order of importance:
1) unrealistic truncation selection,
2) unrealistic assumption of positive mutations, both in quantity and frequency,
3) extinction is ignored or not permitted,
4) an information source is always required to prune any useful information created by a GA.* I claimed GAs are rarely used in engineering. Rei objected and provided a few examples (fallacy of exception supporting the rule).The relevant (IMO) focus of rebuttals hovered around (1) and (4) above. I’ll deal with (1) first, truncation selection:Truncation SelectionRei essentially agreed that commercial GAs use truncation selection, which should have divorced them from the discussion but Rei refused to do so:

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There is no sharp divider [between commercial and research GAs]. Commercial GAs are designed to run *faster* than standard evolution. They're all still GA's, however. A genetic algorithm involves determining an optimal solution through successive generations being based on what worked well in the previous generation with slight changesyour result is guaranteed to be *at least as good*.

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Percy then stated:

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I don't believe either Rei or myself are implying that GAs emulate biological evolution.

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Percy then backtracked a bit and qualified the above by saying that Rei does believe that specifically research GAs emulate evolution. It would have been easier if Rei would have divorced the two type of GAs from the discussion instead of Percy having to do it. But I’ll take it! I then addressed truncation selection in Avida/Tierra (research GAs). I gave an example, which quickly led to strawman arguments from PaulK and Rei. Paul then offered this:

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the fact that even this line included a significant number of deleterious mutations - 18+39 = 57 - shows that selection was certainly not able to eliminate all of the deleterious mutations

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This is yet another strawman, because truncation selection doesn’t mean you necessarily will eliminate all of the deleterious mutations. You can have both truncation selection and deleterious mutations present. More importantly Paul refused to answer how the application of the GA in the paper he cited avoided truncation selection while producing such rapid results of accumulated beneficial mutation. No support was offered to defend his claim, yet I am the one arguing from personal incredulity? Go figure! Paul then gets the irony of the month award for this statement:

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it is just another example of question begging. You fail to deal with my point that you need to actually SHOW that total extinction is so likely under a "realistic" scenario (ignoring the prima facie evidence that life has existed for billions of years without total extinction)

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If you fail to see Paul’s own question begging in the sentence where he accuses me of the same, by golly this is a goooood sign your dogma and blinders are pegging the ‘severe’ meter! Summary on truncation selection: Everyone now agrees (apparently) that it is used in commercial GAs. Commercial GAs should therefore no longer be brought up as evidence for evolution in any way, shape, or form. Someone please inform Rei of this earth-shattering revelation. Now that we have that settled, we are left with the impact and level of truncation selection in research GAs. I have not been offered any evidence, other than asked to look at this file, or look at this research paper. You need to point to specifics within the paper/file and explain your position. Paul offered one that had hope (one that apparently used the random birth setting), yet could not explain why such rapid accumulation of beneficial mutation occurred. I am more than willing to acquiesce this point if it is demonstrated. But funny thing is, all the examples given clearly employed some level of unrealistic truncation selection.BTW, have I ever mentioned that I think Avida as a program is a big joke. No surprise since it was written by a bunch of college hacks! GAs and InformationI will try one last time with Rei. If her answer requires invoking the hook, or pulling the lever that opens the trap floor, or engaging the catapult, then IGNORE mode will be reinstated!Scenario: I am the lead engineer on a project to build an ASIC or FPGA that will perform some function, say regulation of an airplane carburetor, or convert one protocol to another (such as ESCON to Fibre Channel). We decide to use a GA to assist us. Before the GA completes its run, Rei the author of the GA, raises her hand and gleefully says we should use the result of the GA no matter what. She assures us it will be the best solution. After we finish laughing (and calling personnel), we go and check the result of the GA. The cloud of pollution that affected Rei suddenly envelops the rest of the team (envision some Star Trek episode), and we too gleefully decide to use the result of the GA no matter what and do not subject it to test. We then submit the ASIC to fabrication (a time-consuming, critical process that can literally take months). We get the ASIC back, hook it up and at first are pleased. We then notice that it is not quite as efficient as we had hoped, and then discover additional work is required to address an unusual noise problem. We then run it in an actual environment and forget that a certain machine that interfaces to it has intermittent problems due to weak tolerance of the signal level. We tell the head cheese that we blew it and need another run at the ASIC. Our schedules slip badly, and our stock begins to plummet. Eventually, we find ourselves asking Rei if there are any openings at the McDonalds she began working at, or if she could at least share a happy meal.I will again ask Rei, should engineers take a GA output no matter what. Yes or No.Yes - Invoke hook, trap door, or catapultNo - welcome back to the real world!

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For example, your two examples of evolutionists that became creationists, Kenyon studies biophysics, not evolution,

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So for the record, are you prepared to claim that such an accomplished individual who wrote a standard college textbook that dealt with evolution does not know anything about evolution?

