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Author Topic:   Extent of Mutational Capability
dwise1
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Message 111 of 279 (793311)
10-25-2016 2:42 PM
Reply to: Message 48 by Gregory Rogers
10-21-2016 11:31 AM


Re: Greg, Please Don't Give Up Yet!
Greg, what is your background with this "creationism-vs-evolution debate"?
The first thing you should know is that "creation science" itself is a deliberately crafted legalistic deception. For most of the 20th century (circa 1920 to 1968, during which the "monkey laws" were in effect), anti-evolutionists could be open about having purely religious reasons for opposing the teaching of evolution in the schools. But then Epperson v. Arkansas (1968) led to the striking down of the "monkey laws" and after a few failed attempts the anti-evolutionists learned that the courts no longer allowed them to ban evolution for religious reasons. In response, they superficially scrubbed their published materials of all explicit references to the Bible and to God (who suddenly became an "unnamed generic Creator") and dishonestly claimed (ie, lied) to the courts that their objection to evolution was for "purely scientific reasons." That is traditionally known as their playing the game of "Hide the Bible." That deception was exposed in Edwards v. Aguillard (1987), whereupon the anti-evolutionists switched to playing the game of "Hide the Creationism" by calling it "intelligent design" instead of "creation science."
"Creation science" is based on their "Two Model Approach", in which they "define" two "mutually exclusive models", the "creation model" and the "evolution model", and then set about attacking their "evolution model" and proclaiming that that proves their "creation model" without ever having to present, support, or defend that "model" -- in fact, repeatedly in creationist-run debates the creationists steadfastly refuse any discussion of their "creation model". Here is how Dr. Henry Morris, one of the Founding Fathers of "Creation Science", described the "Two Model Approach" to me (my emphasis added):
quote:
"The evolution model, in general terms, is not just Darwinism, but any naturalistic concept of origins (including most of the world's religions, ancient and modern). The creation model, in general terms, is not just the Biblical record, but any cosmogony which postulates a transcendent personal Creator to account for the universe and its basic components. Evolution says one CAN explain the origin and development of all things in terms of continuing, natural processes. Creation says one CANNOT so explain them."
In reality, the "creation model" is very highly restricted to young-earth creationism, which results in the vast majority of theistic creationist ideas (including most Christian ideas about Creation) being lumped into the "only alternative", their "atheistic" "evolution model." So of course they never dare to present or discuss their "creation model", since that would expose their game of "Hide the Bible."
The other consequence of the "Two Model Approach" is that their "evolution model" has virtually nothing at all to do with evolution. At best, it is a caricature misrepresentation of evolution, a strawman for creationists to attack and crow about having defeated while steering clear of actual evolution itself. You yourself presented one such misrepresentation of evolution, also echoed by CRR: the idea that evolution would require animals "evolving from one kind to another", such as a cat "evolving" into a dog (even though from the cat's perspective that would be devolving). As I and others here have described, not only does evolution not say or require that but such an event would be completely contrary to evolution. So when a creationist "disproves" evolution by pointing out that we never see a cat evolving into a dog, he is actually lying to you.
The approach you're taking in your year-old investigation appears to be one of collecting what both sides have to say. You are apparently treating what you collect as being different interpretations of the evidence (a commonly expressed creationist position and argument). But that cannot work when one side (the creationists) bases its "interpretations" on a misrepresentation of the other side. It would be like someone "disproving" Christianity by misrepresenting Communion as being nothing but cannabalism. Or "true Christians" redefining what Christianity is in order to claim that Catholics are not Christians -- a friend listens regularly to The Jesus Christ Show and it really gets Jesus angry whenever he hears that nonsense about Catholics not being Christians.
So part of your investigation also needs to pay attention to whether both sides are being honest and truthful in what they say about the other side. In particular, are creationists being honest and truthful about how they represent evolution? Or are they misrepresenting it in order to turn it into a strawman thus deceiving you and themselves?

