Tuesday, October 12, 2010

Ken Miller and Chromosome Fusion

In the 2005 Kitzmiller v. Dover Area School District court case, federal judge John Jones was heavily influenced by the first expert witness, evolutionist Ken Miller. As Jones later recalled, he “was taken to school.” Unfortunately what Miller “taught” Jones was a series of scientific misrepresentations. Miller focused on two examples from molecular biology: a pseudogene and a fused chromosome. In both cases Miller gave Jones many facts but the lessons were carefully tailored to misrepresent both the science and evolutionary theory.

As I explained here, Miller’s pseudogene example included four key misrepresentations: that the pseudogene has no function and is broken, that the pseudogene DNA sequence has “errors” or “mistakes,” that there is no reason for broken genes aside from common descent, and that the evolutionary interpretation of such pseudogenes is objective science.

As was well known and documented when Miller and the ACLU lawyers devised Miller’s testimony, pseudogenes that had been investigated often exhibited functional roles, such as gene expression, gene regulation, generation of genetic diversity. Pseudogenes were found to be involved in gene conversion or recombination with functional genes. Pseudogenes sequences were found to be conserved with reduced nucleotide variability, excess synonymous over nonsynonymous nucleotide polymorphism, and other features that are expected in genes that have functional roles.

Any expert witness testifying on such a narrow topic would have been well aware of these well known results which were published by leading researchers in top tier scientific journals. And yet Miller gave no such perspective to the Dover court, and instead unequivocally represented his pseudogene example as non functional and broken. That was the evolutionary interpretation of pseudogenes, not what the scientific evidence was indicating.

And even if Miller’s selected pseudogene was truly broken, that would not mandate an evolutionary explanation as Miller unequivocally stated to the court. Miller told judge Jones that a pseudogene found in different cousin species, with common mutations, “must mean that these two organisms are descended with modification from another organism” and “leads us to just one conclusion,” which is evolution’s common descent. But this too was a lie, as any expert witness on this topic would know of the many instances of pseudogenes with mutations common to multiple species that do not fit the evolutionary pattern. In these cases even evolutionists must admit that common descent does not explain the mutations.

Perhaps most importantly, Miller’s pseudogene testimony misrepresented the evolutionary argument as objective science whereas Miller and the evolutionists, when not in federal court, make one religious argument after another. The religious foundation of evolution goes back to 18th century Enlightenment and before, and would automatically expel evolution from our public schools.

Miller’s pseudogene argument was just another example of a centuries-long history of religious mandates for evolution. Miller had been making such religious arguments for many years before Dover. He argued that life revealed features “that no engineer would stand for” so they must have evolved. That may be true, but such knowledge cannot come from objective science.

As Miller informed the Dover court, his pseudogene example was “just a mess.” That’s one of his favorite ways of making evolution’s religious argument. As he wrote more than 10 years before Kitzmiller:

In short, this sixth gene [the same pseudogene Miller testified of in the Dover court] is a mess, a nonfunctional stretch of useless DNA. From a design point of view, pseudogenes are indeed mistakes. So why are they there? Intelligent design cannot explain the presence of a nonfunctional pseudogene, unless it is willing to allow that the designer made serious errors, wasting millions of bases of DNA on a blueprint full of junk and scribbles.

It is a powerful argument, but it is not scientific. Miller routinely makes these religious arguments in his books and presentations, but they were carefully edited out for his testimony to the Dover court.

The ACLU lawyers and evolutionists argued that Intelligent Design is a religious theory because there was religious intent. They carefully traced this in early documents. But in evolutionary theory no such careful tracing is needed. The religious claims are boldly pronounced by evolutionists all through their literature. Darwin’s book was chocked full of religious claims, and today’s evolutionists are no different.

This hypocrisy of evolutionary thinking was equally evident in the second of the two examples Miller presented to the Dover court. In that example, Miller showed evidence that two of our chromosomes have been fused together and claimed it was powerful evidence for evolution: “the closer that we can get to looking at the details of the human genome, the more powerful the evidence has become.”

But from a scientific perspective, the fusion event occurred in, and spread through, the human population. There is no evolutionary relationship revealed. Even if evolution is true, this fusion event would give us no evidence for it. The fused chromosome did not arise from another species, it was not inherited from a human-chimp common ancestor, or any other purported common ancestor.

The reason why evolutionists find this argument to be so powerful is, once again, from a religious perspective. According to evolutionists, the evidence mandates evolution because it disproves creation and design. As evolutionist Barry Starr explains:

An alternative explanation is that the designers fused the two chromosomes together when they created humans. ...

The difficulty with this idea is that there is no obvious advantage to having 46 chromosomes instead of 48. ...

And even if there were, a designer who can easily put in the 60 million or so differences between humans and chimpanzees should be able to accomplish whatever results a chromosome fusion gives more elegantly than sticking two ape chromosomes together.

The power of the argument is not that evolution is confirmed, but rather than design is falsified. As Denis Alexander elaborates in his book Creation or Evolution, the fused chromosome “reveals our shared ancestry with the apes.” [211] Of course the chromosome reveals no such thing. It provides no more evidence for evolution than any other similarity. Starr, Alexander and the evolutionists may as well be discussing similarities we share with the apes in our bones or our biochemistry. But the evolutionists focus on cases such as the fused chromosome because these cases provide far more powerful religious evidence. As Alexander explains:

The suggestion that God has planted misleading ‘molecular fossils’ in our bodies is parallel to the suggestion that God planted misleading physical fossils in the rocks to test the faith of the believer. The obvious and profound theological problem with such a suggestion, as we considered in Chapter Six, is that it makes God into a deceiver on a grand scale. It would mean believing in a God who deliberately confuses people, making it look certain that we had shared common ancestry with the apes, when really this was not the case. [213]

And likewise Miller, when not deceiving federal judges, makes this same argument about the very evidence he presented in the Dover court:

So all we have to do is to look at our own genome, look at our own DNA, and see, do we have a chromosome that fits these features?

We do. It's human chromosome number 2, and the evidence is unmistakable. We have two centromeres, we have telomere DNA near the center, and the genes even line up corresponding to primate chromosome numbers 12 and 13.

Is there any way that intelligent design or special creation could explain why we have a chromosome like this? The only way that I can think of is if you're willing to say that the intelligent designer rigged chromosome number 2 to fool us into thinking that we had evolved. The closer we look at our own DNA, the more detailed a glimpse we get of our own genome, the more powerful the evidence becomes for our common ancestry with other species.

In his testimony, Miller told the Dover court that:

the closer that we can get to looking at the details of the human genome, the more powerful the evidence has become.

And when out of court, he makes the same statement:

The closer we look at our own DNA, the more detailed a glimpse we get of our own genome, the more powerful the evidence becomes for our common ancestry with other species.

The difference is he carefully omits the religion when in court. Nor did Miller reveal to the court that evolution is in no way required to explain the chromosome fusion evidence.

Miller also omitted several other inconvenient truths. Judge Jones said he received the equivalent of a degree in the expert testimony, but that degree didn’t include the fact that, beyond speculation, evolution has no explanation for how chromosomes evolved in the first place. And Miller did not explain the great number (more than a thousand) genes unique to the human genome. Again, beyond speculation evolution does not explain the rapid appearance of these novel genes. Indeed, as one evolutionist admitted, the secret to evolving a human from a chimp is to make fast changes in just the right places:

The way to evolve a human from a chimp-human ancestor is not to speed the ticking of the molecular clock as a whole. Rather the secret is to have rapid change occur in sites where those changes make an important difference in an organism’s functioning.

Finally, Miller presented the chromosome fusion evidence as a “beautiful” confirmation of an evolutionary prediction. What he didn’t explain to the court is that science is full of theories known to be false which yet make all kinds of confirmed predictions.

The Kitzmiller trial was one long series of misrepresentations. Yes judge Jones was schooled, but he didn’t learn the truth.

259 comments:

  1. Poor poor Cornelius. Relegated to obscurity at Biola, doing no research, producing no results, having to content himself with throwing rocks from the sidelines at real scientists.

    If Cornelius was any more glowing green with jealousy of Dr. Miller's success, he could be seen from space.

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  2. "Intelligent design cannot explain the presence of a nonfunctional pseudogene, unless it is willing to allow that the designer made serious errors, wasting millions of bases of DNA on a blueprint full of junk and scribbles."

    Is perceived by Cornelius as a religious argument? Why is that? I supposed because he presumes the designer is god, and any reference to design mist be religious. Miller is simply arguing that the observation does not match design prediction.

    I think he, or others, have gone on to describe the issues with the "sloppy designer." It is an appropriation of the observations and predictions of evolution. Sure, you could have a designer that likes nested hierarchy, and retention of non-functional bits. But these are not explained or predicted by design. The observation is not unique or inherent to design, it just can't exclude design by a designer who mimics evolution. At that point, aren't you at theistic evolution? What distinguishes the sloppy designer that makes everything seem evolved from a guiding hand through evolution?

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  3. How legitimate is it for a judge to "be schooled" by either party in a case? It is one thing to hear both sides of a case and evaluate them, but to "be schooled" by one party? Sounds like he already had his mind made up before the trial started. With some of the decisions that this generation of judges have made, I guess it shouldn't come as a surprise.

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  4. Cornelius said: "...as any expert witness on this topic would know of the many instances of pseudogenes with mutations common to multiple species that do not fit the evolutionary pattern."

    Can you name these instances? It's odd, you keep saying this over and over and over and yet you never provide an example.

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  5. Neal wrote: How legitimate is it for a judge to "be schooled" by either party in a case? It is one thing to hear both sides of a case and evaluate them, but to "be schooled" by one party?

    Neal, Judge Jones was simply acknowledging that Ken Miller is a terrific teacher. The judge really enjoyed learning some biology from him. There is nothing wrong with that.

    But what about the other side? The testimony of the ID experts was boring. Here is an excerpt from Margaret Talbot's Darwin in the Dock:

    ...on the penultimate day of the trial, when Scott Minnich, a professor of microbiology at the University of Idaho who was testifying for the intelligent-design side, showed a slide of the bacterial flagellum, Judge Jones offered the dry understatement "We've seen that." Minnich, who up until then had struck a staid, even sombre tone, acknowledged the sentiment: "I kind of feel like Zsa Zsa Gabor's fifth husband. As the old adage goes, I know what to do, but I just can't make it exciting."

    Whose fault is it that the judge did not find it as exciting as Ken Miller's presentation?

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  6. The Dover trial transcripts are fascinating. I would recommend reading all the arguments from both sides.

    http://ncse.com/files/pub/legal/kitzmiller/trial_transcripts/2005_0926_day1_am.pdf

    Here is Dr. Miller testifying...

    13 Q. Now, are you able to give us some examples
    14 of how modern genetics has applied to evolutionary
    15 theory?
    16 A. Well, I can give you quite a few of
    17 examples. Would you like me to use a demonstrative
    18 that would be useful to the Court?
    19 Q. And you have, at my request, prepared a
    20 series of slides that will help you to explain this?
    21 A. Yes, I have, as a matter of fact. I thought
    22 that I would start illustrating this by looking at
    23 hemoglobin. Hemoglobin is the protein that makes your
    24 blood red. It's the oxygen-carrying protein found in
    25 red blood cells
    ...
    3 Q. Could you give us another example?
    4 A. Sure, I'm very happy to. The next slide,
    5 this is another test of the evolutionary hypothesis of
    6 common ancestry.
    7 We have, as I'm sure most people know, 46
    8 chromosomes in our human cells. That means we have 23
    9 pairs of chromosomes because you get 23 from mom and
    10 you get 23 from dad, so we've all got 46 total. We've
    11 got 23 pairs.
    12 Now, the curious thing about the great apes
    13 is they have more. They have, as you can see from the
    14 slide, 48 chromosomes, which means they have 24 pairs.
    15 Now, what that means, Mr. Walczak, is that you and I,
    16 in a sense, are missing a chromosome, we're missing a
    17 pair of chromosomes. And the question is, if
    18 evolution is right about this common ancestry idea,
    19 where did the chromosome go?
    20 Now, there's no possibility that that common
    21 ancestry which would have had 48 chromosomes because
    22 the other three species have 48, there's no
    23 possibility the chromosome could have just got lost or
    24 thrown away. Chromosome has so much genetic
    25 information on it that the loss of a whole chromosome
    1 would probably be fatal. So that's not a hypothesis.
    2 Therefore, evolution makes a testable
    3 prediction, and that is, somewhere in the human genome
    4 we've got to be able to find a human chromosome that
    5 actually shows the point at which two of these common
    6 ancestors were pasted together.

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  7. Throught provoker,

    No one questions the ability of Darwinists to tell a good story. With so little evidence their whole foundation is a well rehearsed show. It seems the whole framework is designed to stick to poor human reasoning like velco. Critical and independent thinking about the theory in detail leaves the open minded skeptical.

    Darwin should certainly be given credit for turning the tables on his skeptics without evidence. He left it up to his critics to show that it couldn't happen. Slick.

    Ken Miller is also a pretty smooth talker... 'See my tie clip?' 'See the type III secretion system?' Irreducible complexity dismissed.

    Since Judge Jones was schooled by Miller as to what Irreducible Complexity was (incorrectly), he was left to dismiss a definition of IC that was not even correct.

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  8. Neal Tedford said...

    How legitimate is it for a judge to "be schooled" by either party in a case? It is one thing to hear both sides of a case and evaluate them, but to "be schooled" by one party? Sounds like he already had his mind made up before the trial started.


    It's not unusual at all that a judge wouldn't have detailed technical knowledge of a subject before the start of a case, and would take the opportunity to learn from experts. What judges are highly skilled in is being able to tell a well reasoned and well supported argument versus a bunch of ad hoc hand waving.

    Miller presented a well though out, well supported case for evolution. The IDiot experts tried their same fact free tap dancing that worked with the unskilled in critical thinking lay public and fell flat on their collective face. The judge saw right through the IDiot smoke screen, and his ruling reflected his disgust with their lah-di-dah clown show in no uncertain terms.

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  9. Since you're such an expert on ID Tedford, why don't you give us the 'correct' definition of IC. Behe has used at least three different ones in the last few years.

