Tuesday, June 3, 2014

A Clever Spliceosome Mechanism Was Just Reported

And a Massive Violation of Occam’s Razor

In the seventeenth century clocks were a favorite comparison with the complex workings of nature. In the eighteenth century the analogy switched to watches. Now, with the latest crystal structure mapping of the incredible spliceosome machine, which edits newly transcribed gene transcripts, we’re back to clocks. But this time the complexity services evolution rather than design. First for an explanation of the results:

A grandfather clock is, on its surface, a simple yet elegant machine. Tall and stately, its job is to steadily tick away the time. But a look inside reveals a much more intricate dance of parts, from precisely-fitted gears to cable-embraced pulleys and bobbing levers.

Like exploring the inner workings of a clock, a team of University of Wisconsin-Madison researchers is digging into the inner workings of the tiny cellular machines called spliceosomes, which help make all of the proteins our bodies need to function.

The spliceosome is truly an amazing molecular machine. In fact one of the new findings was a clever, unique interlocking mechanism between a protein and RNA in the spliceosome. And what does such complexity suggest to evolutionists?

Could this be a challenge for the theory that cannot even explain how a single protein could have evolved, let alone a massive molecular machine such as the spliceosome?

By no means. In fact, the evolutionists simply concluded that evolution must be even smarter than we thought it was. For such a clever mechanism must mean that protein and RNA have (somehow) evolved together in a much more coordinated fashion than was previously thought:

What's so cool is the degree of co-evolution of RNA and protein. It's obvious RNA and protein had to be pretty close friends already to evolve like this.

Funny how a contradiction is cool. In fact what is cool is the mechanism itself that was discovered. Its hypothetical evolution is what philosophers call a multiplied entity. Evolutionists are constantly adding their unnecessary explanatory mechanisms which add nothing to the science except an unlikely origins narrative.

Mechanisms such as these remind us that biology, like clocks, is full of parts that fit together. That means that both parts are required for the mechanism to work.

That easily contradicts evolution’s blind action, which can’t even reroute a nerve. How could it luckily evolve two parts together? What is needed is a gradual pathway of functional intermediates. Needless to say evolutionists know of no such pathway. That doesn’t mean it doesn’t exist, but it does raise the question of how evolutionists can be so certain that it exists. Particularly when evolution cannot even explain how a single protein could have evolved.

Religion drives science, and it matter.

306 comments:

  1. Cornelius Hunter: How could it luckily evolve two parts together?

    Incredulity is not an argument. There is more than sufficient evidence that irreducibly complex structures can evolve, even if we don't know the specifics of every particular case.

    Your own link points out that "The structure yields clues about the relationship and the relative ages of RNA and proteins."

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    1. Can you point me in the direction of the "more than sufficient evidence that irreducibly complex structures can evolve" please? I have not seen this yet so would be quite interested.

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    2. Dr JDD: Can you point me in the direction of the "more than sufficient evidence that irreducibly complex structures can evolve" please?

      An common example is the mammalian middle ear.

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    3. Zachriel: if something can be reduced to various parts and still show function or confer some small advantage (if at least, neutral adaptation) then by definition it is not "irreducibly complex" surely?

      Perhaps the argument is better structured then that there are systems we observe in biology that we have no evidence that individual components of can provide function or any selective advantage at all without the other respective components also present.

      These are best thought of in the molecular sense rather than gross morphological sense, because the molecular realm (protein, nucleotide) drives the morphology.

      Therefore, when in simple organisms we observe molecular machines consisting of multiple proteinaceous components, and these individual protein components serve no apparent function without the others, we can make an observation that this appears to be an irreducibly complex structure.

      While this is not proof of design or disproof of evolution, if evolution cannot provide a mechanism of how such a molecular machine could arise through known evolutionary mechanisms, then it poses a problem in the theory. The implication then is that if such a problem cannot be overcome at some point in the future, the theory fails as accounting for the OOL from naturalistic means. This is because evolution is a theory cast down as an all encompassing mechanism for biological life.

      While we can argue that because we do not understand how such a particular molecular machine with multiple protein components that are interdependent arose, with increasing evidence of complexity and necessity of varying components comes decreasing likelihood of chance arisal. When we combine this with mathematical models of searching through sequence space and possibilities through chance of a functional sequence with correct protein folds to enable protein-protein interactions that suffice for a functional machine, we must either come to a point of conclusion. Either the chances are conceivable in the time-frame given, or they are not.