This message is a reply to:
 Message 48 by Gregory Rogers, posted 10-21-2016 11:31 AM Gregory Rogers has not replied

  
dwise1
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Posts: 5930
Joined: 05-02-2006
Member Rating: 5.8


Message 113 of 279 (793314)
10-25-2016 2:52 PM
Reply to: Message 110 by Tangle
10-25-2016 2:12 PM


Re: Clades
It makes you wonder whether all/most species whilst they're in the process of speciation meet up breed, move away, meet again etc etc and either finally separate for good like lions and tigers but can in principal interbreed or one outcompetes the others
That interbreeding happens a lot. A number of examples of canine hybrids and feline hybrids happen in the wild -- see my Message 9 for links. And a local creationist seems to love his "chicken or the egg" argument in which his answer is "two chickens", but they need to completely re-evolve their reproductive systems simultaneously, or so he claims (it makes absolutely no sense to me either). In reality, chickens (Gallus gallus domesticus) are still able to interbreed with their ancestral species, the red jungle fowl (Gallus gallus), such that it's now very difficult to find a red jungle fowl that is not a chicken hybrid (https://en.wikipedia.org/wiki/Red_junglefowl#Hybridisation).
Yes, life can be very messy.
Edited by dwise1, : "to find" and added a Wikipedia link

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dwise1
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Posts: 5930
Joined: 05-02-2006
Member Rating: 5.8


(1)
Message 158 of 279 (793554)
11-01-2016 11:08 PM
Reply to: Message 150 by PaulK
11-01-2016 5:52 AM


Sorry, PaulK. I'm using your board as a springboard to address Greg.
Greg, I hope that you have not wandered off and that your intentions are still honest. That you are honestly seeking the truth about creation/evolution.
Oh look, a Creationist is quote-mining. Let's look at the context:
Quote-mining is a major creationist cottage industry. It involves digging through all kinds of scientific sources, including science popularizations (eg, the primary sources for the creationist leap-second claim (my own page on that claim), that less than a million years ago the earth would have been spinning impossibly fast, were quite literally Popular Science and Reader's Digest), in order to find passages to misquote in order to make it appear that scientists actually agree with creationist claims. Of course, any writings by a well-known scientist are prime targets for this treatment. Even without changing a single word in the fragment they quote.
So, you may ask how, if they do not change the actual wording, that would constitute misquoting. Here is an example that you should understand; the following quote is a hypothetical argument I'm just now making up against the existence of God:
quote:
Did you know that even the Bible says that God does not exist? that's true! Right there in the Bible it says, and I quote: "There is no God." That is straight out of the King James Bible, word for word!
And if you open up your KJV Bible to Psalm 14:1, you will indeed see those exact same words. Yet I misquoted that verse. Can you see how and why it is a misquote? A deliberately deceptive misquote? It is because I had lifted it out of context. Here it is within its context:
quote:
The fool hath said in his heart, There is no God.
The author was not saying what he himself thought or believed, but rather presenting what he imagines the opposing side would say. Ironically, a number of creationist misquotes involve quoting what their author thought the opposing side would say.
Lying through quote-mining is achieved by several techniques. Lifting out of context is one. Sometimes they will hide the context in ellipses (...). I tracked down one misquote which hide several pages in that ellipsis, such that that "one sentence" was spliced together from sentence halves pages apart and talking about different things.
Another technique is to quote the source using scientific terminology and then applying everyday meanings to that quote. Their "scientific quotes" "refuting" the existence of transitional forms make heavy use of that one.
Another technique is to misrepresent what evolution is or entails or says and then quote scientists explicitly disproving that misrepresentation. For example, both you and CRR brought up the mistaken idea about evolution that evolution would require a cat to evolve into a dog (even though a cat would consider that to be a case of de-evolving), so you could then misrepresent any actual biologist stating honestly and truthfully that that is impossible as that biologist speaking against evolution.
The bottom line for approaching any creationist quotation is to go to original source and see what it actually says. For example, one very effective debate strategy against Dr. Duane Gish was to present two transparencies side-by-side on the overhead projector (this was circa 1980). On one side was Gish quoting sources in his books. On the other side was what those sources had actually written. The audience, consisting mostly of creationists, was appalled at Gish's dishonesty.
talkorigins is a newsgroup, an early Internet precursor to Web forums. They created a website to act as an archive site for the newsgroup postings and it grew from there with many articles having been added. The TalkOrigins Archive is a very excellent source of information when investigating creationist claims and the "creation/evolution controversy".
On that site is the Quote Mine Project. I've not read it yet, but it looks like it has a lot of information.