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  10. Some of the Cross Examination of Dr. Miller...

    http://ncse.com/files/pub/legal/kitzmiller/trial_transcripts/2005_0926_day1_pm.pdf

    Q. You debated Dr. Behe and others in various forums debating intelligent design, is that correct?
    A. Yes, that is correct.
    Q. During these debates, you were presenting your scientific argument against intelligent design, and Dr. Behe was presenting his scientific argument in support of intelligent design?
    A. Absolutely.
    ...
    Q. It was a presentation something similar to what we saw today with the slides and the discussion of scientific evidence. You advancing your claim and Dr. Behe advancing his claim?
    A. The presentation certainly did include slides. Being a microscopist by training, somebody who takes pictures for a living, I find myself incapable of talking without slides. So therefore, I certainly included them. And I made arguments based on the scientific method.
    But once again, a great deal of what I brought to the Court's attention this morning simply did not exist back when we had this little discussion at Haverford College.
    Q. You agree Dr. Behe will have probably a point by point opposition to the evidence that you presented previously and the new evidence that you presented today?
    A. I actually wouldn't want to speculate on Dr. Behe's testimony.
    Q. Has that been the practice of your prior debates, you put up your scientific evidence, then Dr. Behe will put up his scientific evidence, demonstrating the support for each of your claims?
    A. I suppose that's a fair summary of any debate, which is that each side tries to marshal the evidence and the arguments that are in favor of their side.
    Q. And Dr. Behe was relying on scientific evidence, correct?
    A. Dr. Behe certainly relied on elements from the literature, from the scientific evidence. It's important to understand that scientific evidence, factual evidence, as I mentioned earlier, are isolated things. There's a fact here and a fact there. How you tie them together is really what the practice of science
    is all about. In these discussions and debates, it's my recollection -- and there have been a lot of them. We've had a lot to say to each other.
    Q. So you have a cottage industry going here between the experts?
    A. I don't know if it is a cottage industry or not, but certainly Mike and I see each other quite a [b]it. I think it's fair to say that he relies on certain elements of scientific fact to marshal his arguments. And the point that I think is relevant is basically that he makes, in his books and his writings, and he makes in
    these debates, a large number of claims regarding irreducible complexity, regarding the biochemical argument from design that have been repeatedly falsified by experiments, by observations in nature, and that's
    the point that I try to make in these debates, that these claims have been examined, considered by the scientific community, and generally falsified.
    Q. He disagrees with you?
    A. I'm sure that he disagrees with me, but, of course, he'll get a chance to say that himself, and I wouldn't want to speculate. Perhaps he'll get up here in a couple days and say, you know, I listened to everything Dr. Miller said and, by God, he's got it exactly right.
    THE COURT: We'd have a real story then, wouldn't we?
    THE WITNESS: Exactly.
    MR. MUISE: I doubt that will happen.
    BY MR. MUISE:
    Q. Do you think that will happen, Dr. Miller?
    A. I'd much rather make a bet on the outcome of the world series this year than to make that kind of bet.
    Q. That's probably a safer bet.
    A. Absolutely.

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  11. "...he was left to dismiss a definition of IC that was not even correct."

    Boy, it's just really too bad that there was no one able to take the stand who could set the record straight by giving the correct definition. Having some kind of expert, like maybe the person that originated the term would have just been so awesome for the ID side. It's so unfair that that couldn't happen. So very very unfair.

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  12. Thought Provoker said, "a large number of claims regarding irreducible complexity, regarding the biochemical argument from design that have been repeatedly falsified by experiments, by observations in nature, and that's
    the point that I try to make in these debates, that these claims have been examined, considered by the scientific community, and generally falsified."

    What Ken Miller meant by falsified what flashing his tie clip and mentioning the research with type 3 secretions systems. Like showing that since a lug nut is a component of an engine then an engine is not irreducibly complex.

    Venture, it was not a fair trial. Judge Jones was schooled by one party in the case. Schooling shows favoritism. As we see in this blog, evolution is very much about word definitions and rhetorical skills and how they have various uses to accommodate the situation.

    Thorton,

    Behe says that he would change very little of his Darwins Black Box book. His definition of IC is there and hasn't changed to my knowledge.

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  14. http://ncse.com/files/pub/legal/kitzmiller/trial_transcripts/2005_0927_day2_am.pdf

    14 Q. But in terms of your personal beliefs you
    15 believe that that is consistent with God's
    16 overall plan the way evolution operates?
    17 A. I believe that God is the author of nature,
    18 and therefore I believe that things that happen
    19 in nature are consistent with God's overall
    20 plan, and evolution is a natural process.
    21 Q. And you see evolution as being consistent
    22 with your religious beliefs?
    23 A. Yes, sir, I do.

    6 Q. So you don't ascribe to philosophical
    7 naturalism, correct?
    8 A. As I understand philosophical naturalism,
    9 it is a doctrine that says that the physical
    10 world is all there is, and the only way we have
    11 of learning anything about the nature of
    12 existence is the scientific way, and if that is
    13 what philosophical naturalism means, no, sir, I
    14 am not a philosophical naturalist.
    15 Q. Now, when you read the Book of Genesis, you
    16 take that to be a spiritually correct account of
    17 the origins of our species, correct?
    18 A. I take all of the Bible, including the Book
    19 of Job, the Book of Psalms, New Testament, and
    20 Genesis to be spiritually correct.
    21 Q. And you find repeatedly verses that say
    22 that God commanded the waters of the earth and
    23 the soil of the earth to bring forth life, and
    24 from an evolutionary point of view you believe
    25 that's exactly what happened?
    1 A. Well, I just don't find them. They're
    2 there. And the way in which I look at Genesis
    3 is that Genesis as I read it, and unfortunately
    4 I don't read Hebrew, my co-author does, and he's
    5 frequently discussed Genesis with me, but as I
    6 read English translations of Genesis I see a
    7 series of commands of the Creator to the earth
    8 and its waters to bring forth life and, you
    9 know, without requiring, my church certainly
    10 doesn't, without requiring Genesis to be a
    11 literal history, you know, that's pretty much
    12 what happens, which is that the earth and its
    13 waters and so forth brought forth life.
    14 Q. And that's consistent with evolutionary
    15 theory?
    16 A. In the broad figurative poetic sense it is
    17 consistent with natural history, which underlies
    18 evolutionary theory.

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  15. Dr. Behe's direct testimony...

    http://ncse.com/files/pub/legal/kitzmiller/trial_transcripts/2005_1017_day10_pm.pdf

    20 Q. Did [Mayr] break out these five claims in this
    21 One Long Argument that you're referring to?
    22 A. Yes, he did. He went on to say, well what
    23 are those ideas that are grouped together under
    24 Darwin's theory? He called them, he identified
    25 five different components, the first of which is
    1 "evolution as such." He says this is the theory
    2 that the world is not constant or recently
    3 create nor perpetually cycling, but rather is
    4 steadily changing. So what we might call change
    5 over time.
    6 Q. Is that a theory or is it an empirical
    7 observation of facts? How would you describe
    8 that?
    9 A. Well, yeah, I myself would call that more
    10 an observation rather than a theory. We see
    11 that the earth seems to have changed over time.
    12 The second --
    14 13 Q. Go ahead.
    14 A. The second aspect of Darwin's theory that
    15 Mayr discerned was common descent. This is the
    16 theory that, "Every group of organisms descended
    17 from a common ancestor and that all groups of
    18 organisms, including animals, plants, and
    19 microorganisms, go back to a single origin of
    20 life on earth." The third point is something
    21 called multiplication of species. This theory
    22 explains the origin of enormous organic
    23 diversity.
    24 I won't read the rest of the quote there,
    25 but it's just a question why are there so many
    1 species, the multiplication of species. The
    2 fourth component of Darwin's theory according to
    3 Mayr is something called gradualism. According
    4 to this theory, "Evolutionary change takes place
    5 through the gradual change of populations and
    6 not by the sudden saltational production of
    7 new individuals that represent a new type." So
    8 gradualism, things thing gradually over time.
    9 And the last component according to Mayr is
    10 natural selection. According to this theory,
    11 "Evolutionary change comes through the abundant
    12 production of genetic variation, the relatively
    13 few individuals who survive, owing to
    14 particularly well adapted combinations of
    15 inheritable characters, give rise to the next
    16 generation." So this is what's commonly called
    17 survival of the fittest.
    18 Q. Is this strength of the scientific evidence
    19 equal for each of these five separate claims?
    20 A. No, they vary greatly in the strength of
    21 evidence that's behind each of those.

    Q. I want to return to Ernst Mayr and ask you
    2 are the parts of Darwin's theory as he's listed
    3 here well tested?
    4 A. No, they are not. If you look at the
    5 top ones, evolution as such, common descent,
    6 multiplication of species, those are all well
    7 tested. The claim of gradualism is in my
    8 opinion rather mixed. There's evidence for,
    9 and some people argue against it. But the
    10 component of Darwin's theory natural selection
    11 which is sometimes viewed as the mechanism that
    12 Darwin proposed for evolution is very poorly
    13 tested and has very little evidence to back
    14 it up.

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  16. More Dr. Behe direct...

    http://ncse.com/files/pub/legal/kitzmiller/trial_transcripts/2005_1017_day10_pm.pdf

    17 Q. Sir, I'd like at this point for you to
    18 define irreducible complexity, and we have a
    19 slide here.
    20 A. Yes, in my article from the journal Biology
    21 and Philosophy, I defined it this way. "By
    22 irreducibly complex, I mean a single system
    23 which is necessarily composed of several well
    24 matched interacting parts that contribute to the
    25 basic function, and where the removal of any one
    1 of the parts causes the system to effectively
    2 cease functioning."
    3 Q. Now, you have up there "necessarily"
    4 in italics. Is there a reason for that?
    5 A. Yes, the definition that I gave in Darwin's
    6 Black Box did not have those italicized words
    7 necessarily, but after the books came out and an
    8 evolutionary biologists at the University of
    9 Rochester named Allen Orr pointed out that it
    10 may be the case that if you had a system that
    11 was already functioning, already doing some
    12 function, it's possible for a part to come
    13 along and just assist the system in performing
    14 its function, but after several changes perhaps
    15 it might change in such a way that the extra
    16 part has now become necessary to the function of
    17 the system but that could have been approached
    18 gradually.
    19 And I, in thinking about it I saw that he
    20 was thinking of examples that I did not have
    21 in mind when I wrote the book. So I kind of
    22 tweaked the definition here in this article to
    23 try to make it clear and try to exclude those
    24 examples that I didn't have in mind.
    25 Q. Is it a common practice within the science
    1 community for a scientist to adjust, modify, or
    2 tweak their theories based on criticisms that
    3 they get from other scientists?
    4 A. Oh, sure. That's done all the time.
    5 Nobody is perfect, nobody can think of
    6 everything at once, and a person is always
    7 grateful for criticism and feedback that helps
    8 to improve an idea.
    9 Q. Does criticism undermine the idea that
    10 you were trying to convey by irreducible
    11 complexity?
    12 A. No, it didn't. It clarified it, and after
    13 his, after reading his SI I saw that he was
    14 thinking of things that I did not have in mind.
    15 So I tried to clarify that.
    16 Q. You have this system in underlying
    17 capitalized and in red. What's the purpose
    18 for that?
    19 A. Well, that to me has turned into a point
    20 of confusion because some people, including
    21 Professor Miller, have been focusing the
    22 discussion on the parts of the system and saying
    23 if one removes a part and then can use the part
    24 for some other purpose, then they say that means
    25 that it's not irreducibly complex, but that is
    1 not the definition I gave to irreducible
    2 complexity, that is not the concept of
    3 irreducible complexity that I described in
    4 Darwin's Black Box. I said that if you take
    5 away one of the parts from the system, the
    6 system, the function of the system itself ceases
    7 to work, and whether one can use the part for
    8 anything else is beside the point.
    9 Q. So then it is fair to say Dr. Miller's uses
    10 the wrong definition of your concept and then
    11 argues against that different definition to
    12 claim that your concept is incorrect?
    13 A. Yes. It's a mischaracterization, yes.

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  18. Neal Tedford asked, "How legitimate is it for a judge to "be schooled" by either party in a case?"

    That is a good question to ask. It appears from your comments, however, that you started by assuming an answer that was convenient to your preconceived beliefs, and have not seriously attempted to answer your own question. This is an unfortunately common characteristic of creationists, in my experience. Here, as with biology, your preconceptions are incorrect.

    It is not only "legitimate" for the court to be educated by the parties, it is the proper and expected procedure. Parties don't *want* judges to do all their learning in chambers. They want to educate the court themselves, as part of the adversarial process. There is an enormous body of law and procedure dedicated to how exactly this should be done. Generally it's done through expert witnesses. This was the case at Dover. Both parties had equal opportunities to present their experts. The creationists were hobbled by the vacuity of their position, not by any procedural hanky-panky.

    A cursory look at the real world shows that educated men and women, presented with actual evidence, almost universally reject creationism in favor of objective and empirical science. Why would you expect the court to buck that trend? Active creationism, as opposed to passive ignorance, seems to flourish only in isolated and insular communities like bible colleges and countercultural churches. It has very little traction among people who actually know facts about biology. Those educated people who do cling to creationism have obvious and transparent ulterior motives, be it their religious faith or their careers as professional dissenters. The Dover court had no such reason to reject the evidence before it.

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  19. 16 The second point is this. The second
    17 mischaracterization is this. He says, "The
    18 observation that there are as yet no detailed
    19 evolutionary explanations for certain structures
    20 in the cell, while correct, is not a strong
    21 argument for special creation that is 'design.'"
    22 Here Professor Miller is doing something more
    23 understandable. He's essentially is viewing my
    24 theory through the lens of his own theory. So
    25 all he sees is essentially how it conflicts with
    1 his own theory and thinks that that's all there
    2 is to it.
    3 But as I have explained throughout the day
    4 today, if we could go to the next slide, that
    5 an inability to explain something is not the
    6 argument for design. The argument for design is
    7 when we perceive the purposeful arrangement of
    8 parts, the purposeful arrangement of parts such
    9 as we see in the flagellum, such as we see the
    10 molecular machinery such as described in that
    11 special issue of Cell and so on.

    ReplyDelete
  20. 12 We can go to the next slide, this is a copy
    13 of the first slide of Professor Miller's, the
    14 third mischaracterization is this. He says, "As
    15 Michael Behe has made clear, the biochemical
    16 argument from design depends upon a much bolder
    17 claim, namely that the evolution of complex
    18 biochemical structures cannot be explained even
    19 in principle." This is a mischaracterization.
    20 It's essentially absolutizing my argument.
    21 It's making overstating my argument in order to
    22 make it seem brittle, to make it more easily
    23 argued against.
    24 Q. Have you addressed such a claim in Darwin'S
    25 Black Box?
    1 A. Yes, if you read Darwin's Black Box you
    2 see that I say the following, "Even if a system
    3 is irreducibly complex and could not have been
    4 produced directly, however one cannot definitely
    5 rule out the possibility of an indirect
    6 circuitous route. As the complexity of an
    7 interacting system increases though, the
    8 likelihood of such an indirect route drops
    9 precipitously."
    10 So here I was arguing well, there's a big
    11 problem for Darwinian theory. These things
    12 can't be produced directly, but nonetheless
    13 you can't rule out an indirect route, but
    14 nonetheless building a structure by changing
    15 its mechanism and changing its components
    16 multiple times is very implausible and the
    17 likelihood of such a thing, the more complex
    18 it gets, the less likely it appears. So the
    19 point is that I was careful in my book to
    20 qualify my argument at numerous points, and
    21 Professor Miller ignores those qualifications.
    128 22 Q. Do these qualification also demonstrate
    23 the tentative nature in which you hold your
    24 theories?
    25 A. Yes, that's right. I always -- well, I try
    1 to state it in what I thought was a reasonable
    2 way and in a tentative way as well.
    3 Q. I believe we have a couple of more slides
    4 from Dr. Miller that you --
    5 A. Yes, this is essentially a continuation.
    6 These will be slides number 2 and 3 from his
    7 slides on the flagellum. This is just a
    8 continuation of his overstated arguments.
    9 He says, "The reason that Darwinian evolution
    10 can't do this is because the flagellum is
    11 irreducibly complex," and he quotes my
    12 definition of irreducible complexity from
    13 Darwin's Black Box, and continue on the next
    14 slide.
    15 And he states that, "That claim is the
    16 basis of the biochemical argument for design."
    17 But again that is not the basis for the
    18 biochemical argument for design. The basis
    19 for the biochemical argument for design is the
    20 purposeful arrangement of parts. Irreducible
    21 complexity shows the difficulties for Darwinian
    22 processes in trying to explain these things.
    23 Q. Now, Dr. Miller claims that natural
    24 selection can explain the flagellum. Do
    25 you agree with that claim?
    1 A. I'm sorry, can you restate that?
    2 Q. Dr. Miller claims that natural selection
    3 can explain the bacterial flagellum. Do you
    4 agree with that claim?
    5 A. No, I disagree, and we go on to the next
    6 slide, which is another one of Professor
    7 Miller's slides from his presentation on the
    8 bacterial flagellum, and he tried to explain
    9 molecular machines using kind of simple concepts
    10 to try and make it more understandable to a
    11 broad audience. So for example on the
    12 right-hand side which he labels "Evolution,"
    13 he has little colored hexagons, which are exist,
    14 which are separated, and then he has the
    ... big snip ...
    [but] the components of
    6 molecular machines are not little colored
    7 squares. They are not little colored hexagons.
    8 They are very complex entities...