      The ~150-protein rich spliceosomal complex is surely one that with its necessities for multiple protein:protein interactions and its function in a critical stage of cell survival and replication make the case for Darwinism much weaker.

      This is not a god of the gaps argument, it is a critical assessment of a proposed mechanism for OOL.

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    4. Dr JDD: if something can be reduced to various parts and still show function or confer some small advantage (if at least, neutral adaptation) then by definition it is not "irreducibly complex" surely?

      Actually, that is the definition of irreducibly complex. It can't be reduced further and still have function.

      Dr JDD: These are best thought of in the molecular sense rather than gross morphological sense, because the molecular realm (protein, nucleotide) drives the morphology.

      If the claim is that irreducibly complex structures *can't* evolve, then any example is a counterexample.

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    5. Zachriel: Perhaps I should define what I mean as irreducibly complex. I believe there are 2 meanings.

      1) Irreducibly complex for a specified function
      2) Irrudecibly complex for any function

      It is definition #2 I am getting at, which perhaps is different to most. In the inner ear formation there are functional parts that have function apart from trapping sound wave vibrations for noise, and then apparently gain function for that. I say apparent because functional steps in between do not prove one arose from the other. I would not consider that definition #2 of irreducibly complex.

      What I would consider #2 definition is for example, a molecular machine where >10 protein or nucleotide components are necessary for function of a machinery mechanism, yet if you remove any of those components it fails to work. Further, if you separate out those components, the individual proteins do not have roles (function) separate to the macromolecular complex function.

      Thus what we would expect to see for macromolecular complexes of specific functionality where each component is necessary, would be lower organisms have less of the components than higher ones, and a progression in complexity.

      Now we do see that for many things, not as simply as that, but broadly. But there are plenty of instances where we do NOT observe that. Therefore those are truly irreducibly complex - you need all the components (many), and individually those components are non-functional and offer no advantage.

      Many scientists have competently shown how long it takes for the arisal of just a few amino acid changes to confer a new protein fold, for example. Yet such a complex structure would require many of these, simultanseously because the individual components do not confer advantage so would not be selected for unless all are present.

      It only takes one molecular machine that satisfies the above criteria to place the times and available sequence space for mutation and fixation to an unsurmountable level to cause rejection of the evolutionary theory to fully explain the OOL. That is what people forget - just one single complexity that cannot be explained by evolutionary mechanisms means no longer is it an all-encompassing theory of OOL and therefore cannot fully explain the biology of life as it claims to.

      I would argue given the calculations of the likes of Douglas Axe, Michael Behe and even naturalistic evolutionists in order to generate the coordinated mutations needed just to get 1 quite different protein, that there are many examples of complex molecular machinery that cast severe doubt over the capabilities of Darwinistic mechanisms to explain their existance.

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    6. Dr JDD: In the inner ear formation there are functional parts that have function apart from trapping sound wave vibrations for noise, and then apparently gain function for that.

      In a modern mammal, if you remove any of the ossicles, the middle ear no longer functions.

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    7. Zacheriel: Thanks for that. So are there examples throughout the fossil record/in the natural world where we see lack of ossicles, and other parts associated with the middle ear that serve no other function without the ossicles? Is that in the record? Can you please point me to such a mammal/finding if so? Thanks.

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    8. Dr JDD: So are there examples throughout the fossil record/in the natural world where we see lack of ossicles, and other parts associated with the middle ear that serve no other function without the ossicles?

      Today they are only functional as an irreducibly complex structure, that is, they meet your definition of "irreducibly complex for any function".

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    9. But you do not have stages in the fossil record where you see lack of say one or two functional parts of this system, with other parts present that offer no function? Thus you are making an extrapolation and an inference from othe similar functional yet less complex structures, that they changed to give new more complex and functional ones? No actual demonstratable stages of that? Then it is a mere inference and assumption, and it does not fit my definition #2 of irreducible complex system that has been shown to evolve from its constituent parts (that lacked function on their own).

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    10. Dr JDD: But you do not have stages in the fossil record where you see lack of say one or two functional parts of this system, with other parts present that offer no function?

      That's correct.

      Dr JDD: Thus you are making an extrapolation and an inference from othe similar functional yet less complex structures, that they changed to give new more complex and functional ones?

      That's correct.