{When you search for God, y}ou can't go to the people who believe already. They've made up their minds and want to convince you of their own personal heresy.
("The Jehovah Contract", AKA "Der Jehova-Vertrag", by Viktor Koman, 1984)
Humans wrote the Bible; God wrote the world.
(from filk song "Word of God" by Dr. Catherine Faber, http://www.echoschildren.org/CDlyrics/WORDGOD.HTML)
Of course, if Dr. Mortimer's surmise should be correct and we are dealing with forces outside the ordinary laws of Nature, there is an end of our investigation. But we are bound to exhaust all other hypotheses before falling back upon this one.
(Sherlock Holmes in The Hound of the Baskervilles)
Gentry's case depends upon his halos remaining a mystery. Once a naturalistic explanation is discovered, his claim of a supernatural origin is washed up. So he will not give aid or support to suggestions that might resolve the mystery. Science works toward an increase in knowledge; creationism depends upon a lack of it. Science promotes the open-ended search; creationism supports giving up and looking no further. It is clear which method Gentry advocates.
("Gentry's Tiny Mystery -- Unsupported by Geology" by J. Richard Wakefield, Creation/Evolution Issue XXII, Winter 1987-1988, pp 31-32)
It is a well-known fact that reality has a definite liberal bias.
Steven Colbert on NPR

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dwise1
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Posts: 5930
Joined: 05-02-2006
Member Rating: 5.8


(3)
Message 159 of 279 (793555)
11-02-2016 12:03 AM
Reply to: Message 156 by RAZD
11-01-2016 11:22 AM


This is a two-step feedback response system that is repeated in each generation, like walking on first one foot and then the next. It repeats every generation.
Based on evidence observed this occurs in virtually every breeding population in every generation, and we can thus say with high confidence that at least one new mutation survives in at least one individual from one generation to the next. For the purpose of maths we can say that this has a probability of >0.99, so we can use 0.99 and be conservative.
The probability of another new mutation surviving in the following population is also, conservatively speaking, 0.99
The probability of both occurring is not 0.98, because they are separate instances and one does not depend on the other. This is like flipping a coin, each flip has an 0.5 probability of being heads (or tails) and every subsequent flip has the same probability because it does not rely on the results of the first flip.
Good enough start, but I'm afraid it slipped away from you.
Close to three decades ago, I was so skeptical of Dawkins' WEASEL program in his "The Blind Watchmaker" that I wrote my own implementation of it. When it outperformed even his program (mine was in compiled Pascal, whereas his was in interpreted BASIC), I still could not believe it so I analyzed the actual probabilities. Both my program and my analysis of it are at http://cre-ev.dwise1.net/monkey.html. In all that time, the only criticism of my analysis was that my count of iterations was off by one -- ie, an insignificant minor error which does not affect the outcome.
Basically, the probability of approaching the target was very small, but the probability of every single iteration failing was vanishingly small, so arriving at the target in extremely short time became inevitable.
Most probability exercises involve a particular series of independent events all happening in a particular sequence. For example, to get a particular sequence of 100 fair coin tosses (ie, P=0.5, not weighted for tails since the heads side is heavier) the probability is p100 or 7.89-31, AKA very improbable. To express it algebraically:
P = P0 P0 P1 ... Pn
= pn
But that's not what we are talking about. We are talking about a population and about the probability of at least one of them succeeding. What we want to know is the probability of at least one member of the population succeeding. We do not want:
P = PA AND PB AND ... AND Pn
What we do want is:
P = PA OR PB OR ... OR Pn
For that, I borrowed from Boolean Algrebra's de Morgan's Theorem:
C = A AND B is equivalent to NOT(C) = NOT(A) OR NOT(B)
Hence, given Q = 1-P -- i.e., the probability of P being false:
P = PA OR PB OR ... OR Pn
becomes
Q = QA AND QB AND ... AND Qn
So to calculate the probability of failure if all failure probabilities are the same, we get:
Q = = qn
From which we can calculate P = 1 - Q
So, let's assume the probability of a beneficial mutation occurring in an individual as being 1/1000 or 0.001. Let's furthermore assume a population size of 1000.
So, q = 1-0.001 = 0.999
Q = q1000 = 0.367695
P = 1-Q = 0.6323
Pretty good odds, don't you think?
Now let's assume a larger population size, like 10,000, which in the wild shouldn't be too unreasonable:
Q = q10 000 = 4.517-5
P = 1-Q = 0.99995483
Approaching dead certainty, wouldn't you agree? And that's ignoring the fact that you could skip several generations without success. We're actually calculating the probability for success in successive generations, which is much less likely.
Of course, my MONKEY, like Dawkins' WEASEL, does not simulate evolution, but rather it compares two different kinds of selection: single-step selection and cumulative selection. The target is the alphabet in alphabetical order. Single-step selection involves trying to put the alphabet together randomly in one attempt and, when that fails, start all over from scratch. I calculated that in order to have one in a million chance of success, you have to run the program on a supercomputer (performing 1,000,000 attempts per second, hence running 1000 or 10000 times faster than the fastest PC) for many several times the 14-billion-year ago of the universe. Yet both MONKEY and WEASEL succeed within seconds (or within a half-hour in the case of the original WEASEL), every time without fail. By using cumulative selection, which is based on evolution. Single-step selection is based on creation out of nothing, creation ex nihilo.
Even though single-step selection has absolutely nothing to do with how evolution works, creationists continually try to saddle us with that loser of theirs.