    ReplyDelete
  21. Again, I encourage everyone to read for themselves; Think for themselves.

    The trial transcripts can be found at...

    http://ncse.com/creationism/legal/kitzmiller-trial-transcripts

    ReplyDelete
  22. Thorton said...
    Poor poor Cornelius. Relegated to obscurity at Biola, doing no research, producing no results, having to content himself with throwing rocks from the sidelines at real scientists.

    If Cornelius was any more glowing green with jealousy of Dr. Miller's success, he could be seen from space.


    Another ad hominem from an evolutionist. Dr Hunter must have hit a nerve.

    ReplyDelete
  23. Dr. Hunter, you wrote:
    "Of course the chromosome reveals no such thing. It provides no more evidence for evolution than any other similarity."

    Sir, you're delusional. The fused chromosome is a DIFFERENCE, not a similarity. You're so determined to push the Big Lie that the evidence only represents vague similarity that you can't see that.

    You can't explain the differences, so even the differences are similarities. Orwell would be proud.

    "Starr, Alexander and the evolutionists may as well be discussing similarities we share with the apes in our bones or our biochemistry."

    Yes, except that they were discussing a difference. Do you not understand the difference between a difference and a similarity?

    Now for another Big Lie:

    "... And Miller did not explain the great number (more than a thousand) genes unique to the human genome."

    WHAT? Are you really that ignorant?

    Wanna bet your house that there are more than a thousand genes that have no ortholog in the chimp?

    ReplyDelete
  24. I"m a little confused. First they say that the similarities between chimp and human genomes are evidence for evolution. Then they say that the differences are evidence for evolution. Its "head I win, tales you lose."

    ReplyDelete
  25. natschuster: First they say that the similarities between chimp and human genomes are evidence for evolution. Then they say that the differences are evidence for evolution.

    The Theory of Evolution posits that humans and chimpanzees share a relatively recent common ancestory, hence they have inherited many common traits, but are each modified from that common ancestor.

    In any case, it's not just the similarities and differences, but that they fit a nested hierarchy with other organisms.

    ReplyDelete
  26. natschuster said...

    I"m a little confused. First they say that the similarities between chimp and human genomes are evidence for evolution. Then they say that the differences are evidence for evolution. Its "head I win, tales you lose."


    Yep, you're confused alright.

    The similarities when compared with the genomes of other mammals establish homo sapiens' place on the tree of common descent and establish our relationships with other ape lineages - bonobos, chimps, gorillans, etc.

    The differences show the evolutionary changes that have happened since the human-chimp split some 4-6 MYO. The number of differences and the known mutation rate correlate with fossil and other genetic data to establish the approximate split date. The fact that unique mutations to common genes also map to unique feature (like the mutated foxp2 speech gene in humans) is additional evidence.

    So both the similarities and differences are evidence for evolution.

    ReplyDelete
  27. Neal Tedford said...

    What Ken Miller meant by falsified what flashing his tie clip and mentioning the research with type 3 secretions systems. Like showing that since a lug nut is a component of an engine then an engine is not irreducibly complex.


    Clueless Tedford misses the boat again.

    No one in the scientific community says IC structures don't exist. What science shows is that there are observed evolutionary mechanisms that can produce IC structures.

    Behe's idiotic claim is that IC structure can only come about by the adding of multiple parts which must work together at every stage to produce the specific IC function. Evolution is under no such constraints. Evolution can add parts, or delete part, or modify parts, or modify functions of individual parts, or modify the efficiency of the function, or modify the function of the whole structure.

    To get an IC structure, all you have to do is

    1) add a part
    2) make it necessary.

    The 2) can be the deletion, modification of function, etc. There are dozens of examples of this process in the primary literature.

    Miller's tie clip was a perfect example of a part that was co-opted for one function and used in another function, something Behe completely left out of his cartoon scenario.

    It's like claiming that springs used in the car's valves were only created especially for that engine, and I show you the use of a spring in a retractable pen.

    ReplyDelete
  28. C. Hunter: Pseudogenes sequences were found to be conserved with reduced nucleotide variability, excess synonymous over nonsynonymous nucleotide polymorphism, and other features that are expected in genes that have functional roles.
    It doesn't make much sense to talk about conservation, nucleotide variability and excess synonymous over nonsynonymous nucleotides when at the same time common ancestry, variation over time and selection for synonymous codons is denied.

    ReplyDelete
  29. When examined and understood rationally, the (purported) chromosmal fusion is solid scientific evidence for ID -- and interventionist ID, at that. Or even for the dreaded creationism. AND, it is solid scientific evidence against Darwinism.

    ReplyDelete
  30. Ilion

    Being, as I am, clearly irrational I'm not sure that I understand your claim about the chromosomal fusion.

    Your claim that its discovery is "solid scientific evidence for ID" implies that if ID is true, then just such a fusion is expected to be found. In other words you are implying that ID makes a clear prediction about the existence of such a fusion. Could you explain in detail exactly why ID predicts that such a fusion should exist?

    Also, your claim that its discovery is "solid scientific evidence against [evolution]" implies that if evolution is true then just such a fusion should not be found there. In other words you are implying that evolution also makes a clear prediction about the existence of such a fusion, though your implied prediction seems to clash with the experts' opinions on what evolution apparently predicts. Could you explain in detail exactly why evolution predicts that such a fusion should not exist?

    ReplyDelete
  31. If we listen to evolutionists then there was only ONE book ever written- all other books are descended from that book via copying errors.

    As for evos and IC- why is it there isn't any evidence that genetic accidents can accumulate in such a way as to CONSTRUCT multi-part systems?

    As for nested hierachies- that is only expected in a design scenario, as only dsigners have the ability to construct things in that manner.

    ReplyDelete
  32. Chromosome fusion-

    What advantage did it provide?

    IOW what is the blind watchamker explanation for how/ why it became fixed?

    Or are bald assertions the best you have?

    Pseudogenes- why the heck would those be kept around and intact enough to be used as genetic markers?

    You don't have any explanation for that either.

    ReplyDelete
  33. Joe G: If we listen to evolutionists then there was only ONE book ever written- all other books are descended from that book via copying errors.

    A collection of artifacts rarely form a singular nested hierarchy. Books are no exception. Books can be arranged in a number of consistent and useful nested hierarchies, including Dewey Decimal Classification and the Library of Congress Classification.

    Joe G: As for nested hierachies- that is only expected in a design scenario, as only dsigners have the ability to construct things in that manner.

    Well, no. A nested hierarchy is the natural consequent of descent along uncrossed lines, even when variation is random.

    ReplyDelete
  34. Miller:
    "Intelligent design cannot explain the presence of a nonfunctional pseudogene, unless it is willing to allow that the designer made serious errors, wasting millions of bases of DNA on a blueprint full of junk and scribbles."

    That is false.

    ID does not say mutations cannot occur which disable genes.

    The point being now we know their tactics so the next trial it won't bode well for them.

    ReplyDelete
  35. Joe G: IOW what is the blind watchamker explanation for how/ why it became fixed?

    Fixation can occur in finite populations due to chance alone.

    ReplyDelete
  36. If we listen to evolutionists then there was only ONE book ever written- all other books are descended from that book via copying errors.

    Zachriel:
    A collection of artifacts rarely form a singular nested hierarchy.

    Non-sequitur.

    As for nested hierachies- that is only expected in a design scenario, as only dsigners have the ability to construct things in that manner.

    Zachriel:
    Well, no.

    Yes it is.

    A nested hierarchy is the natural consequent of descent along uncrossed lines, even when variation is random.

    Prove it.

    To datew all we have is your say-so- and we all know that is meaningless.

    Also the ToE does NOT posit uncrossed lines.

    ReplyDelete
  37. IOW what is the blind watchamker explanation for how/ why it became fixed?

    Zachriel:
    Fixation can occur in finite populations due to chance alone.

    That ain't science- but thanks for admitting you don't have an explanation.

    ReplyDelete
  38. Joe_G:

    " what is the blind watchamker explanation for how/ why it became fixed?

    Or are bald assertions the best you have?

    Pseudogenes- why the heck would those be kept around and intact enough to be used as genetic markers?

    You don't have any explanation for that either.
    =====

    Perhaps you can now understand the importance of their fascination of and why they spend on so much time devoted(wasted) on the study and research of eastern religious philosophy and it's New Age concepts. Clearly it is important for them when real world answers are lacking. It's the ultimate gap filler.

    Summed up, "What Is Truth" ???

    ReplyDelete
  39. Zachriel: A nested hierarchy is the natural consequent of descent along uncrossed lines, even when variation is random.

    Joe G: Prove it.

    The simplest way would be to take a sequence, then allow it to duplicate with a random letter change in one the offspring. So if the founder genome was

    ,,,,,,,,,,,,,,,,

    Then its offspring might be

    ,,,,,,,,,,,,,,,,
    ,,,,,B,,,,,,,,,,

    We then let the offspring continue to divide and see what sort of pattern it forms.

    For a bit more understanding of the process, we might alter the size of the genome, the mutation rate, or even limit the population through random selection. (Is there a fixed font option for this blog?)

    ReplyDelete
  40. Zachriel: Fixation can occur in finite populations due to chance alone.

    Joe G: That ain't science-

    It's mathematics.

    The probability of fixation of a specific neutral mutation is equal to its proportion in the population. Hence, the smaller the population, the greater the chance of fixation. Probability of fixation of a stream of neutral mutations is equal to the mutation rate.

    ReplyDelete
  41. Zachriel: Fixation can occur in finite populations due to chance alone.

    Joe G: That ain't science-but thanks for admitting you don't have an explanation.

    Zachriel:
    It's mathematics.

    Nope- it is evo nonsense.

    Heck experimentation shows even in a stable environment fixation doesn't take place.

    ReplyDelete
  42. Zachriel:
    The simplest way would be to take a sequence, then allow it to duplicate with a random letter change in one the offspring. So if the founder genome was

    ,,,,,,,,,,,,,,,,

    Then its offspring might be

    ,,,,,,,,,,,,,,,,
    ,,,,,B,,,,,,,,,,

    We then let the offspring continue to divide and see what sort of pattern it forms.

    For a bit more understanding of the process, we might alter the size of the genome, the mutation rate, or even limit the population through random selection. (Is there a fixed font option for this blog?)


    No nested hierarchy there.

    ReplyDelete
  43. And a line is a lineage, which is a sequence.

    And zacho has already said that a sequence is not a nested hierarchy.

    ReplyDelete
  44. As for evos and IC- why is it there isn't any evidence that genetic accidents can accumulate in such a way as to CONSTRUCT multi-part systems?

    Shouldn't that be telling us something?

    ReplyDelete
  45. Joe G: Heck experimentation shows even in a stable environment fixation doesn't take place.

    Sure it does, such as antibiotic resistance in bacteria, or pesticide resistance in insects. But especially in eukaryotes, with complex genomes, there can be a number of countervailing influences when selecting for an arbitrary trait.

    Joe G: And a line is a lineage, which is a sequence.

    Of course, a single lineage in a tree of descent is not a nested hierarchy. The nested hierarchy is the relationship between the leaves of all the branches on the tree.

    Joe G: As for evos and IC- why is it there isn't any evidence that genetic accidents can accumulate in such a way as to CONSTRUCT multi-part systems?

    There is, but you are still hung up on very simple aspects of evolution.

    Joe G: No nested hierarchy there.

    So you claim that if we run the simulation with random mutation, it will not form a discernable nested hierarchy?

    ReplyDelete
  46. Heck experimentation shows even in a stable environment fixation doesn't take place.

    Zachriel:
    Sure it does, such as antibiotic resistance in bacteria, or pesticide resistance in insects.

    Artificial selection- and even then there isn't any guarantee of fixation.

    And a line is a lineage, which is a sequence.

    Zachriel:
    Of course, a single lineage in a tree of descent is not a nested hierarchy.

    What tree?

    There isn't any evidence of a tree.

    As for evos and IC- why is it there isn't any evidence that genetic accidents can accumulate in such a way as to CONSTRUCT multi-part systems?

    Zachriel:
    There is,

    No thnere isn't.

    If there were you would just present it

    Zachriel:
    but you are still hung up on very simple aspects of evolution.

    And another false accusation.

    Zachriel:
    So you claim that if we run the simulation with random mutation, it will not form a discernable nested hierarchy?

    What would this nested hierarchy be based on?

    Can you define the levels and sets?

    Do it.

    ReplyDelete
  47. Joe G: Artificial selection- and even then there isn't any guarantee of fixation.

    So, fixation can occur under selection. It can also occur due to drift per well-established mathematical laws. You might start with Hardy-Weinberg (1908).

    Joe G: What tree?

    The pattern.

    Joe G: What would this nested hierarchy be based on?

    The letters and positions in the genome.

    ReplyDelete
  48. I guess it wouldn't help resident moron Joe G much to point out that fixation corresponds to an absorbing state in a Markov chain model of neutral evolution in finite populations.

    Wright-Fisher processes

    ReplyDelete
  49. Artificial selection- and even then there isn't any guarantee of fixation.

    Zachriel:
    So, fixation can occur under selection.

    It may under ARTIFICIAL selection.

    No evidence for natural selection doing it.

    What tree?

    Zachriel:
    The pattern.

    The pattern is a lineage

    What would this nested hierarchy be based on?

    Zachriel:
    The letters and positions in the genome.

    LoL!

    IOW you STILL don't have any idea how to form a nested hierarchy.

    ReplyDelete
  50. Joe G: Do it.

    We want to make sure you agree this is a valid test. Will the results of replication and random mutation lead to a random pattern of traits in the descendents, or will the traits be nested?

    We want to make sure the goal posts are firmly planted before we kick the ball.

    ReplyDelete
  51. troy,

    The fruit-fly experiment pretty much refutes your "math".

    Evidence troy, not math games.