      Dr JDD: No actual demonstratable stages of that?

      Actual demonstrable states.

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    11. There isn't any evidence that unguided evolution produced the mammalian inner ear. Zachriel doesn't know how many mutations it took nor what genes were involved. IOW there isn't any science behind the claim

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    12. There isn't any "evidence" or science?

      You'll need to unpack that, Joe.

      For example what is your explanation for how science works, in practice? What is the role that evidence plays, in science? Please be specific.

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  2. Likewise, credulity is not an argument. There is more than sufficient evidence that the (darwinian/random with respect to need) evolution of complex structures is implausible. Not impossible, mind you. But implausible.

    And thats what we are in the business of accessing: the plausibility of an explanation, not its possibility. (Darwinian/random with respect to need) evolution is a highly implausible scenario for the development of life.

    The best plausibility claim (darwinian/random with respect to need) evolution can make is for variation of what already exists. IOW, plausibly explaining 1%, meh maybe 2% of biology.

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    1. Steve: Likewise, credulity is not an argument.

      Quite so, but as we pointed out, there is substantial evidence that irreducibly complex structures can evolve.

      Steve: There is more than sufficient evidence that the (darwinian/random with respect to need) evolution of complex structures is implausible.

      And that evidence? Any idea why generations of biologists haven't reached your conclusion?

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    2. Any idea why those alleged generations of biologists cannot find support for unguided evolution? And no, there isn't any evidence that unguided evolution can produce irreducibly complex structures. Zachriel is all bluff and bluster.

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  3. Dr Hunter,

    That easily contradicts evolution’s blind action, which can’t even reroute a nerve.


    Perhaps, but likewise neither could the " designer" then.

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  4. Zach:

    Has anyone ever actually scene the evolution of a irreducibly complex system or structure? In our experience working with machines and such we find that it is really hard to make things that are irreducibly complex without intelligent input,

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    1. natschuster: Has anyone ever actually scene the evolution of a irreducibly complex system or structure?

      While evolution of complex features normally takes much too long for direct observation, we have evidence that such structures have evolved (e.g. mammalian middle ear), as well as theoretical support for how such a process may occur.

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    2. How do you know that the mammalian inner ear evolved via Darwinian process. Maybe it was intelligently guided evolution?

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    3. natschuster: Maybe it was intelligently guided evolution?

      So, let's make sure we understand your position. Are you agreeing that the mammalian middle ear evolved (and by extension, common descent and adaptation), but you are just disagreeing with the mechanism?

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    4. I'm agreeing that there was change over time. how it happened. I can't say. I wasn't there when it happened. The explanation that fits the actual record best is a series of separate creations. My point is that you can't conclude that intelligence was not involved.

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    5. natschuster: The explanation that fits the actual record best is a series of separate creations.

      Every species in the fossil record? Every beetle? Why is there such an obvious succession, and why do they form a nested hierarchy?

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    6. Nat,

      The explanation that fits the actual record best is a series of separate creations. My point is that you can't conclude that intelligence was not involved


      Without a how it does not seem very explanatory, isn't that your problem with the ToE, the how. What mechanisms do you propose?

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    7. Zach:

      I was only talking about the series of proto-mammals, but I guess it applies to the whole fossil record. And there are so many because a designer would stick with a design that works, There is an obvious succession just like in the evolution of technology. And I'm not sure how different the nested hierarchy in life is from artifacts.

      Vel:

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    8. natschuster: There is an obvious succession just like in the evolution of technology.

      Technology does evolve in its fashion, but artifacts don't form a distinct nested hierarchy.

      natschuster: And I'm not sure how different the nested hierarchy in life is from artifacts.

      When we group by traits, nearly all organisms *objectively* form a specific nested hierarchy. Artifacts do not. Consider that we can categorize books in many different, equally rational ways, Dewey Decimal, Library of Congress, or just plain alphabetical.

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    9. Nat:

      I was only talking about the series of proto-mammals,


      How does a proto- mammal become a present day mammal?

      And there are so many because a designer would stick with a design that works

      Not in human design, designers are constantly experimenting with new designs,

      There is an obvious succession just like in the evolution of technology.

      Technology evolves because of an increase in knowledge, is life on earth the result of the designer learning on the job as well?

      And I'm not sure how different the nested hierarchy in life is from artifacts.