{When you search for God, y}ou can't go to the people who believe already. They've made up their minds and want to convince you of their own personal heresy.
("The Jehovah Contract", AKA "Der Jehova-Vertrag", by Viktor Koman, 1984)
Humans wrote the Bible; God wrote the world.
(from filk song "Word of God" by Dr. Catherine Faber, http://www.echoschildren.org/CDlyrics/WORDGOD.HTML)
Of course, if Dr. Mortimer's surmise should be correct and we are dealing with forces outside the ordinary laws of Nature, there is an end of our investigation. But we are bound to exhaust all other hypotheses before falling back upon this one.
(Sherlock Holmes in The Hound of the Baskervilles)
Gentry's case depends upon his halos remaining a mystery. Once a naturalistic explanation is discovered, his claim of a supernatural origin is washed up. So he will not give aid or support to suggestions that might resolve the mystery. Science works toward an increase in knowledge; creationism depends upon a lack of it. Science promotes the open-ended search; creationism supports giving up and looking no further. It is clear which method Gentry advocates.
("Gentry's Tiny Mystery -- Unsupported by Geology" by J. Richard Wakefield, Creation/Evolution Issue XXII, Winter 1987-1988, pp 31-32)
It is a well-known fact that reality has a definite liberal bias.
Steven Colbert on NPR

This message is a reply to:
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Replies to this message:
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dwise1
Member
Posts: 5930
Joined: 05-02-2006
Member Rating: 5.8


Message 169 of 279 (793617)
11-02-2016 3:46 PM
Reply to: Message 161 by Gregory Rogers
11-02-2016 8:26 AM


Vestigial, Vesmigial!
Closing the topic should be left up to the administrators. When the originator arbitrarily closes a topic it is seen as being very rude, though you could request that an administrator close it before its time. The process involves an administrator first placing the topic into summation mode, wherein anyone who had participated can submit one and only one final message which sums up their thoughts about the topic and how it went. After all the summation messages have been posted, the admin will then close the topic. However, one can later request that the topic be reopened. Of course, if the topic is spinning out of control, an admin can close it much more abruptly. In such cases, it is also not uncommon for an admin to close a topic temporarily in order to encourage the participants to cool down before continuing.
the ID and Creationist response here is to say that the limb is not vestigial, but has a natural function, serving as an attachment point for muscles that both male and female cetaceans need to reproduce.
That is an example of creationists lying by shifting the meanings of words. Such "semantic shifting" is very widely used in creationist quote-mining (see Message 158 above). It's an attempt at "word magick", making something go away by redefining its name. Such "word magick" is a dishonest and deceptive practice best left to lawyers {1}.
In this case, there is a very strict definition for "vestigial" to mean that that feature serves absolutely no purpose whatsoever, and the practical definition used by scientists to mean that it no longer serves its original purpose and hardly any other purpose. It's the difference between being of very little use and absolutely no use whatsoever.
Hence the cetacean vestigial pelvis is indeed vestigial because it no longer serves to support the hind legs, which no longer exist (though can occasionally still be expressed {2}). The fact that some muscles still attach to what's left of that atrophied feature does nothing to eliminate the fact that the pelvis is vestigial and tells us something of the whales' evolutionary past, just like the vestigial pelvis in some snakes.
The best way to test this is, I would say, to examine the limb itself: looking at bone structure, basic design, etc., what are the evidences as to its background: are there clear indications, parallels, of limbs of a land-mammal; alternatively, is there clear evidence that it has, and has only ever had, the sole function of an attachment point for reproductive organs.
As Dr Adequate points out in Message 165 and AZPaul3 in Message 164, look at the fossil record which experts have studied extensively. In the much earlier cetacean ancestors you will find better defined pelvises and hind legs which had started to atrophy away. You will clearly see that those earlier pelvises served the function of articulating those hind legs. Clearly, being an attachment point for reproductive organs was never the sole function of the pelvis.
You can research this in the paleontology journals in the periodicals section your local university library, just as Merle Hertzler had done. He was a young-earth creationist I met on CompuServe in 1993-1994. He was the first honest creationist I had encountered since I had started trying to discuss this issue circa 1984. Not only did he do his best to discuss creationist claims (an extremely rare quality in creationists) but he would also research not only his claims but also the responses he got. As happens all too often to honest creationists, he learned that his claims were false and in a year's time he ended up on the other side arguing against creationism. He tells that story on his page, Did We Evolve?. Basically what happened was that an "evolutionist" had referred him to a book in which there was a citation in a paleontology journal, so he went to look that up. And he found more and more evidence that the creationists had always told him did not exist. I seem to recall that the citation had to do with cetacean fossils.
A further angle would be to compare other sea creatures to see if they have a comparable external mechanism.
Do you mean fish? Their reproductive systems are nothing those of mammals -- remember, whales are not fish, but rather mammals and as such have reproductive organs like other mammals and not at all like those of fish who basically do all their egg fertilizing in the open water. Though I'm not familiar with shark reproduction, especially considering that some are viviparous (ie, give live birth).
But still, since fish have no limbs in their evolutionary history, there would be no reason to expect them to have vestigial pelvises. Remember that evolution works by modifying what's already there. Unlike in designing a car, you cannot just completely redesign and replace an entire component in an animal; rather you are stuck with modifying what it already has (eg, in cars we completely changed how the engine is mounted and had to completely redesign how the radiator fan is powered, in cars we replaced the old pneumatically powered intermittant windshield wipers with a completely new electronic design). So as you compare the limbs of amphibians, reptiles, mammals, birds, both modern and fossil, you will see the same bones in the same relative positions over and over again. Their sizes and shapes will vary, but they are the same bones and you can trace them back to certain fossil fish.