    Chromosome fusion-

    What advantage did it provide?

    IOW what is the blind watchamker explanation for how/ why it became fixed?

    Or are bald assertions the best you have?

    Pseudogenes- why the heck would those be kept around and intact enough to be used as genetic markers?

    You don't have any explanation for that either.


    As Zachriel has admitted is was all due to sheer dumb luck- and that ain't science.

    ReplyDelete
  52. Joe G: No evidence for natural selection doing it.

    Antibiotics and antibiotic resistance occur in nature, and local populations of bacteria can become fixed for antibiotic resistance.

    Joe G: The pattern is a lineage

    The posited pattern is a branching tree. Try to keep up (Darwin, 1859).

    Joe G: IOW you STILL don't have any idea how to form a nested hierarchy.

    The letters and positions are the traits in the simulation. In this case, they are neutral changes, such as synonymous mutations in biological genomes.

    ReplyDelete
  53. Zachriel:
    Will the results of replication and random mutation lead to a random pattern of traits in the descendents, or will the traits be nested?

    It depends if the mutations are random and it also depends on the program.

    However it is clear just by looking at prokaryotes that descent with mod does not expect a nested hierarchy.

    Zachriel:
    We want to make sure the goal posts are firmly planted before we kick the ball.

    Said the person who routinely runs around with said goalposts.

    ReplyDelete
  54. No evidence for natural selection doing it.

    Zachriel:
    Antibiotics and antibiotic resistance occur in nature, and local populations of bacteria can become fixed for antibiotic resistance.

    Evidence please.

    The pattern is a lineage

    Zachriel:
    The posited pattern is a branching tree. Try to keep up (Darwin, 1859).

    THERE ISN'T ANY EVIDENCE FOR SUCH A TREE.

    Try to keep up.

    ReplyDelete
  55. Joe G: As Zachriel has admitted is was all due to sheer dumb luck- and that ain't science.

    Please do not misrepresent our position. Neutral mutations can fix according to well-established mathematical laws. That doesn't say one way or the other whether the particular mutation is neutral or not. Selection is often an important consideration.

    ReplyDelete
  56. As Zachriel has admitted is was all due to sheer dumb luck- and that ain't science.

    Zachriel:
    Please do not misrepresent our position.

    I'm not- you said:

    Fixation can occur in finite populations due to chance alone.

    Sheer dumb luck.

    Zachriel:
    Neutral mutations can fix according to well-established mathematical laws.

    The fruit-fly experiment demonstrates otherwise.

    IOW what you have on paper doesn't appear to translate to real-life.

    Go figure...

    ReplyDelete
  57. Joe G: It depends if the mutations are random and it also depends on the program.

    The mutations are random. The algorithm has already been described. Will the results of replication and random mutation lead to a random pattern of traits in the descendents, or will the traits be nested? (We'll use a genome length of 20 for four generations.)

    ReplyDelete
  58. It depends if the mutations are random and it also depends on the program.

    Zachriel:
    The mutations are random.

    Apologies but your word is meaningless here.

    Zachriel:
    The algorithm has already been described.

    I would need to see it.

    ReplyDelete
  59. Joe G: I would need to see it.

    This is the algorithm. You are free to implement it yourself. Take a sequence, then duplicate with a random letter change in one the two offspring. So if the founder genome was

    ,,,,,,,,,,,,,,,,,,,,

    Then its offspring might be

    ,,,,,,,,,,,,,,,,,,,,
    ,,,,,B,,,,,,,,,,,,,,

    We then let the offspring continue to divide and see what sort of pattern it forms. We'll use a genome length of 20 for four generations.

    Will the results of replication and random mutation lead to a random pattern of traits in the descendants, or will the traits be nested?

    ReplyDelete
  60. Geez Zacho, I could take that "B" and change it back to the original:

    ,,,,,,,,,,,,,,,,,,,,
    ,,,,,B,,,,,,,,,,,,,,
    ,,,,,,,,,,,,,,,,,,,,

    Now what?

    ReplyDelete
  61. Yes, there is a small chance of convergence or reversion. That depends on genome length and the number of generations. Will the results of replication and random mutation (with the parameters above) lead to a random pattern of traits in the descendants, or will there likely be a discernable nesting of traits.

    ReplyDelete
  62. Zachriel:
    Yes, there is a small chance of convergence or reversion.

    Why small?

    But that is moot- I have refuted your premise.

    ReplyDelete
  63. As for evos and IC- why is it there isn't any evidence that genetic accidents can accumulate in such a way as to CONSTRUCT multi-part systems?*

    Shouldn't that be telling us something?


    * Zachriel has made a bald claim that such evidence exists yet he hasn't produced it. Go figure...

    ReplyDelete
  64. Joe G:

    "The fruit-fly experiment pretty much refutes your "math".

    Evidence troy, not math games."

    You are too stupid to understand either, Joe. For the onlookers, here you can find some info about the famous Buri experiment on genetic drift and fixation in Drosophila.

    Peter Buri 1956. Gene frequency in small populations of mutant Drosophila. Evolution 10:367–402.

    ReplyDelete
  65. troy is saying a recent experiment that shows no fixation is superseded by an experiment 54 years ago in which the technology for gene comparison didn't exist.

    It looks like troy is too stupid to actually provide positive evidence for its position.

    ReplyDelete
  66. Joe G: Why small?

    It's a matter of probability, contingent on genome length, mutation rate, and number of generations. With our example, there are a total of 15 replications over four generations. The genome length is 20 and there are twenty-six letters. The chance of reversion is small, but not vanishingly small. If we increase the genome size, then the probability decreases. We could use a larger genome, but that isn't necessary to reach a reasonable answer to the question.

    Will the results of replication and random mutation lead to a random pattern of traits in the descendants, or will there likely be a discernable nesting of traits.

    ReplyDelete
  67. Why small?

    Zachriel:
    It's a matter of probability, contingent on genome length, mutation rate, and number of generations.

    IOWb you don't know.

    Zachriel:
    The chance of reversion is small, but not vanishingly small.

    The chance of reversion is the same as any other change.

    Zachriel:
    Will the results of replication and random mutation lead to a random pattern of traits in the descendants, or will there likely be a discernable nesting of traits.

    It will only lead to a nested hierarchy if it was designed to do so.

    I have proven it doesn't lead to a nested hierarchy if not designed to do so.

    ReplyDelete
  68. "Consequently, the probability of fixation in wild populations should be even lower than its likelihood in these experiments."

    Burke, Dunham et al, “Genome-wide analysis of a long-term evolution experiment with Drosophila,” Nature 467, 587-590

    ReplyDelete
  69. Zachriel: It will only lead to a nested hierarchy if it was designed to do so.

    You didn't answer the question. Will the results of replication and random mutation lead to a random pattern of traits in the descendants, or will there likely be a discernable nesting of traits.

    ReplyDelete
  70. It will only lead to a nested hierarchy if it was designed to do so.

    Zachriel:
    You didn't answer the question.

    That is the answer.

    . Will the results of replication and random mutation lead to a random pattern of traits in the descendants, or will there likely be a discernable nesting of traits.

    It should not lead to any nesting- and I proved that.

    Time to deal with that and move on...

    ReplyDelete
  71. Joe G: It should not lead to any nesting-

    It clearly does. For instance, if position 8 mutates to a C, then C8's descendants will inherit that trait. When we look at the leaves after four generations, they will group. If an immediate descendant of C8 mutates a J in position 6, then J6's descendants will inherit that trait. After four generations, this is what we have (sorry, no fixed font):

    ,,,,,,,,,,,,,,,,,,,,
    ,,,,N,,,,,,,,,,,,,,,
    ,,,,,,,,,,,,,,,,A,,,
    ,,,,,,,,,,,B,,,,A,,,

    ,,,,F,,,,,,,,,,,,,,,
    ,,,,F,,,,,,,,,D,,,,,
    ,,,,F,Z,,,,,,,,,,,,,
    ,,,,F,Z,,K,,,,,,,,,,

    ,,,,,,,C,,,,,,,,,,,,
    ,,,,,,,C,,,,,V,,,,,,
    ,,,,,,,C,,,,,,,T,,,,
    ,,,,,,,C,,,,,,,T,,,V

    ,,,,,J,C,,,,,,,,,,,,
    ,,,,,J,C,,,,,,,,,,,Q
    ,,,,,J,C,,,,,,,,,,G,
    ,,,,,J,C,,,,,,,,,,GX

    Among the various groupings, within C8 we group J6. Within J6, we group G19. Other runs have similar results.

    ,,,,,,,,,,,,,,,,,,,,
    ,,,,E,,,,,,,,,,,,,,,
    ,,,,,,,,,,,,,Q,,,,,,
    ,,,,,,,,,,,,,Q,X,,,,
    ,T,,,,,,,,,,,,,,,,,,
    ,T,,,S,,,,,,,,,,,,,,
    ,T,,,,,I,,,,,,,,,,,,
    ,T,,,O,I,,,,,,,,,,,,
    Z,,,,,,,,,,,,,,,,,,,
    Z,,Y,,,,,,,,,,,,,,,,
    Z,,,,,,,,,,,,,,,,,,C
    Z,,,,,,,,,,,,,D,,,,C
    Z,,,,,,,,,,,B,,,,,,,
    Z,,,,,,,,,,,B,B,,,,,
    Z,,,,,,,,,,,B,,T,,,,
    Z,,,,,E,,,,,B,,T,,,,

    Non-random and highly patterned. But feel free to make your own implementation.

    ReplyDelete
  72. Zachriel:
    But feel free to make your own implementation.

    I already have- no nested hierarchy.

    And I doubt your example had anything to do with random mutations.

    ReplyDelete
  73. Zachriel:
    For instance, if position 8 mutates to a C, then C8's descendants will inherit that trait.

    No guarantee on that- as I have demonstrated.

    ReplyDelete
  74. The issue of the fixation of human chromosome 2 is addressed in a series of essays over at the Panda’s Thumb, collectively called “The Rise of Human Chromosome 2”:

    The Dicentric Problem-

    http://pandasthumb.org/archives/2009/02/the-rise-of-hum.html

    The Fertility Problem -

    http://pandasthumb.org/archives/2009/02/the-rise-of-hum-1.html

    Fixation within a Deme-

    http://pandasthumb.org/archives/2009/05/the-rise-of-hum-2.html

    Beyond the Deme-

    http://pandasthumb.org/archives/2009/09/the-rise-of-hum-3.html

    Dave Wisker

    ReplyDelete
  75. Joe G: No guarantee on that- as I have demonstrated.

    A discernable pattern, even with the rare reversion. Certainly not random.

    Joe G: And I doubt your example had anything to do with random mutations.

    You are more than welcome to make your own implementation. You can even do it with paper, pencil and a randomizer of some sort sufficient to select a random base and letter.

    But most any reader can follow the discussion in our previous comment and understand that the descendants of C8 will inherit that characteristic, and among those descendants, J6 will leave its characteristic mark, as well.

    ReplyDelete
  76. Allopatrick,

    Thanks- now all Dave has to do is get that pap published and science may care about it...

    ReplyDelete
  77. Zachriel:
    A discernable pattern, even with the rare reversion. Certainly not random.

    As I said reversions ahve the same chance as all other changes.

    IOW it is as rare as any change.

    And I doubt your example had anything to do with random mutations.

    Zachriel:
    You are more than welcome to make your own implementation.

    I did and didn't get the pattern you claimed.

    Zachriel:
    But most any reader can follow the discussion in our previous comment and understand that the descendants of C8 will inherit that characteristic,

    There is no reason why the descendents would get that trait.

    Reversions have the same chance as any other change.

    ReplyDelete
  78. Joe G: As I said reversions ahve the same chance as all other changes.

    That is incorrect, of course. The expected rate of base mutation is only 3/4. In any case, the pattern is easily discernable in each of hundreds of trials.

    Joe G: I did and didn't get the pattern you claimed.

    Show us some results, so we can see if you are implementing it correctly. Oh, here's the complete generational breakdown of our example.

    0
    ,,,,,,,,,,,,,,,,,,,,

    1
    ,,,,,,,,,,,,,,,,,,,,
    ,,,,,,,C,,,,,,,,,,,,

    2
    ,,,,,,,,,,,,,,,,,,,,
    ,,,,F,,,,,,,,,,,,,,,
    ,,,,,,,C,,,,,,,,,,,,
    ,,,,,J,C,,,,,,,,,,,,

    3
    ,,,,,,,,,,,,,,,,,,,,
    ,,,,,,,,,,,,,,,,A,,,
    ,,,,F,,,,,,,,,,,,,,,
    ,,,,F,Z,,,,,,,,,,,,,
    ,,,,,,,C,,,,,,,,,,,,
    ,,,,,,,C,,,,,,,T,,,,
    ,,,,,J,C,,,,,,,,,,,,
    ,,,,,J,C,,,,,,,,,,G,

    4
    ,,,,,,,,,,,,,,,,,,,,
    ,,,,N,,,,,,,,,,,,,,,
    ,,,,,,,,,,,,,,,,A,,,
    ,,,,,,,,,,,B,,,,A,,,
    ,,,,F,,,,,,,,,,,,,,,
    ,,,,F,,,,,,,,,D,,,,,
    ,,,,F,Z,,,,,,,,,,,,,
    ,,,,F,Z,,K,,,,,,,,,,
    ,,,,,,,C,,,,,,,,,,,,
    ,,,,,,,C,,,,,V,,,,,,
    ,,,,,,,C,,,,,,,T,,,,
    ,,,,,,,C,,,,,,,T,,,V
    ,,,,,J,C,,,,,,,,,,,,
    ,,,,,J,C,,,,,,,,,,,Q
    ,,,,,J,C,,,,,,,,,,G,
    ,,,,,J,C,,,,,,,,,,GX

    Not random. Not random, at all.

    ReplyDelete
  79. As I said reversions ahve the same chance as all other changes.

    Zachriel:
    That is incorrect, of course.

    Nope it is quite correct.

    I did and didn't get the pattern you claimed.

    Zachriel:
    Show us some results

    I did- the "B" reverted back and therefor the nested hierarchy is ruined.

    ReplyDelete
  80. Joe, those essays aren't original research. They simply discuss the probability of fixation under already established cytogenetic and population genetics knowledge, as opposed to the ID approach of simply waving hands.

    Dave Wisker

    ReplyDelete
  81. Dave:
    They simply discuss the probability of fixation under already established cytogenetic and population genetics knowledge, as opposed to the ID approach of simply waving hands.

    And that is fine and dandy.

    However there is this population of fruit-flies- actual experimental data-that seem to contradict your conclusions.

    ReplyDelete
  82. That said the fusion could be an actual event- something that did become fixed- 48 down to 46.

    Fine, but that still isn't evidence of common ancestry between chimps and humans.

    IOW the original population of humans- Adam and Eve- had 48- then somewhere along that line the fusion occurred and became fixed just as you said.

    Another possibility is the fusion was designd in as part of a package that provides reproductive isolation for similarly designed genomes/ organisms.

    And as for waving ahnds- that is what you guys do- you think you are jedi knights who can wave their hands and people will just take you word for it.

    That only works with weak-minded fools- troy, thorton, zachriel, et al....