      Perhaps you could do a quick nested hierarchy of iPods to find out

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    10. If one includes all of the alleged transitionals then life would not form an objective nested hierarchy. Geez evolutionists are the most dishonest people there are. Period. Zachriel is particularly dishonest- why bother Zach? Everyone knows that you are deluded.

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  5. Per Darwinists, every fact is conformable to evolution. This renders the theory unfalsifiable, and, so, completely irrelevant; i.e., trivial.

    In physics or math, a polynomial equation with zeros for all of its coefficients, which adds up to zero, is considered to be an independent equation, and can be used to solve ANY equation where the independent equation is substituted in as the value of the variable. This is usually called the trivial solution. Only non-trivial solutions are of interest.

    But, I really shouldn't be this hard on Darwinism because, for example, if they were to find a cell whose chromosomes flashed out, non-stop, the words "Darwin was wrong," then, and perhaps only then, would they give up on their hero's completely out-dated, and incoherent, theory.

    Speaking of the theory's incoherence, here's a question for our Darwinist friends: in the only diagram that shows up in the entirety of the Origin of Species we find that it shows "species" along the bottom, and "genera" (as kinds of 'bundles' of species) at the top.

    Now, if we were to begin a new diagram with "genera" at the bottom, logically, we would end up with "families" 'bundled' at the top, and so forth. Darwin acknowledges this in his text. However, when talking about it in his text, he stops the progression at the level of "classes". That is, when you start with a 'diagram' with "orders" at the bottom and end with "classes" 'bundled' at the top, you're then forced to stop right there. Why? What's the logic?

    But there is no logic for the cessation. Certainly none is given by Darwin. Instead, there are only problems. And Darwin, surely knowing of the problems associated with his proposed progression, but, it seems, unwilling to face them, simply stops there.

    Well, the logical continuation would have you begin with "classes" at the bottom and end with "phyla" at the top. With this the incoherence and foolishness of his proposal begins to appear since it is impossible to "evolve" body-plans ("phyla") without the "body-plans" already existing.
    [BTW: This is tantamount to presuming that 'life has begun'---thus avoiding the OOL dilemna---and then going from there to say that by "little steps" life begins to evolve.]

    And, to make matters worse, the final 'diagram' would have "phyla" at the bottom, and "kingdoms" at the top. Now, since there are more "species" at the bottom of Darwin's 'diagram' than at the top, this would mean there would be more "kingdoms" than "phyla", and more "phyla" than "classes," which is, of course, incomprehensible and incoherent.

    This is, of course, to the attentive reader, the problem that Stephen Meyer points to in Darwin's Doubt, and is there identified as the "top-down" phylogenetic tree inferred from Darwinism instead of the "bottom-up" phylogenetic tree we should expect evolved life to produce.

    This is nothing but bald-faced incoherence on Darwin's part, and something that he was not, I would submit, intellectually honest enough to recognize and admit. And we've been forced to live with the nonsense ever since.

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    1. Lino Di Ischia: Per Darwinists, every fact is conformable to evolution.

      That is incorrect. For instance, if were to invert the fossil succession, it would contradict the Theory of Evolution.

      Lino Di Ischia: Speaking of the theory's incoherence, here's a question for our Darwinist friends: in the only diagram that shows up in the entirety of the Origin of Species we find that it shows "species" along the bottom, and "genera" (as kinds of 'bundles' of species) at the top.

      Actually, it's the ancestor of the genus at the bottom, and species at every level.

      Lino Di Ischia: it is impossible to "evolve" body-plans ("phyla") without the "body-plans" already existing.

      Why is that?

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    2. Zachriel

      Lino Di Ischia: Per Darwinists, every fact is conformable to evolution.

      "That is incorrect. For instance, if were to invert the fossil succession, it would contradict the Theory of Evolution."

      And I suppose you're going to say evolutionists would not spin that inversion in favour of evolution. Let's at least try to be honest here, Zachriel.

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    3. Nic,
      And I suppose you're going to say evolutionists would not spin that inversion in favour of evolution. Let's at least try to be honest here, Zachriel.


      Any examples of something that would contradict your theory?

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    4. Nic: And I suppose you're going to say evolutionists would not spin that inversion in favour of evolution.

      Nothing in the modern Theory of Evolution could possibly explain that result. It's like a rabbit in the Precambrian. All sorts of things would contradict the Theory of Evolution.

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    5. Zachriel,

      "Any examples of something that would contradict your theory?"