Footnote 1:
An excellent example of lawyers redining words is found in the story of the Lintillas in The Hitchhiker's Guide to the Galaxy:
quote:
Lintilla is a rather unfortunate woman who has (as of Fit the Eleventh of the radio series) been cloned 578,000,000,000 times due to an accident at a Brantisvogan escort agency. While creating six clones of a wonderfully talented and attractive woman named Lintilla (at the same time another machine was creating five hundred lonely business executives, in order to keep the laws of supply and demand operating profitably), the machine got stuck in a loop and malfunctioned in such a way that it got halfway through completing each new Lintilla before it had finished the previous one. This meant that it was for a very long while impossible to turn the machine off without committing murder, despite lawyers' best efforts to argue about what murder actually was, including trying to redefine it, repronounce it, and respell it in the hope that no one would notice.
From Fit the Eleventh:
quote:
Arthur Dent: Why are there three of you?
Lintillas: Why is there only one of you?
Arthur Dent: Er ... (He is totally stumped by this)
Footnote 2:
It would be interesting to look at the development of whale embryos. For example, baleen whales have no teeth, but they still have genes for teeth and during embryonic development they start to form teeth which are then reabsorbed. Similarly, chickens have genes for teeth which we can cause to be expressed; in experiments fetal mouse gum tissue was placed on the jaws of chick embryos which caused teeth to start to form.
So my question is whether we see hind legs and the associated pelvis start to form in a whale embryo. I think that we should see that, since some individual whales have been found with vestigial hind legs (ie, not fully formed nor functional).

This message is a reply to:
 Message 161 by Gregory Rogers, posted 11-02-2016 8:26 AM Gregory Rogers has not replied

  
dwise1
Member
Posts: 5930
Joined: 05-02-2006
Member Rating: 5.8


Message 170 of 279 (793625)
11-02-2016 5:04 PM
Reply to: Message 161 by Gregory Rogers
11-02-2016 8:26 AM