    ReplyDelete
  83. "Another possibility is the fusion was designd in as part of a package that provides reproductive isolation for similarly designed genomes/ organisms."


    The fact that heterozygotes for the fusion only have slightly lowered fitness is evidence against that hypothesis.

    ReplyDelete
  84. "However there is this population of fruit-flies- actual experimental data-that seem to contradict your conclusions"

    How so?

    Dave Wisker

    ReplyDelete
  85. That should have read "human heterozygotes for fusions often have only slightly lowered fitness"

    ReplyDelete
  86. "Another possibility is the fusion was designd in as part of a package that provides reproductive isolation for similarly designed genomes/ organisms."

    Dave:
    The fact that human heterozygotes for fusions often have only slightly lowered fitness is evidence against that hypothesis.

    Umm the designer would know which fusion would be OK and which wouldn't.

    But anyway what about YOUR scenario?

    Doesn't that also apply- lowered fitness?

    Now you are trying to tell us that something that lowered fitness not only survived but thrived to the point of becoming fixed.

    Come on- are you serious?

    ReplyDelete
  87. "However there is this population of fruit-flies- actual experimental data-that seem to contradict your conclusions"

    Dave:
    How so?

    Fixation of new alleles appears very, very unlikely.

    No evidence for such a thing in the lab with sexually reproducing populations.

    That's how...

    ReplyDelete
  88. "Another possibility is the fusion was designd in as part of a package that provides reproductive isolation for similarly designed genomes/ organisms."

    IOW it was designed in to prevent humans from successfully mating with chimps.

    ReplyDelete
  89. "Doesn't that also apply- lowered fitness?

    Now you are trying to tell us that something that lowered fitness not only survived but thrived to the point of becoming fixed.

    Come on- are you serious? "

    You didnt read the essays. LOL. I knew it.

    Dave Wisker

    ReplyDelete
  90. Joe G: I did- the "B" reverted back and therefor the nested hierarchy is ruined.

    ,,,,,,,,,,,,,,,,,,,,
    ,,,,,B,,,,,,,,,,,,,,
    ,,,,,,,,,,,,,,,,,,,,

    Oh, so that was meant to be 'random'. Where's the rest of the pattern over four generations?


    If your monitor draws a circle, but one of the pixels is out of place, are you saying you can't discern the pattern, that it appears random to you?

    ReplyDelete
  91. For those who think Joe knows what he is talking about ("Now you are trying to tell us that something that lowered fitness not only survived but thrived to the point of becoming fixed"), consider the classic paper by Wright and Kerr in 1954, in which the Bar mutation became fixed in several small lines of Drosophila, despite very strong selection against it.

    Wright S & WE Kerr (1954). Experimental studies of the distribution of gene frequencies in very small populations of Drosophila melanogaster. II. Bar. Evolution 8(3): 225-240

    Dave Wisker

    ReplyDelete
  92. JoeTard said...

    "Another possibility is the fusion was designd in as part of a package that provides reproductive isolation for similarly designed genomes/ organisms."

    IOW it was designed in to prevent humans from successfully mating with chimps.


    Hey JoeTard:

    Horses have 64 chromosomes. Donkeys have 62. Zebras have between 32 and 46, depending on the species.

    Were all the zebra species with different chromosome numbers created separately?

    Why is it that zebras and horses (and other equines) can produce healthy hybrids (called zebroids) ?

    ReplyDelete
  93. Joe G said...

    IOW the original population of humans- Adam and Eve- had 48- then somewhere along that line the fusion occurred and became fixed just as you said.


    "the original population of humans- Adam and Eve"

    Oops! Joe makes a Freudian slip, confirms that's really a Biblical literalist. His "ID has nothing to do with religion" spiel is so much disingenuous hooey.

    Way to come out of the closet Joe!

    ReplyDelete
  94. Thorton,

    It is a common misconception that hybrids coming from populations with differing chromosome numbers must either be sterile or suffer from greatly reduced fertility. Many do, of course, but many also do not.

    Dave Wisker

    ReplyDelete
  95. Allopatrik said...

    Thorton,

    It is a common misconception that hybrids coming from populations with differing chromosome numbers must either be sterile or suffer from greatly reduced fertility. Many do, of course, but many also do not.

    Dave Wisker


    I know that, but JoeTard doesn't.

    ReplyDelete
  96. "Another possibility is the fusion was designd in as part of a package that provides reproductive isolation for similarly designed genomes/ organisms."

    PART OF THE PACKAGE.

    Not only that if there were a fusion tat could cause reproductive isolation the designer would know about it.

    ReplyDelete
  97. throton:
    Oops! Joe makes a Freudian slip, confirms that's really a Biblical literalist.

    Umm no- I was just presenting their poition to demonstrate the nonsense of Wisker's position.

    ReplyDelete
  98. Dave:
    It is a common misconception that hybrids coming from populations with differing chromosome numbers must either be sterile or suffer from greatly reduced fertility.

    Umm first I said it was PART OF THE PACKAGE- but also a designer would know if there was one fusion would could cause such isolation.

    ReplyDelete
  99. Zachrie:
    Oh, so that was meant to be 'random'.

    Yes it was.

    Where's the rest of the pattern over four generations?

    More of the same- letters coming and going.

    No nested heirarchies...

    ReplyDelete
  100. Dave:
    You didnt read the essays. LOL. I knew it.

    Yes I did- LoL!

    ReplyDelete
  101. And in the end all you ahve is "it just did" become fixed- even though the odds were stacked against it.

    ReplyDelete
  102. Joe G said...

    throton:
    Oops! Joe makes a Freudian slip, confirms that's really a Biblical literalist.

    Umm no- I was just presenting their poition to demonstrate the nonsense of Wisker's position.


    LOL! you're lying like a rug JoeTard!

    Joe Gallien the Biblical literalist!

    Don't worry Joe, Pastor Tedford will love you even more!

    ReplyDelete
  103. "And in the end all you ahve is "it just did" become fixed- even though the odds were stacked against it. "

    Which Wright and Kerr showed can happen without resorting to design.

    Dave Wisker

    ReplyDelete
  104. And as for waving ahnds- that is what you guys do- you think you are jedi knights who can wave their hands and people will just take you word for it.

    JoeG,
    It's you who are hiding behind an obscure pseudonym, in an obscure corner of the web, without a single publication to your credit. Take a look at the mirror before you project!

    ReplyDelete
  105. jbeck,

    I'm not hiding- and your position doesn't have any publications that support it.

    ReplyDelete
  106. Dave:
    Which Wright and Kerr showed can happen without resorting to design.

    And a much more recent paper says it doesn't happen.

    What do we trust? Work from 5 decades ago or work from this century?

    ReplyDelete
  107. From Dave's cited paper:

    "Populations of 4 males and 4 females per generation are so exceedingly small that experiments such as the present may seem to have no implications for evolution
    in nature."


    Nice job Dave...

    ReplyDelete
  108. YEC Joe G said...

    jbeck,

    I'm not hiding- and your position doesn't have any publications that support it.


    That's right Biblical literalist Joe. All these publications have had nothing but blank pages for the last 75 years.


    * American Journal of Botany
    * American Journal of Human Genetics
    * American Museum of Natural History Research Library
    * American Scientist
    * Animal Biodiversity and Conservation
    * Anatomischer Anzeiger
    * Anatomy, Anthropology, Embryology, and Histology
    * Annals of Anatomy
    * Biological Bulletin
    * Biological Journal of the Linnean Society
    * Biological Procedures Online
    * BioMed Central journals
    * BioScience
    * Botanical Review
    * Bulletin of the Ecological Society of America
    * Canadian Society for Forensic Science Journal
    * Cell
    * Chinese Science Bulletin
    * Comptes Rendus de l’Académie de Sciences
    * Current Science
    * Ecological Society of America Journals
    * European Journal of Cell Biology
    * Evolution
    * Evolution: Education and Outreach
    * Florida Entomologist
    * Forensic Science International
    * Genetics
    * Genome Research
    * Integrative and Comparative Biology
    * International Journal of Plant Sciences
    * Journal of Biological Research
    * Journal of Biology
    * Journal of Evolutionary Biology
    * Journal of Experimental Biology
    * Journal of Forensic Sciences
    * Journal of Genetics
    * Journal of Mammalian Evolution
    * Journal of Mammalogy
    * Journal of Molecular Evolution
    * Journal of Tropical Biology
    * Maryland Essays in Human Biodiversity
    * Molecular Biology and Evolution
    * Molecular Phylogenetics and Evolution
    * Nature
    * Natural History
    * New Scientist
    * Philosophical Transactions of the Royal Society
    * Plos: Public Library of Science
    * Proceedings of the American Philosophical Society
    * Proceedings of the National Academy of Sciences
    * Proceedings of the Oklahoma Academy of Science
    * Proceedings of the Royal Irish Academy
    * Quarterly Review of Biology
    * Raffles Bulletin of Zoology
    * Science
    * Scientific American
    * South African Journal of Science
    * Tentacle
    * Theoretical Applied Genetics
    * Transactions of the Royal Society of London
    * Turkish Journal of Zoology
    * Zoological Studies

    Do you believe in a literal Noah's Ark too YEC Joe? We know you believe in Biblical created 'kinds'.

    ReplyDelete
  109. OK child molesting thorton,

    Pick out ONE paper that demonstrates blind, undirected chemical processs can construct a functioning multi-part system.

    IOW once again you prove all you have are lies and equivocation.

    ReplyDelete
  110. BIG LOL!

    Man, look at Joe's spittle fly!

    OK YEC Joe,

    Pick out ONE paper that demonstrates Adam and Eve were the original human population.

    ReplyDelete
  111. This comment has been removed by the author.

    ReplyDelete
  112. Big LOL! Indeed.

    I see child molesting thorton has an evotardgasm once its bluff is called...

    Par for the course.

    ReplyDelete
  113. Child molesting thorton is upset because it lost its "primo" job as a mall cop trainee because it was soliciting sex from little boys in the mall bathrooms.

    Get over it...

    ReplyDelete
  114. Zachriel: Where's the rest of the pattern over four generations?

    Joe G: More of the same- letters coming and going.

    That's what we want to see.

    ReplyDelete
  115. More of the same- letters coming and going.

    Zachriel:
    That's what we want to see.

    Good for you.

    I want to see a testable hypothesis for your position but you are too much of a coward to produce one.

    ReplyDelete
  116. 0
    ,,,,,,,,,,,,,,,,,,,,

    1
    ,,,,,B,,,,,,,,,,,,,,

    2
    ,,,,,,,,,,,,,,,,,,,,


    3
    ,,,,A,,,,,,,,,,,,,,,

    4
    ,,,,,,,,,,,,,,,,,,,,

    5
    D,,,,,,,,,,,,,,,,,,,

    6
    D,,,A,,,,,,,,,,,,,,,

    7
    ,,,,A,,,,,,,,,,,,,,,

    8
    ,,,,,,,,,,,,,,,,,,,,

    ReplyDelete
  117. Joe -

    apologies for interjecting in this discussion with Zachriel, who is more than competent in carrying out this discussion -

    but you do realise that the odds of random mutation producing a reversion in the mutated daughter sequence are 1/20 * 1/26 = 0.0019 in each second generation.

    As the number of (pairs of) generations increase, the multiplicative odds approach zero (0.019, 3x10-6, 7x10-9, 1x10-11 etc).

    ReplyDelete
  118. Venture Free: "Could you explain in detail exactly why evolution predicts that such a fusion should not exist?"

    Of course I can; I'd not have said what I said, otherwise. But I expect you to do most of the heavy lifting. I already *know* how Darwinists (and creationists, for that matter) tend to react when given the explanation. I'm curious to see whether a Darwinist can work his way through the reasoning under his pwn steam.

    1) Do you understand the concept "differential reproductive success"? -- and, if you don't, then you have some nerve demanding that I justify myself to you.

    2) Do you *grasp* how vitally important that concept is to the formalization (*) of 'modern evolutionary theory?'

    2a) Such that, to *deny* "differential reproductive success" is to formally (*) deny 'modern evolutionary theory' itself? -- This does not imply that to affirm "differential reproductive success" is to affirm 'modern evolutionary theory' (I expect, based on the content of your post, that you'll have difficulty grasping *that* side point).

    3) Do you grasp that if the proponent of 'modern evolutionary theory' must assert some ad hoc suspension of the principle of "differential reproductive success," so as to attempt to save 'modern evolutionary theory' from falsification, then he has actually admitted it to be falsified?

    (*) I'm making a point about "formalization" because in actual fact, the only non-negotiable point of 'modern evolutionary theory' is the (generally hidden) premise that "It just happened."

    ReplyDelete
  119. Joe G: ,,,,,,,,,,,,,,,,,,,,

    The genome isn't replicating. You won't get a nested hierarchy unless there is branching. There should be one in the zero generation, two in the first generation, four in the second generation, eight in the third generation, and sixteen in the fourth generation.

    With your lineal example, as Paul pointed out, the odds of that being random mutation is vanishingly small.

    ReplyDelete
  120. Joe G: IOW what is the blind watchamker explanation for how/ why it [the purported chromosomal fusion] became fixed?

    Zachriel: Fixation can occur in finite populations due to chance alone.

    Joe G: That ain't science- but thanks for admitting you don't have an explanation.

    Oh, it's even worse than that. The Darwinist, in his intellectual dishonesty, holds himself free to at any time inject *himself* into his fanciful Just-So Story so as to supply the necessary agency to get it to work out as has foregone "conclusion" requires.

    ReplyDelete
  121. Allopatrik: The issue of the fixation of human chromosome 2 is addressed in a series of essays over at the Panda’s Thumb ...

    Surely, you being a bit free and easy with that word 'addressed.' Panda's Thumb? Addressing a serious difficulty to 'modern evolutionary theory?' What next, the Holy Talk Origins?

    ReplyDelete
  122. Joe falls back almost immediately to the standard ID tactic,quote mining:

    From Dave's cited paper:

    "Populations of 4 males and 4 females per generation are so exceedingly small that experiments such as the present may seem to have no implications for evolution
    in nature."

    Nice job Dave...


    Of course, Wright and Kerr had a little more to say on the matter:

    Populations of 4 males and 4 females per generation are so exceedingly small that experiments such as the present may seem to have no implications for evolu- tion in nature. It must be borne in mind, however, that changes in the underlying multifactorial genetic structure of species probably occur so slowly that an apprecia- able change in a thousand generations must be considered as an explosively rapid process. Study in the laboratory of the factors that can contribute to such change is prac- ticable only by stepping up the rates by at least one hundred fold. Thus the in- teraction between a weak selective ad- vantage of one isoallele over another and a slight random drift, due to inbreeding, can be simulated by using alleles with selective differentials of ten percent or more instead of perhaps only one tenth of a percent or even one hundredth of a percent in populations of only one percent or even one tenth of one percent of the size of a typical natural deme

    Dave Wisker

    ReplyDelete
  123. Joe's lame attempt at quote mining aside, Wright and Kerr's work is empirical confirmation of a prediction about genetic drift from population genetic theory, namely, that drift can bring alleles to fixation despite strong selection against them.