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Gary Parker was always a creationist and apparently fabricated the story of his "conversion" from evolution to creationsm

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You rely/trust an internet hack for your information? I perused his page and found what I expected, the usual poor scholarship nonsense full of unsubstantiated, hazy innuendo from a Talk.Origins wacko. I have met Gary Parker, and I trust his version, some of which you’ll find here:Acts and Facts Magazine | The Institute for Creation Research

Hey, Fred: my twice-asked question still awaits you at post 43 -
http://EvC Forum: Favorable Mutations? Help me!! -->EvC Forum: Favorable Mutations? Help me!!

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You rely/trust an internet hack for your information? I perused his page and found what I expected, the usual poor scholarship nonsense full of unsubstantiated, hazy innuendo from a Talk.Origins wacko. I have met Gary Parker, and I trust his version, some of which you’ll find here:

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Acts and Facts Magazine | The Institute for Creation Research

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The description of his "pre-conversion" attitude is exactly what I would write if I were a creationist looking to foster a condescending, pitying attitude among fellow creationists toward those poor, deceived evolutionists. What it does not resemble, in the slightest, is the actual beliefs of anyone I have ever known, spoken to, or read the writings of, who is convinced of the validity of the theory of evolution. As many do, he focuses on the supposed emotional and religious attachment that evos have to the theory, and glosses over the material objections - a supposed preponderance of problems that turned him away from evolution, while apparently causing no problems for all his classmates. As I see it, peer pressure after his conversion was the primary factor in his change of heart regarding the origins of life.
I'm not saying that none of this story happened as Parker tells it. However, it is without a doubt heavily embellished for the sake of his audience, and flavored more as a tale of comfort for the faithful than an instructive catalog of events as they occurred.

Well let's start by pointing out that Fred's original "straman" assertion has been already debunked by direclty quoting what he said.

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Paul then gets the irony of the month award for this statement:

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it is just another example of question begging. You fail to deal with my point that you need to actually SHOW that total extinction is so likely under a "realistic" scenario (ignoring the prima facie evidence
that life has existed for billions of years without total extinction)

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If you fail to see Paul’s own question begging in the sentence where he accuses me of the same, by golly this is a goooood sign your dogma and blinders are pegging the ‘severe’ meter!

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Well it is certainly a fact that life has been around for a long time and the scientiifc consensus (based on evidence!) is that it has been around for billions of years. We have evidence that life is evolving now and evidence that is has evolved in the past. So on the face of it we do have prima facie evidence that life HAS been evolving for billions of years.Fred on the other hand won't even explain WHY it is "unrealistic" not to allow total extinction as he claims.And he still doesn't. So we can scratch that argument by Fred and a pure fabrication on his part.On to the serious stuff.

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This is yet another strawman, because truncation selection doesn’t mean you necessarily will eliminate all of the deleterious mutations. You can have both truncation selection and deleterious mutations present. More importantly Paul refused to answer how the application of the GA in the paper he cited avoided truncation selection while producing such rapid results of accumulated beneficial mutation. No support was offered to defend his claim, yet I am the one arguing frompersonal incredulity? Go figure!

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This is an admission by Fred that he does not understand how Avida works. If you remember Fred claimed to have studied Tierra and Avida and those studies were the basis for his claims about truncation selection. When challenged on Avida Fred could only point to a single birth option which he claimed produced truncation selection - and could not even explain that.Because Fred can't argue from knowledge or understanding (proving that his study was clearly inadequate) he has decided to set up his unsupported assertions as the default and demand disproof.In doing so he sets up more questions. If truncation selection is so unrealistic then why would it have to be AVOIDED ? Where is the reason to suspect truncation selection at all ? It seems to be based on the view that truncation selection is necessary to get good results - and absolutely nothing else. But that assumption has yet to be supported - the burden then is on Fred to either support hisassertion or to show that there somehow the Avida run requires *unrealistic* truncation selection. Until he does it constitutes prima facie evidence against his assertionFred also fails to mention that the only results he reported were those for the MOST successful line, and even these included a number of deleterious mutations which obviously were not immediatately selected out - the most successful line by definition has done well above the average. He also accused the authors of the paper of fraud with no grounds at all other than his refusal to accept the results.[edited]
As for Fred's "strawman" assertion well THAT is ironic. Fred claimed that the selection was very efficient and - as stated above - I pointed out that the number of deleterious mutations found in the MOST successful line indicated that the selection was not that efficient after all. In short it was never about truncation selection. So Fred's strawman accusation is itself a strawman. Beat that for irony, Fred.Fred, it is up to you to support your assertions. If the best you can do is claim that the counter evidence doesn't amount to proof - while not even offering evidence to support your own claims - then you simply don't have a case. Simply trying to gloss over that fact as you do in your comments on my posts won't work.[This message has been edited by PaulK, 10-08-2003]