Vestigiality
Regarding the definition of "vestigial", refer to the Wikipedia article, Vestigiality. In the introductory first section:
quote:
Vestigiality refers to genetically determined structures or attributes that have lost some or all of their ancestral function in a given species, but have been retained during the process of evolution.[1] Assessment of the vestigiality must generally rely on comparison with homologous features in related species. The emergence of vestigiality occurs by normal evolutionary processes, typically by loss of function of a feature that is no longer subject to positive selection pressures when it loses its value in a changing environment. The feature may be selected against more urgently when its function becomes definitively harmful. Typical examples of both types occur in the loss of flying capability in island-dwelling species.
And the first paragraph of the Overview section:
quote:
Vestigial features may take various forms; for example they may be patterns of behavior, anatomical structures, or biochemical processes. Like most other physical features, however functional, vestigial features in a given species may successively appear, develop, and persist or disappear at various stages within the life cycle of the organism, ranging from early embryonic development to late adulthood.
Vestigiality, biologically speaking, refers to organisms retaining organs, which have seemingly lost the entirety of the original function. The issue is controversial and not without dispute; nonetheless, vestigial organs are common, evolutionary knowledge. In addition, the term vestigiality is useful in referring to many genetically determined features, either morphological, behavioral, or physiological; in any such context however, it need not follow that a vestigial feature must be completely useless. A classic example at the level of gross anatomy is the human vermiform appendix though vestigial in the sense of retaining no significant digestive function, the appendix still has immunological roles and is useful in maintaining gut flora.
So the definition of "vestigial" does not require that trait to be absolutely useless, whereas the creationist redefinition does require that. In that way, creationists try to redefine vestigiality out of existence in order to create "evidence" against evolution. They are creating a false claim and a deceptive argument.
Again, the lesson learned is that you need to learn about the science in question so that you can evaluate what both sides say about it. It is not enough to simply collect arguments, but you must also determine the worthiness of those arguments.

This message is a reply to:
 Message 161 by Gregory Rogers, posted 11-02-2016 8:26 AM Gregory Rogers has not replied

  
dwise1
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Posts: 5930
Joined: 05-02-2006
Member Rating: 5.8


(3)
Message 187 of 279 (793670)
11-03-2016 10:26 AM
Reply to: Message 179 by Tangle
11-03-2016 3:43 AM


Re: The Maths
From Musgrave's post cited in your quote, Weasels, ReMine, and Haldane's dilemma:
quote:
There has been some discussion on the newsgroups talk.origins and sci.bio.evolution over the last year or so regarding Walter ReMine's claims that a version of Dawkins' "weasel" program, which demonstrates the efficacy of selection, nevertheless demonstrates a serious limitation on the rate of evolution, in agreement with Haldane's Dilemma, a rate so low that Mr. ReMine claims this makes the current accounts of human origins (and other higher vertebrates) implausible
. . .
Fortunately, Will Pratt of the University of Nevada found a copy, and as a result Robert Williams was able to get a copy of David Wise's program MONKEY (see http://www-personal.monash.edu.au/~ianm/whale.htm), which ReMine used. As I also noted earlier, after running it several times, and looking at the code, I couldn't find any hint of Haldane's Dilemma in the program. What was I missing?
The answer is actually blindingly simple, and is an embarrassment to Mr. ReMine.
. . .
Can you see where ReMine has made his error? I actually wasted a couple of hours comparing the effects of mutation rates on different programs before I realized it, but it should have been blindingly obvious (so I'm stupid, okay, but I was expecting something subtle).
Here's the key line: "Then we reduce the reproduction rate to that of the higher vertebrates, say to n=6."
Well, knock me down with a stick of mortadella and call me Jake. Mr. ReMine doesn't know how these programs work! In the vast majority of weasel simulations, including Wise's, the program takes a string, makes x copies of it with single letter mutations in one or more copies of the string, then chooses the best string and makes x copies of that with mutations, then chooses the best string from those copies, and makes x copies ad infinitum until the target string is reached. In many of these programs, the value x is a user entered variable called "number of offspring" or similar wording.
The important thing to note is that in Wise's program, Dawkins' original, Wesley Elsberry's weasel.pl and my WEASEL4.BAS (see sig) the "reproduction rate", i.e. number of offspring, IS ALSO THE POPULATION SIZE! Of course you will see only slow substitution in any of these programs when you only have 5 offspring, as there is only a TOTAL POPULATION of 5 strings at any one time![1]
Of course, in the real world, most organisms have populations of more than 5 individuals :-). Trying to compare the substitution rate in a population of 5 indviduals with the substitution rate in a population of between 10,000 to 100,000 individuals is a pretty big blunder to make, even allowing for the other problems in trying to compare this program with a real population. The information about "offspring" number isn't hidden, it's clear in the description given by Dawkins and in David Wise's documentation.
ReMine's argument totally collapses, without even having to point out the other, obvious problems.
I am that David Wise and MONKEY is my program (http://cre-ev.dwise1.net/monkey.html). Not only do I describe what MONKEY does, but I also analyzed the probabilities involved. I even provide the source code (then written in Pascal, but now also converted to C). What the program does is so easy to understand and information is so freely available, it boggles the mind how creationists like Remine and Royal Truman can get it so wrong. They have to be trying very hard to misunderstand it. They certainly have strong motivation to misunderstand everything: protecting their faulty theology from reality.
Verily it was written: "Everybody's got something to hide, except for me and my MONKEY!"