    Let's keep in mind, however, that selection against heterozygotes for chromosome fusions in humans is not severe. In addition, there is a mechanism which favors fusions during meiosis in human females. That is, human heterozygotes for chromosome fusions preferentially end up with fusions in their eggs--rather than the expected 50/50 split--a phenomenon known as meiotic drive. As my essay shows, meiotic drive increases the probability of fixation of this kind of chromosomal rearrangement, especially in smaller demes where genetic drift can also have a strong effect.

    Joe hasn't even begun to address the issues over human chromosome 2, and the best Ilion has ever done is cite a university webpage used to teach undergrads general cytogenetic principles regarding chromosome rearrangements, where none of the specific conditions that I point out are considered. Readers here are encouraged to see a debate I had with Ilion over this on ARN.

    http://www.arn.org/ubbthreads/showflat.php?Cat=0&Board=13&Number=30335905&fpart=1&PHPSESSID=

    They can judge for themselves who is actually addressing the issue.

    ReplyDelete
  124. Dave:
    Joe's lame attempt at quote mining aside, Wright and Kerr's work is empirical confirmation of a prediction about genetic drift from population genetic theory, namely, that drift can bring alleles to fixation despite strong selection against them.

    Yes if we artificially cull the populations.

    Dave:
    Joe hasn't even begun to address the issues over human chromosome 2

    Nice projecion.

    All you have is it happened by chance and you sur as hell don't know what benefit, if any, it had.

    ou don't have any way to test your claims and what I said are just as likely as your scenarios.

    ReplyDelete
  125. Paul:
    but you do realise that the odds of random mutation producing a reversion in the mutated daughter sequence are 1/20 * 1/26 = 0.0019 in each second generation.

    Shit happens.

    That is evolution for ya.

    And that is my point- EVOLUTION DOES NOT HAVE A DIRECTION.

    Whatever survives to reproduce survives to reproduce.

    ReplyDelete
  126. This comment has been removed by the author.

    ReplyDelete
  127. Populations of 4 males and 4 females per generation are so exceedingly small that experiments such as the present may seem to have no implications for evolution
    in nature.


    Joe G: Nice job Dave...

    Bottlenecks in effective population size are not unusual in nature. The smaller the population the more important drift can be compared to selection.

    ReplyDelete
  128. Joe G: ,,,,,,,,,,,,,,,,,,,,

    Zachriel:
    The genome isn't replicating.

    Geez are you stupid.

    You just cut out one generation.

    Zachrie:
    There should be one in the zero generation, two in the first generation, two in the first generation, four in the second generation, eight in the third generation, and sixteen in the fourth generation.

    Why is that?

    You never sad anything aboutn that before.

    IOW it appears you are moving the goalposts- again.

    ReplyDelete
  129. Chromosome 2-

    OK the fusion occurs-

    How may individuals are likely to come up with this same fusion?

    My bet is one and only one.

    So now what has to happen- well that one has to be able to live and succesfully mate.

    And what are the chances that the fusion gets passed down?

    Obviously the more offspring the better the chances.

    But what are those probabilities?

    This is what evos don't want t diuss.

    Ya se if they try you will stheir position is nothing but sheer dumb luck- against all odds the fusion became fixed.

    And that is all thy really have...

    ReplyDelete
  130. Joe G: S#!t happens.

    Your results are obviously flawed. These are typical results of lineal descent based on the previous parameters.

    ,,,,,,,,,,,,,,,,,,,,
    ,,,,,,,,X,,,,,,,,,,,
    ,,,,,,A,X,,,,,,,,,,,
    ,,,E,,A,X,,,,,,,,,,,
    ,R,E,,A,X,,,,,,,,,,,

    ,,,,,,,,,,,,,,,,,,,,
    ,,,,,,,,,,J,,,,,,,,,
    ,,,,,,,,,,JP,,,,,,,,
    ,,,,,,V,,,JP,,,,,,,,
    ,,,,,,V,,,JPC,,,,,,,

    ,,,,,,,,,,,,,,,,,,,,
    ,,,,,,,,,,Z,,,,,,,,,
    ,,,,F,,,,,Z,,,,,,,,,
    ,,,,F,,,,,Z,,,,,,,X,
    G,,,F,,,,,Z,,,,,,,X,

    There is a reasonable likelihood of a previously mutated base being mutated again, but with your results, where the same bases are hit over and over again, the chances are vanishingly small.

    To be generous, your implementation was faulty. You may want to check and publish new results. In any case, we were discussing branching descent, and your algorithm ignores that facet of the problem.

    ReplyDelete
  131. Zachriel: There should be one in the zero generation, two in the first generation, two in the first generation, four in the second generation, eight in the third generation, and sixteen in the fourth generation.

    Joe G: Why is that? You never sad anything aboutn that before.

    Repeated twice above:

    Take a sequence, then duplicate with a random letter change in one the two offspring. So if the founder genome was

    ,,,,,,,,,,,,,,,,,,,,

    Then its offspring might be

    ,,,,,,,,,,,,,,,,,,,,
    ,,,,,B,,,,,,,,,,,,,,

    We then let the offspring continue to divide and see what sort of pattern it forms.

    Also, from above:

    With our example, there are a total of 15 replications over four generations. The genome length is 20 and there are twenty-six letters.

    And this:

    Oh, here's the complete generational breakdown of our example.

    0
    ,,,,,,,,,,,,,,,,,,,,

    1
    ,,,,,,,,,,,,,,,,,,,,
    ,,,,,,,C,,,,,,,,,,,,

    2
    ,,,,,,,,,,,,,,,,,,,,
    ,,,,F,,,,,,,,,,,,,,,
    ,,,,,,,C,,,,,,,,,,,,
    ,,,,,J,C,,,,,,,,,,,,

    3
    ,,,,,,,,,,,,,,,,,,,,
    ,,,,,,,,,,,,,,,,A,,,
    ,,,,F,,,,,,,,,,,,,,,
    ,,,,F,Z,,,,,,,,,,,,,
    ,,,,,,,C,,,,,,,,,,,,
    ,,,,,,,C,,,,,,,T,,,,
    ,,,,,J,C,,,,,,,,,,,,
    ,,,,,J,C,,,,,,,,,,G,

    4
    ,,,,,,,,,,,,,,,,,,,,
    ,,,,N,,,,,,,,,,,,,,,
    ,,,,,,,,,,,,,,,,A,,,
    ,,,,,,,,,,,B,,,,A,,,
    ,,,,F,,,,,,,,,,,,,,,
    ,,,,F,,,,,,,,,D,,,,,
    ,,,,F,Z,,,,,,,,,,,,,
    ,,,,F,Z,,K,,,,,,,,,,
    ,,,,,,,C,,,,,,,,,,,,
    ,,,,,,,C,,,,,V,,,,,,
    ,,,,,,,C,,,,,,,T,,,,
    ,,,,,,,C,,,,,,,T,,,V
    ,,,,,J,C,,,,,,,,,,,,
    ,,,,,J,C,,,,,,,,,,,Q
    ,,,,,J,C,,,,,,,,,,G,
    ,,,,,J,C,,,,,,,,,,GX

    Not random. Not random, at all.

    In any case, the discussion has to do with branching descent.

    ReplyDelete
  132. Shit happens.

    Zachriel:
    Your results are obviously flawed.

    Nope.

    But nice try- I do undersad that is all you have though- bald accusations.

    Zachriel:
    There is a reasonable likelihood of a previously mutated base being mutated again, but with your results, where the same bases are hit over and over again, the chances are vanishingly small.

    Irrelevant- ya se it could happen, and all it takes is once to ruin your premise.

    Zachriel:
    To be generous, your implementation was faulty.

    To be generous, you are a moron.

    Zchriel:
    In any case, we were discussing branching descent, and your algorithm ignores that facet of the problem.

    No it doesn't- each new generation is a new branch.

    You are just upset because I demonstrated your claim is bogus.

    Deal with it...

    ReplyDelete
  133. Zachriel:
    Take a sequence, then duplicate with a random letter change in one the two offspring.

    Now tht is movong the goalposts!

    Why stop at two

    Why not 9 or 99?

    ReplyDelete
  134. Zachriel:
    Oh, here's the complete generational breakdown of our example.

    Your example is faulty and does not follow the reality of evolution.

    ReplyDelete
  135. OK so Dave Wisker has a study from 1954 in which fruit-flies were artificially culled to keep the population very, very low.

    I cite a paper from this year which contradicts the findings of that very old paper and dave just ignores it.

    Typical.

    ReplyDelete
  136. Zachriel: Your results are obviously flawed.

    Joe G: Nope.

    We certainly didn't expect you to build and debug a simulation, but once you have, then it is reasonable that the implementation is accurate. The chance of repeatedly hitting the same base that was previously mutated is very small. Changing it back to its original value each time is vanishingly unlikely. But it's simple to find out. Run your simulation again and show us the new results. You might want to publish the code, too.

    Joe G:

    That's like saying you can't recognize a pattern zf a couple of letters are out ow place.

    Joe G: No it doesn't- each new generation is a new branch.

    We're discussing a bifurcating tree. Try to keep up (Darwin, 1859).

    Zachriel: Take a sequence, then duplicate with a random letter change in one the two offspring.

    Joe G: Now tht is movong the goalposts!

    That is the original description of the algorithm from above, which we have repeated several times for your reading pleasure.

    Joe G: Why stop at two? Why not 9 or 99?

    That's fine. That's another parameter we can manipulate. We are mostly concerned with bifurcation, as that is the posited process for most evolutionary divergence, also for bacterial replication; however, you will still get a nested hierarchy even if there are multiple offspring. The limiting factors are the length of the genome, the rate of mutation, and the number of generations. But such a discussion is seemingly beyond your kin, but if you are interested, just say so.

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  137. Zachriel:
    The chance of repeatedly hitting the same base that was previously mutated is very small.

    The chance of ANY mutation occurring is very small.

    nd evevry position has the equal chance of being changed.

    Zachriel:
    Changing it back to its original value each time is vanishingly unlikely.

    So is the chance of having a chromosome fusion becoming fixed.

    Zachriel:
    We're discussing a bifurcating tree. Try to keep up (Darwin, 1859).

    Darwin was wrong- ther isn't any evidencefor such a tree.

    IOW apparently you are an asshole also.

    Also Zacho YOU said a family tree does NOT produce a nested hierarchy.

    Yet now you present a family tree as a neted hierarchy.

    IOW you are either a fool or very dishonest.

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  138. And Zacho STILL doesn't get it- even if there is just a very small chance of a reversion that alone refutes its claims.

    ReplyDelete
  139. Joe G: The chance of ANY mutation occurring is very small.

    A typical human has more than a hundred new mutations, while bacteria have about one mutation per thousand replications.

    Joe G: And evevry position has the equal chance of being changed.

    Which is why we know your results are not reasonably random.

    Joe G: Darwin was wrong- ther isn't any evidencefor such a tree.

    We could have that discussion. But we have to understand the pattern at issue first. Based on the algorithm described above, will the results of replication and random mutation lead to a random pattern of traits in the descendants, or will there likely be a discernable nesting of traits?

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  140. Joe G: even if there is just a very small chance of a reversion that alone refutes its claims.

    That's like saying you can't recognize a pattern zf a couple of letters are out ow place. It's like saying we can't identify the shape of the Earth because it's not a perfect sphere.

    The correlation may be less than 100%, but still be discernable.

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  141. How did the chromosome fusion happen? Wouldn't the same homologous chromosomes have to fuse in a male and a female proto-human, and then those two had to mate? And, aren't we lucky, the fusion had no bad effects. Please correct me if I'm wrong.

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  142. "How did the chromosome fusion happen? Wouldn't the same homologous chromosomes have to fuse in a male and a female proto-human, and then those two had to mate? And, aren't we lucky, the fusion had no bad effects. Please correct me if I'm wrong."

    No, it only had to happen in one individual – to be more precise, it would have happened in one gamete (whether a sperm or an ovum), and that gamete would have fused with a normal gamete from the opposite sex thereby producing one individual who was heterozygous for the fusion.

    That is, the first individual to possess the purported fusion would have had one fused chromosome and the two corresponding unfused chromosomes.

    HOWEVER, you still can’t get from there to here naturalistically, in accord with Darwinism.

    But, you can get from there to here non- naturalistically. You can get from there to here if there is a knowledgeable agent who is overseeing the breeding of individuals who are homozygous for the fusion … and the subsequent segregation of them from the original stock and from the intermediate heterozygous state.

    There are all sorts of contradictions to Darwinism represented in this purported fusion – and Darwinists, being Darwinists, are more than willing to retroactively insert themselves into a Just-So Story as the (hidden) agent making the necessary choices and exercising the necessary control to get from there to here.

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  143. "How did the chromosome fusion happen?"

    Who knows. Chromosomal fusions happen all the time -- I'm not going to look it up to make sure I'm remembering the number correctly, but I think about 1 in 900 humans have a chromosomal fusion.

    It is reasonable to assume that the rates of de novo chromosomal fusions amongst humans have been relatively constant over time. And, we know that there have been thousands of isolated and nearly isolated populations of humans throughout history.

    Yet, there are no chromosomal races amongst humans. So, time for more Darwinist Just-So Stories.

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  144. Allopatrik: "Typical Ilion. All hat and no cattle."

    I know better than to waste my time on intellectually dishonest persons -- one cannot reason with a man who will say simply anything.

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  145. JoeG says:"The chance of ANY mutation occurring is very small."

    The chance a specific mutation occurring in an individual is small (e.g. a reversion). The chance of an unspecified mutation occurring is very high. That is precisely what makes your willful misinterpretation of Zachriel's nested hierarchy simulation so very flawed.

    Also Zacho YOU said a family tree does NOT produce a nested hierarchy

    A (human or otherwise within species) family tree does not produce a nested hierarchy if there is a lot of interbreeding between lineages.

    Yet now you present a family tree as a neted hierarchy.

    What was presented was not a family tree in the sense of a human family tree (which I assume is the type of thing you mean). Different lineages in human family trees can interbreed (i.e. different families of humans). Non-random interbreeding might still result in some of the same patterns of nesting, but not necessarily an overall robust pattern, and not one that is robust to future collapse.

    By contrast, in the tree of life, different lineages do not (or at least very rarely) interbreed (the same in Zachriel's example). This makes these patterns robust. A nested hierarchy results.

    even if there is just a very small chance of a reversion that alone refutes [his] claims.

    Absolutely not. Provided enough DNA was sequenced what you suggest could work at most for the odd individual in one or two generations in the occasional lineage by chance. The odds over time make such a probability effectively zero (as already explained above).

    What you suggest could be trivially true for a few mutations in sites when viewed in isolation but not for the overall genome-wide pattern of mutations that could be observed. This has no bearing on the evolutionary tree of life.

    Given sufficient time such that the lineages have speciated, forming part of a nested hierarchy, they will match the patterns predicted by Zachriel provided appropriate DNA has been sequenced (i.e. genes that evolve on a timescale appropriate for whatever species are under consideration).

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  146. You're question-begging, Paul.

    Oh! Silly me, you're a DarwinDefender. Of course you're question-begging!

    ReplyDelete
  147. nat wrote:
    "How did the chromosome fusion happen? Wouldn't the same homologous chromosomes have to fuse in a male and a female proto-human, and then those two had to mate?"

    No.

    "And, aren't we lucky, the fusion had no bad effects. Please correct me if I'm wrong."

    You're wrong.

    Say, Nat, do you believe Dr. Hunter's claim of more than a thousand genes present in humans with no ortholog in chimps?

    Or do you think it's a lie, but don't want to know the truth?

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  148. Paul:
    The chance a specific mutation occurring in an individual is small (e.g. a reversion).

    And that is what makes your position very unlikely.

    Ya see it takes an accumulation of specific mutations in order to build something.

    Or do you think just any accumulation of mutations can change a reptile ear and jaw into a mammalian inner ear?

    Also Paul nested hierarchies requyire a direction- one of unique and unreversable traits.

    Yet it is a given that evolution does NOT have such a direction.

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  149. The chance of ANY mutation occurring is very small.

    Zachriel:
    A typical human has more than a hundred new mutations, while bacteria have about one mutation per thousand replications.

    Thanks for proving my point.

    And evevry position has the equal chance of being changed.

    Zachriel:
    Which is why we know your results are not reasonably random.

    Because it follows biological reality?

    Darwin was wrong- ther isn't any evidencefor such a tree.

    Zachriel:
    We could have that discussion.

    Doubtful- you seem incapable of having one.

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  150. Joe G: The chance of ANY mutation occurring is very small.

    The chance of a mutation occurring is virtually certain in every human birth.

    Zachriel: Which is why we know your results are not reasonably random.

    Joe G: Because it follows biological reality?

    Anyone with a bit of knowledge of probability can see your results were not the result of a random process. Here are your results (assuming they were meant to be eight lineal generations):

    0) ,,,,,,,,,,,,,,,,,,,,
    1) ,,,,,B,,,,,,,,,,,,,,
    2) ,,,,,,,,,,,,,,,,,,,,
    3) ,,,,A,,,,,,,,,,,,,,,
    4) ,,,,,,,,,,,,,,,,,,,,
    5) D,,,,,,,,,,,,,,,,,,,
    6) D,,,A,,,,,,,,,,,,,,,
    7) ,,,,A,,,,,,,,,,,,,,,
    8) ,,,,,,,,,,,,,,,,,,,,

    Not only were your results not likely the result of a random process, they represented lineal descent, not branching descent. We would be happy to help you debug your code, though.

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  151. The chance of ANY mutation occurring is very small.

    Zachriel:
    The chance of a mutation occurring is virtually certain in every human birth.

    Non-sequitur.



    Zachriel:
    Anyone with a bit of knowledge of probability can see your results were not the result of a random process.

    Nice try- however too bad it is nothing but a bald assertion.

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  152. 1- The ToE would be fine without any branching

    2- The ToE does NOT posit uncrossed lines

    3- Evolution does NOT have a direction of unique and unreversed traits.

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  153. And Zachriel, your position relies on the premise that even the very improbable is indeed likely.

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  154. "And Zachriel, your position relies on the premise that even the very improbable is indeed likely."

    Darwinism relies upon question-begging and other specific logical fallacies.

    And, importantly, Darwinism relies upon "arguing" both 'A' and 'not-A' -- to the Darwinist, everything and its opposite is "proof" of Darwinism. In this regard, Darwinism is like Freudianism and Marxism.

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  155. NatSchuster: "And, aren't we lucky, the fusion had no bad effects. Please correct me if I'm wrong."

    Joaozinho: "You're wrong."

    Joaozinho is ignorant ... or dishonest.

    An individual who is heterozygous for a chromosomal fusion has a significantly reduced level of fertility as compared to its fellows who are not so afflicted, or compared to its fellows who are homozygous for the chromosomal fusion.

    A specific chromosomal fusion may have other deleterious effects (for instance, some cancers are caused by somatic chromosomal fusions), but a chromosomal fusion occurring during gametogenesis *always* reduces the fertility (even to the point of total infertility) of any resulting, and descendant, individuals who are heterozygous for the fusion. Darwinists *know* this - and they typically refuse to admit it.

    Now, while this purported chromosomal fusion may have generated some other deleterious effect than just reduced fertility, we can't know either that it did or that it didn't -- though, we can observe that there appear (I have to say 'appear,' because of course not all apes have been karyotyped) to be no populations of chimpanzees of other apes possessing this specific fusion. Considering how common chromosomal fusions are, and considering that the Darwinists assert that the purported fusion in *our* chromosomes is undeniable proof that we are naturalistically descended from some earlier ape, is not this lack a profound mystery? Is it not a profound mystery that there are no known populations of humans in which a similar fusion between any of the five acrocentric chromosomes of our karyotype have become fixed?

    So, getting back to the main point, in a mating between two individuals who are heterozygous for a chromosomal fusion the reduced fertility of each reinforces the reduced fertility of the other. That is, a mating between two individuals who are heterozygous for a chromosomal fusion is less likely to produce viable offspring than that between a heterozygous individual and a homozygous individual (either with our without the fusion) and far less likely to produce viable offspring than that between two homozygous individuals (again, either with our without the fusion).


    NOW, any scenario which seeks to explain-and-justify the assertion that human ancestors had 48 chromosomes and that a chromosomal fusion at some point in our lineage explains how it is that we have 46, rather than 48, must take into account that reduced fertility of the individuals who are heterozygous (that is, having 47 chromosomes) for the purported chromosomal fusion.

    There are, of course, more things that a rational explanation must account for; but that is the biggie: that is the problem which kills Darwinism - for, to get his favored “explanation” to work, the Darwinist always ends up *denying* the truth of some key formal point(s) of Darwinism, most commonly “differential reproductive success.”

    AND, any scenario-explanation which is purported to be rational may *never* engage in question-begging or any other logical fallacy. BUT, the Darwinists simply cannot get from there to here without engaging in logical fallacies -- including injecting themselves into their imaginative scenario as the hidden agent who is making the decisions to guide the scenario to its "proper" conclusion. THAT IS, by injecting themselves into their imaginative scenarios (they do it constantly), Darwinists implicitly repudiate the naturalism upon Darwinism is built and depends, and for which it, by intention, supplies the creation myth.

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  156. Joe G: The chance of ANY mutation occurring is very small.

    Zachriel: The chance of a mutation occurring is virtually certain in every human birth.

    Joe G: Non-sequitur.

    any, one or some indiscriminately of whatever kind.

    The chance of mutations occurring in humans is a virtual certainty. All humans are mutants. Maybe instead of "any mutation" you meant "a specific mutation."

    Zachriel: Anyone with a bit of knowledge of probability can see your results were not the result of a random process.

    Joe G: Nice try- however too bad it is nothing but a bald assertion.

    It's quite obvious from the results. However, you are more than welcome to provide another run of the algorithm or a description of the code.

    Joe G: 1- The ToE would be fine without any branching 2- The ToE does NOT posit uncrossed lines

    The Theory of Evolution has included branching descent since its inception (Darwin, 1859).

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  157. 1- The ToE would be fine without any branching

    2- The ToE does NOT posit uncrossed lines

    3- Evolution does NOT have a direction of unique and unreversed traits.


    Zachriel:
    The Theory of Evolution has included branching descent since its inception (Darwin, 1859).

    Non-sequitur.

    IOW your response doesn't even address what i said.

    Typical.

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  159. Joe G: Non-sequitur.

    Joe G: The ToE does NOT posit uncrossed lines

    Yes, it does. The hypothesis explains the observed nested hierarchy of character traits.

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  160. The ToE does NOT posit uncrossed lines.

    Zachriel:
    Yes, it does.

    Please provide the scientific paper that states exactly that.

    The image you linked to doesn't support your claim.

    Zachriel:
    The hypothesis explains the observed nested hierarchy of character traits.

    Except evolution does not posit a direction of unique and unreversed traits and a nested hierarchy demands it.

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  161. Joe G: Please provide the scientific paper that states exactly that.

    Darwin, Origin of Species, 1859.

    Joe G: The image you linked to doesn't support your claim.

    It does depict branching descent. The bifurcations are clearly shown.

    Joe G: Except evolution does not posit a direction of unique and unreversed traits and a nested hierarchy demands it.

    The Theory of Evolution doesn't posit a 100% correlation. That doesn't mean the pattern isn't evident.

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  162. Joe G: Please provide the scientific paper that states exactly that.

    Zachriel: Darwin, Origin of Species, 1859.

    Without even backtracking to find out the antecedent of ‘that,’ this assertion is a howler. Darwin’s opus is not even close to being scientific. Nor is it logical -- it is, as has been said, “one long argument” … but it’s not a logical argument.

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  163. Joe G:Except evolution does not posit a direction of unique and unreversed traits and a nested hierarchy demands it.

    Zachriel:The Theory of Evolution doesn't posit a 100% correlation. That doesn't mean the pattern isn't evident.

    Translation: everything - and its opposite - is “proof” of Darwinism.

    ===
    Joe G:Except evolution does not posit a direction of unique and unreversed traits and a nested hierarchy demands it.

    Joe, you really ought to teach yourself to stop saying and thinking ‘evolution’ when you mean 'evolutionism.' The "evolution vs creationism" dichotomy which is reflected in your statement is itself an instance of Darwinistic propaganda and misinformation.

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  164. Allopatrik: "Readers here are encouraged to see a debate I had with Ilion over this on ARN."

    So that's who you are.

    It is, in fact, logically impossible to engage in rational examination of an issue ('debate,' if you prefer that word) with a man who is intellectually dishonest ... and you, my good man, are intellectually dishonest to the core, when it comes to anything touching upon Darwinism.


    Allopatrik: "Joe's lame attempt at quote mining aside, Wright and Kerr's work is empirical confirmation of a prediction about genetic drift from population genetic theory, namely, that drift can bring alleles to fixation despite strong selection against them."

    Translation: "everything and its opposite is 'proof' of Darwinism." Or, to put it less bluntly and in more scientistic speech, there is no conceivable fact or observation which can, in principle, falsify 'modern evolutionaly theory'. That is to say, 'modern evolutionaly theory' is *not* scientific -- it is, rather, on a par with Freudianism or Marxism.

    This example of typically Darwinistic "reasoning" -- that 'A' and 'not-A' are simultaneously true -- ought to be enough in itself to convince any rational being that Darwinism is illogical; which is to say, that it is necessarily false.


    Allopatrik: "Let's keep in mind, however, that selection against heterozygotes for chromosome fusions in humans is not severe."

    Riiight!

    That why, despite that about 1 in 900 human births bear a chromosomal fusion (generally de novo, are they not?), and that we may reasonably assume that this ratio holds across time and space, there are no populations amongst humans in which a chromosomal fusion is fixed.

    Again, "everything and its opposite is 'proof' of Darwinism."


    Even aside from the question of fixation (in some sub-population) of any specific chromosomal fusion, IF it were indeed true "that selection against heterozygotes for chromosome fusions in humans is not severe," THEN by now most living human beings should possess at least one chromosomal fusion -- but, in fact, we observe just the opposite.

    This isn't calculus, people, or even algebra; it's simple arithmetic.

    FOR, Allopatrik has asserted that humans afflicted with a chromosomal fusion have, on average, nearly as many offspring as humans with a normal karyotype. Which is to say, he asserts that chromosomal fusions tend to stick around from one generation to the next. THUS, as new fusions are constantly being generated in each new generation, AND AS the assertion is that the fusions generated in prior generations are not being strongly selected out of the population(s) of humans, but rather are mostly carrying forward into the present generation, THEN in each new generation the ratio of individuals possessing the standard human karyotype must decrease, and the ratio of individuals possessing one or more chromosomal fusions must increase.

    BUT, this is not what we observe in the real world. You know, the one where DarLogic (tm) has to bow both to fact and to actual logic.


    Did I not assert at the start of this post that Allopatrik is intellectually dishonest in his defense of Darwinism? This is an example of what I meant -- he will assert *anything,* no matter how blatantly illogical and/or contrary to fact it is, if he thinks it will promote belief in, or silence criticism of, Darwinism.

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  166. This comment has been removed by the author.

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  167. Allopatrik: "In addition, there is a mechanism which favors fusions during meiosis in human females. That is, human heterozygotes for chromosome fusions preferentially end up with fusions in their eggs--rather than the expected 50/50 split--a phenomenon known as meiotic drive."

    Allopatrik *knows* that he is asserting bull -- he *knows* he is giving the reader half-truths, and false a understanding. He *knows* that "meiotic drive," even were it as robust as some Darwinists like to claim it is (I wonder, have they "solved" it, yet again, since I lost interest in pursuing the logically impossible task of trying to reason with unreasonable people?), cannot answer the problem of reduced fertility of the heterozygous individuals.

    He is also ignoring the problems (by which I mean sweeping them under the rug while he has the reader distracted elsewhere) resulting from chiasmata (*) forming in the region between the two centromeres -- and I’m sure he must be aware of this issue, for he brought the realization forward in my consciousness. Perhaps he doesn't realize that even in his intellectual dishonesty he sometimes reveals infomation he'd prefer to keep hidden.

    We are, after all, *not* talking about a Robertsonian or centromeric fusion, but rather about a telomeric fusion.

    (*) For the general reader --
    This first image represents a crossover event between a pair of normal chromosomes. This second image represents a crossover event for a telomeric-fusion chromosome and its two unfused/normal homologues, with a chiasma having formed in the region between the two centromeres.


    Allopatrik: "As my essay shows, meiotic drive increases the probability of fixation of this kind of chromosomal rearrangement, especially in smaller demes where genetic drift can also have a strong effect."

    I'm sure Allopatrik's essays will be very amusing when I get around to reading them.


    Allopatrik: "... and the best Ilion has ever done is cite a university webpage used to teach undergrads general cytogenetic principles regarding chromosome rearrangements, where none of the specific conditions that I point out are considered."

    Allopatrik is misrepresenting "the best Ilion has ever done." And, as this misrepresentation is intentional, he must be lying.

    Allopatrik: "Readers here are encouraged to see a debate I had with Ilion over this on ARN. ... They can judge for themselves who is actually addressing the issue."

    And I have already shown the reader, using his own statements in this very thread, that Allopatrik is intellectually dishonest. One cannot debate with a man who will say simply anything.

    =======
    Isn't it odd? Mr Wisker likes to pretend that I have no idea what I'm talking about with respect to human chromosome 2 and its implications for Darwinism. And yet, he wrote all those essays to soothe the troubled souls of rank-and-file DarwinDefenders who may encounter my argument and begin to question Darwinism.

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  168. lion likes to insist that chromosome fusions always have a detrimental effect on fitness. Yet, he has Ben confronted with evidence contradicting him several times. for those who aren't fa,air with the issue, biologists interested in speciation have looked at affects of chromosomal rearrangements on fertility, because that could be a reproductive isolation barrier. However, what they found is, this expect ion is simply not the case. As evolutionary geneticists interested in speciation Jerry Coyne and Allen Orr note:

    A further problem with chromosomal speciation is that it depends critically on the semi sterility of hybrids who are heterozygotes for chromosomal rearrangements. It is not widely appreciated, however, that heterozygous rearrangements theoretically expected to be deleterious (e.g., fusions and pericentric inversions) in reality often enjoy normal fitness, probably because segregation is regular or recombination is prevented

    Coyne J & HA Orr (1998). The evolutionary genetics of speciation. Phil Trans R Soc Lond B 353: 287-305

    When confronted with this another evidence, Ilion just reflexively accuses those who actually know what they are tailing about of intellectual dishonesty.