This message is a reply to:
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Replies to this message:
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dwise1
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Posts: 5930
Joined: 05-02-2006
Member Rating: 5.8


(1)
Message 214 of 279 (794487)
11-16-2016 2:50 PM
Reply to: Message 211 by Dr Adequate
11-14-2016 2:48 PM


Re: The Maths
Please remember that CRR is quoting ReMine on this issue; so if this is false then CRR is not lying, he is being lied to.
True enough. However, even though he is "merely" repeating a lie, it still does remain a lie. And the consequences of that lie being told is exactly the same whether or not CRR knows that it is a lie.

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dwise1
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Posts: 5930
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Message 232 of 279 (797500)
01-22-2017 4:30 PM
Reply to: Message 221 by CRR
01-21-2017 9:46 PM


Re: Look Sharp
Douglas Axe has estimated the chance of a chain of amino acids forming a functional protein is ~1 in 10^77. Denton estimates that no more than 10^40 proteins have ever existed on Earth. So even with those vast probabilistic resources the odds are fantastically small that a protein could have formed by chance. (obviously there are lots of assumptions and boundary conditions in any estimates of this kind). Pro-evolution researchers have done estimates and come up with the chance forming a functional protein as ~1 in 10^50. However that still leaves the chance at ~1/10^10 so it remains fantastically improbable. Note this avoids the sharpshooter fallacy because any functional protein would be success.
You can read more on this in Axe's "Undeniable".
I have seen this claim made for decades, so, no, I will not buy that book just in order to read the same false claim yet again.
Just making bare assertions and bare links instead of presenting the argument is frowned upon here. That is basically what you have done, minus any links (just naming an ID book is less than a bare link).
Here is a reply I posted on CompuServe two decades ago. Please let us know whether Axe's claim is different than Charles Wagner's was and describe how they are different:
quote:
#: 230849 S4/Biology
20-Feb-96 21:15:48
Sb: #229253-Lamarquian Evolution
Fm: David C. Wise 72747,3317
To: charles wagner 72401,2203
> Take for example a hypothetical polypeptide enzyme composed of 20
> different amino acids. These amino acids must be in the correct order and
> of the correct kind for the enzyme to work. The first amino acid has a 1:20
> chance of being correct. Same with the second and third anon... This gives
> us a probability of randomly discovering the correct sequence as about
> 10e20. Now there are about 2000 enzymes needed for a mammal to function.
> This gives us a probability of 10e40000 of finding them all by random
> trial and error. The earth is about 10e17 seconds old. How many mutations
> would have had to occur to get where we are?
Your first mistake is in assuming, quite incorrectly, that one and only one
amino acid sequence would be correct and any variation in that sequence would
be non-functional. Human lysozyme, chicken lysozyme, and bullfrog lysozyme all
have different amino acid sequences and yet are still the same protein,
lysozyme (BTW, human and chimpanzee lysozyme are identical). Human and
rattlesnake cytochrome c differ from each other by about 14 amino acids,
rattlesnake cytochrome c differs even more from cytochrome c in other species
(in the Dayhoff study, which included no other snakes, the rattlesnake protein
happened to be slightly more similar to the human protein than to the other 15
or so species in the study, which gave rise to a particularly and intentionally
deceptive creationist claim), and human and rhesus monkey cytochrome c differ
by 1 amino acid (which the creationist claim carefully avoided mentioning), and
yet it is still cytochrome c. I have a protein database with many more such
examples.
From the class notes of Frank Awbrey & William Thwaites' creation/evolution
class at UCSD (the Institute for Creation Research conducted half the lectures
and Awbrey & Thwaites the other half), we read their response to Duane Gish's
standard argument which you have repeated here. Gish calculates the
probability of a replaceable pool of 20 amino acids randomly forming into
RNAase with 124 amino acid sequences as:
Prob = (1/20)^124 = 1/3.4 x 10^(-166).
His basic assumptions, identical to yours, are:
1. each amino acid is uniquely specified.
2. parts of proteins serve no useful purpose
Evolutionist response:
1. only a few amino acids in a protein are uniquely specified, many are
loosely specified, and many are not specified at all; eg, in hemoglobin,
although sickle cell trait involves only one amino acid substitution, 17