    Dave Wisker

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  169. Please provide the scientific paper that states exactly that.

    Zachriel:
    Darwin, Origin of Species, 1859.

    What I am asking for isn't in that book.

    Go figure.

    The image you linked to doesn't support your claim.

    Zachriel:
    It does depict branching descent. The bifurcations are clearly shown.

    You need to find a scientific paper that states evolutioon predicts uncrossed lines of branching descent.

    You have failed to do so.

    Except evolution does not posit a direction of unique and unreversed traits and a nested hierarchy demands it.

    Zachriel:
    The Theory of Evolution doesn't posit a 100% correlation. That doesn't mean the pattern isn't evident.

    The pattern doesn't have anything to do with the theory.

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  170. Chromosome fusion- chromosome 2

    When did it happen?

    The point being we should either see humans with 48 or chimps with 46 and even some individuals with 47 in both populations.

    Yet we do not.

    That should be evidence that humans always had 46 and apes always had 48- as in it was designed like that.

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  171. Zachriel: The Theory of Evolution doesn't posit a 100% correlation. That doesn't mean the pattern isn't evident.

    Ilíon: Translation: everything - and its opposite - is “proof” of Darwinism.


    If we have a correlation, it means we can make empirical predictions, even if that correlation is not 100%. Indeed, convergence has been a part of the Theory of Evolution since its inception.

    Is the Earth an oblate sphere? Does it follow an elliptical orbit about the Sun?

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  172. Zachriel: Darwin, Origin of Species, 1859.

    Ilíon: Without even backtracking to find out the antecedent of ‘that,’ this assertion is a howler. Darwin’s opus is not even close to being scientific.

    Quite a bit of handwaving there. Of course Origin of Species was scientific. Not only was Darwin already a scientific observer of the first rank when he published Origin of Species, but his theory led to an explosion of scientific research that continues today.

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  173. Ilíon: I think about 1 in 900 humans have a chromosomal fusion.

    The most common chromosomal rearrangement is a Robertsonian translocation, and occur in about 1 in a 1000 human births. Many have Downs Syndrome. Some have normal function, but there is an increased risk in their progeny of abnormalities.

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  174. Joe G: your position relies on the premise that even the very improbable is indeed likely.

    You had claimed to have produced results of lineal descent with random mutation.

    0) ,,,,,,,,,,,,,,,,,,,,
    1) ,,,,,B,,,,,,,,,,,,,,
    2) ,,,,,,,,,,,,,,,,,,,,
    3) ,,,,A,,,,,,,,,,,,,,,
    4) ,,,,,,,,,,,,,,,,,,,,
    5) D,,,,,,,,,,,,,,,,,,,
    6) D,,,A,,,,,,,,,,,,,,,
    7) ,,,,A,,,,,,,,,,,,,,,
    8) ,,,,,,,,,,,,,,,,,,,,

    The results you provided are highly unlikely to be the result of a random process. Notice the clustering of positions (1,5,6) and of letters (A,B,D), and that they revert soon after being changed.

    Please provide your methodology or code. You might want to provide additional results.

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  175. Zachriel:
    Not only was Darwin already a scientific observer of the first rank when he published Origin of Species, but his theory led to an explosion of scientific research that continues today.

    And still there isn't any positive evidence that an accumulation of genetic accidents can construct a functioning multi-part system.

    That should be evidence against the theory...

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  176. Joaozhino:

    So how exactly did the chromosome fusion happen? Two pairs of chromosomes fused, not one pair. And I understand that the fuse supposedly chromosomes are homologous, so they had to fuse in two proto-humans, and then they had to mate.

    And I understand that genes can be up to 20% different and still be considered stronlgy orthologous. They can be 50% different and be considered orthologous. And they can be orhtologous if they have a similar shape. So I'm not sure that labeling genes orthologous means much with thayt mch difference. Please correct me if I'm wrong.

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  177. The above post, is me, natschuster.

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  178. Joe G: "When did [the purported chromosomal fusion which resulted in h.c.2] happen?"

    God only knows.

    Joe G: "The point being we should either see humans with 48 or chimps with 46 and even some individuals with 47 in both populations.
    .
    Yet we do not.
    "

    IF Darwinism were true, then yes, we ought to see human beings with 48, 47, and 46 chromosomes. And, depending on when in "evolutionary history" the purported fusion happened, we might even expect to see the same amongst chimpanzees or even other apes.

    Moreover, IF the Darwinistic Just-So Stories which seek to explain-away what we do not see were true, THEN we should see other chromosomal fusions fixed within sub-populations of humans and of apes.

    But, we do not see any of this.


    Joe G: "That should be evidence that humans always had 46 and apes always had 48- as in it was designed like that."

    What is observed is consistent with that hypothesis. But, it's also consistent with some other hypotheses, including this one: that an intelligent agent intervened (and guided) the breeding of our ancestors at the time of the purported fusion, including keeping the individuals with 2n=46 karyotypes (once such individuals had actually been born) from breeding with either the original stock (the 2n=48 karyotype) or with heterozygous individuals (the 2n=47 karyotype), so as to "get them over the hump" that naturalism simply cannot.

    What that which is observed is not consistent with is Darwinism.

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  179. Yoni: "So how exactly did the chromosome fusion happen? ... so they had to fuse in two proto-humans, and then they had to mate."

    Actually, that isn't necessary.

    The fusion (if there really was one) probably happened during a meiosis event, and the gamete so generated was eventually successful in mating with its corresponding opposite (which had a normal karyotype). Thus, the individual born of this union had a 2n=47 karyotype -- whereas, the normal karyotype for that individual's species was 2n=48.

    The way to (initially) get individuals with the 2n=46 karyotype (which is the standard human karyotype) is to successfully breed individuals of the "intermediate" 2n=47 karyotype.

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  180. Zachriel:
    The results you provided are highly unlikely to be the result of a random process.

    More false accusations.

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  181. Zachriel: The results you provided are highly unlikely to be the result of a random process.

    Joe G: More false accusations.

    It's not an accusation. The clustering makes it quite apparent your results are not the result of random mutation. It could simply be due to a faulty PRNG, a bug in your program, or you misunderstood the described algorithm. Additional results should resolve the issue.

    We didn't see where you provided your code.

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  182. Zachriel:
    It's not an accusation.

    Right it is just a coward crying because his premsie was refuted.

    Zachriel:
    The clustering makes it quite apparent your results are not the result of random mutation.

    If it happened with other families you might have a point.

    However seeing that your position relies on the highly improbable becoming likely you don't have anything to talk about.

    Zachriel:
    We didn't see where you provided your code.

    What an asshole!

    I asked YOU for the code days ago and you balked.

    So I used YOUR instructions as YOU provided them.

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  183. Joe G: I asked YOU for the code days ago and you balked.

    Our code has been posted for years, linked directly on zachriel.com. But where's your code? Your results above cannot be reasonably considered random, but if you will provide additional results and your code, we would have a better idea.

    Zachriel’s Nest of Letters: Not just a similarity, but a family resemblance.

    ...
    Length = Len(Member)
    Letter = Random(0, Length - 1)
    Member = Left(Member, Letter) & Chr(Random(65, 90)) & Right(Member, Length - Letter - 1)
    ...

    Public Function Random(L, u)
    Random = Int((u - L + 1) * Rnd) + L
    End Function

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  184. Zachriel:
    Your results above cannot be reasonably considered random,

    Nice bald assertion.

    As I said and you ignore as if your ignorance helps you-

    YOUR position relies on the fact that the extremely improbable is indeed likely.

    Deal with it and stop being such a whiny little baby.

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  185. LoL!

    From Zacho's own page:

    “A nested-hierarchy is not just a mere similarity, but a family resemblance.”

    Yet a family tree is not a nested hierarchy!

    So a family tree is not a nested hierarchy but Zacho sez UCD, whch is just a big family tree, is a nested hierarchy.

    Strange...

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  186. Still haven't seen your additional results, or your code.

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  187. Ilion asserts that we are not talking about a Robertsonian fusion when considering human chromosome 2. The general reader is hereby cautioned to seek confirmation for Ilion's assertions on this subject:

    G-banding reveals that a Robertsonian translocation in human ancestor switched the long and short arms of the two acrocentric chromosomes that are still found in the other three primates [Gorilla, Chimpanzee & Orangutan]. This translocation created the large metacentric human chromosome 2.

    --Benjamin Pierce (2008). "Transmission and Population Genetics", p.249

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  188. Chromosome fusion- chromosome 2

    When did it happen?

    The point being we should either see humans with 48 or chimps with 46 and even some individuals with 47 in both populations.

    Yet we do not.

    That should be evidence that humans always had 46 and apes always had 48- as in it was designed like that.

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  189. Zachriel:
    Still haven't seen your additional results, or your code.

    Still haven't seen your claims supported by actual research and still haven't seen anything from you that would demonstrate an understanding of evolution.

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  190. The general reader should beware of Ilion's link with the illustration of a telomere-telomere fusion.. The illustration was of a fusion between homologous chromosomes. The fusion that created human chromosome 2 was between non-homologous chromosomes, and has very different meiotic consequences.

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  191. Dave Wisker:
    The fusion that created human chromosome 2 was between non-homologous chromosomes, and has very different meiotic consequences.

    Most likely it was a design feature...

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  192. Joe G: Still haven't seen your claims supported by actual research and still haven't seen anything from you that would demonstrate an understanding of evolution.

    That wasn't the point under contention.

    Zachriel: The simplest way would be to take a sequence, then allow it to duplicate with a random letter change in one the offspring.

    Joe G: No nested hierarchy there.

    And you then provided what you said was the result of a simulation of that process. Not only didn't the results show duplication with one of the duplicates having a mutation, but the lineal descent you posted was clearly not random. When asked for additional results and the code, you deferred, deflected, averted and hurled insults.

    Please provide the additional results and the code, or withdraw your claim.

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  193. Still haven't seen your claims supported by actual research and still haven't seen anything from you that would demonstrate an understanding of evolution.

    Zachriel:
    That wasn't the point under contention.Not only didn't the results show duplication with one of the duplicates having a mutation, but the lineal descent you posted was clearly not random.

    Do you really think that whining like a little baby helps your case?

    Zachriel:
    Please provide the additional results and the code, or withdraw your claim.

    Please stop acting like a little baby- unless you aren't acting- and deal with the FACT that evolution does NOT have a direction of unique and unreversed traits and nested hierarchies based on characteristics requires one.

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  194. JoeG says:
    Please stop acting like a little baby- unless you aren't acting- and deal with the FACT that evolution does NOT have a direction of unique and unreversed traits and nested hierarchies based on characteristics requires one.


    Rather than writing such meaningless invective (e.g. 'Do you really think that whining like a little baby helps your case?'), why not actually provide the code or method used to produce you apparent results as requested?

    That way your methods can be analysed and your results repeated.

    This will be a) be on par with what Zachriel has already done and b) allow for scientific analysis rather than reducing discussion here to naysaying and assertion.

    I assure you, you fool no one with talk like this.

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  195. Paul,

    Do you really think I care?

    Do you think that evolution posits a direction of unique and unreversed traits?

    I don't have the patience to deal with lying evolutionists Paul.

    Oh well...

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  196. Joe G - actually yes, I think you do care. After all you keep returning to spout your ID/creationist assertions. And while you care, you don't appear to have anything of substance with which to support your assertions.

    Unsurprisingly then, when you are asked to do so, you frequently resort to naysaying and insults.

    Point in case, all you have been asked to do here is to present your methods such that they could be compared with those presented by Zachriel. A simple request. Yet, your response has been "I don't have the patience to deal with lying evolutionists Paul." and "Do you really think that whining like a little baby helps your case?" These are not rational responses if you genuinely believed you had the superior case, or even a case at all.

    It is quite clear that Zachriel has presented a model of mutation and duplication in lineages that produce a pattern of nested hierarchy. It is also clear that you have failed to produce a counter model to support your assertion that such a pattern cannot arise under random mutation. Thus, it is clear in conclusion that you have either failed to understand why Zachriel's model produces a nested hierarchy or you are desparately trying to avoid having to admit that you are wrong.

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  197. Paul:
    It is quite clear that Zachriel has presented a model of mutation and duplication in lineages that produce a pattern of nested hierarchy.

    You don't get it-

    answer the question:

    Do you think that evolution posits a direction of unique and unreversed traits?

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  198. Joe G: Do you think that evolution posits a direction of unique and unreversed traits?

    Nope. Darwin discusses this and other problems with reconstructing phylogeny in Origin of Species. Nest of Letters can be used to explore this question. The length of the genome, the rate of mutation and the number of generations help determine the phylogenetic signal.

    Is the Earth an oblate sphere?

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  199. Do you think that evolution posits a direction of unique and unreversed traits?

    Zachriel:
    Nope.

    There you have it- in order to get a nested hierarchy based on traits you need that unique and unreversed traits.

    Therefor the theory of evolution does not predict such a pattern- which is good because we don't see that pattern in the bulk of the biomass.

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  200. Joe G: in order to get a nested hierarchy based on traits you need that unique and unreversed traits.

    In order to get a perfect nested hierarchy, you need to have unique and unreversed traits. This isn't a new insight, though. Darwin made the same point in Origin of Species. You really need to keep up. Instead, what we have is a strong signal of a nested hierarchy with some noise.

    Let's look at it this way. Here's an example of bifurcating descent, which we discussed before.

    ,,,,,,,,,,,,,,,,,,,,
    ,,,,N,,,,,,,,,,,,,,,
    ,,,,,,,,,,,,,,,,A,,,
    ,,,,,,,,,,,B,,,,A,,,
    ,,,,F,,,,,,,,,,,,,,,
    ,,,,F,,,,,,,,,D,,,,,
    ,,,,F,Z,,,,,,,,,,,,,
    ,,,,F,Z,,K,,,,,,,,,,
    ,,,,,,,C,,,,,,,,,,,,
    ,,,,,,,C,,,,,V,,,,,,
    ,,,,,,,C,,,,,,,T,,,,
    ,,,,,,,C,,,,,,,T,,,V
    ,,,,,J,C,,,,,,,,,,,,
    ,,,,,J,C,,,,,,,,,,,Q
    ,,,,,J,C,,,,,,,,,,G,
    ,,,,,J,C,,,,,,,,,,GX

    Are the traits distributed randomly, or are there patterns? It's highly patterned, of course.

    Here's another one, but with a much smaller sequence length and reduced letters to A-D, which increases the chance of convergence. Notice that the D in B,,D is due to random convergence.

    ,,,,
    ,C,,
    ,,,C
    ,,BC
    ,,,D
    ,E,D
    ,,DD
    ,EDD
    ,,,A
    D,,A
    A,,A
    A,AA
    B,,A
    B,,D
    BD,A
    BA,A

    Nevertheless, we can easily recognize that the results are not random, but highly ordered.

    Oh, and you neglected to answer the other question. Is the Earth an oblate sphere?

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