other hemoglobin variants are known which are not harmful -- these have
substitutions at nonessential sites.
2. parts of proteins may well have serve useful functions in primitive
life forms.
A&T point out that there are different classes of amino acids: hydrophyllic,
hydrophobic, charged, uncharged, etc, and that for many amino acid positions it
is the class of amino acid and not the amino acid itself that is important.
Their counter example is of a calcium binding site with 29 amino acid
positions: only 2 positions require specific amino acids, 8 postions can be
filled by any of 5 hydrophobic amino acids, 3 positions can be filled by any
one of 4 other amino acids, 15 of the positions can be filled by virtually any
of the 20 amino acids.
The sequence of the 15 positions is: L* L*L* L*D D* D*G* I*D* EL* L*L* L*
Where:
L* = hydrophobic - Leu, Val, Ilu, Phe, or Met Prob = (5/20)^8
D* = (a) Asp, Glu, Ser, or Asn Prob = (4/20)^3
(b) theoretically also Gls or Thr Prob = (6/20)^3
D = Asp (1/20)
E - Glu (1/20)
G* = Gly or Asp (2/20)
I* = Ilu or Val (2/20)
Total Prob = (a) 3.05 x 10^(-12)
(b) 10.2 x 10^(-12)
By Gish's (and your) method: (1/20)^29 = 1.86 x 10^(-38)
So you see that the world and its probabilities work quite differently that
Duane Gish and you imagine it to.
Your second mistake should have been covered in your biology courses. Each
generation's proteins are not specified de novo and randomly, but rather each
generation inherits the previous generation's encoded sequences with the
possibility of some random changes. Of course, you can now see that several
sites in those sequences can suffer base substitutions very gladly and still
produce functional proteins. Indeed, we repeatedly find that the degree of
difference found between the proteins of different species fits very well what
we would expect had they descended from a common ancestor (AKA "evolved").
These patterns show up even when one tries to demonstrate otherwise, as in the
case of Michael Denton (whose attempts to disprove the standard phylogenetic
trees by grouping species according to the degree of difference between their
corresponding proteins only resulted in the very same standard phylogenetic
trees that he was trying to disprove).
Come to think of it, how does your panspermia account for the patterns of
relatedness shown by protein comparisons, or for pseudogenes, pieces of "junk"
DNA that are only shared by related species?
And as for the very first such protein having to have formed at random,
research by Sidney Fox shows that, when heated, amino acids form quite readily
into short proteins which, in the presence of water, form into microspheres.
These microspheres are very stable, so long as there are no micro-organisms
about to eat them. Many of these microspheres also display catalytic activity.
All that is missing at this point is a mechanism for replicating these thermal
proteins, after which the power of cumulative selection could be brought to
bear.
Which brings us to your third mistake. You assume that life would operate by
single-step selection whereas it is blatantly obvious that life operates by
cumulative selection. As much as you would love to discount my MONKEY, it does
still demonstrate, through a controlled experiment, the immensely vast
probability difference between the single-step and cumulative selection
methods. Your single-step example would indeed be very improbable and require
an immense time-span to produce results, whereas cumulative selection would
succeed in a matter of generations.
Bottom line:
  1. In order to mean anything, a mathematical model must actually describe what it's supposed to be model. These creationist protein probability claims do nothing of the sort.
  2. Nobody but creationists claim that proteins are the products of amino acids just happening to have fallen together by pure chance. Rather, they evolved, which is something quite different.
PS
I mention and contrast single-step selection and cumulative selection. If you are not familiar with those concepts and how they differ, then read the first half of Chapter 3, "Accumulating Small Change", of Richard Dawkins' The Blind Watchmaker.
Or you could go to my page, MONKEY, in which I discuss my own implementation of Dawkins' WEASEL program and link to my MPROBS.DOC file which analyzes and discusses the probabilities involved in cumulative selection. Basically, creationists keep using single-step selection whose probability of success are abysmally small, whereas evolution uses cumulative selection which succeeds with extreme rapidity and certainty. So far, the creationist attempts I've seen to "disprove" both WEASEL and MONKEY rely on lying about how they work (which I discuss on that page).
Edited by dwise1, : PS

This message is a reply to:
 Message 221 by CRR, posted 01-21-2017 9:46 PM CRR has not replied

  
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