      Demonstrating life arising spontaneously from non-life might be a good place to start. Care to make an attempt?

      "Nothing in the modern Theory of Evolution could possibly explain that result. It's like a rabbit in the Precambrian. All sorts of things would contradict the Theory of Evolution."

      It's just that nothing has so far, right?

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    6. Philosopher Peter Godfrey-Smith doubted that a single set of anachronistic fossils, however, even rabbits in the Precambrian, would disprove the theory of evolution outright. The first question raised by the assertion of such a discovery would be whether the alleged "Precambrian rabbits" really were fossilized rabbits. Alternative interpretations might include incorrect identification of the "fossils", incorrect dating of the rocks, and a hoax such as the Piltdown Man was shown to be. Even if the "Precambrian rabbits" turned out to be genuine, they would not instantly refute the theory of evolution, because that theory is a large package of ideas, including: that life on Earth has evolved over billions of years; that this evolution is driven by certain mechanisms; and that these mechanisms have produced a specific "family tree" that defines the relationships among species and the order in which they appeared. Hence, "Precambrian rabbits" would prove that there were one or more serious errors somewhere in this package, and the next task would be to identify those errors.[2]

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    7. Nic: Demonstrating life arising spontaneously from non-life might be a good place to start.

      Were you asking this of velikovskys? In any case, there's no workable theory of abiogenesis at this point.

      Nic: It's just that nothing has so far, right?

      That's correct, depending on how tightly you constrain what is meant by the Theory of Evolution. A theory is an amalgam of different claims, and one or another may be falsified or modified. So we have Darwin's original theory, Neodarwinism, Neutral Theory, Endosymbiotic Theory, all under the rubric of the Theory of Evolution as most of the postulates of Darwin's original theory remain intact.

      Blas: Philosopher Peter Godfrey-Smith doubted that a single set of anachronistic fossils, however, even rabbits in the Precambrian, would disprove the theory of evolution outright.

      What you mean is purported discovery of a rabbit in the Precambrian.

      Blas: The first question raised by the assertion of such a discovery would be whether the alleged "Precambrian rabbits" really were fossilized rabbits.

      So not a rabbit in the Precambrian.

      Blas: Alternative interpretations might include incorrect identification of the "fossils", incorrect dating of the rocks, and a hoax such as the Piltdown Man was shown to be.

      So not a rabbit in the Precambrian.

      Blas: Even if the "Precambrian rabbits" turned out to be genuine ... Hence, "Precambrian rabbits" would prove that there were one or more serious errors somewhere in this package, and the next task would be to identify those errors.

      The Theory of Evolution would be severely tested, and would be very unlikely to survive such a confirmed find. However, you are correct that the discovery of a single piece of purported evidence would not be sufficient to counter the huge bulk of other evidence. That, however, is not the same as saying that the Theory of Evolution is consistent with any evidence whatsoever, which was the claim.

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    8. By the way, let us know when you find such evidence.

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    9. Blas is correct, most view evolutionary theory as unfalsifiable, whether admitted to or not.

      As published originally by Vreeland, a 250 MYA bacterium showed very high sequence identity (99%) with its modern counterpart:
      http://mbe.oxfordjournals.org/content/19/9/1637.long
      Yet replies to this gave one of the main reasons this should be rejected as:
      " If Bacillus strain 2-9-3 is ancient, then a significantly shorter genetic distance to the outgroup is expected as compared to its contemporary relatives, as the latter should have an additional 250 m.y. to accumulate substitutions. Although mutation rates are not always similar across organisms, it is striking that not a single claim of geologically ancient DNA, including that of Bacillus strain 2-9-3, has passed the rate test so far, strongly suggesting that contamination is involved (Hebsgaard et al., 2005)."
      http://geology.gsapubs.org/content/33/1/e93.1.full

      So you see, because it does not fit with evolutionary expectations it is rejected. Those authors did however, give 3 reasons why they believe it was not a genuine 250 MYA organism. However the original authors did reply to this comment quite confidently addressing that initial response to their published work:
      http://geology.gsapubs.org/content/33/1/e93.2.full

      Note what they say regarding this: "Relative rate tests, which suggest that Virgibacillus strain 2-9-3 is not geologically ancient, are based on the assumption that evolution follows a predictable mutation rate and that the rate is known. The rates being used by the researchers cited are based on nucleotide substitutions in laboratory-grown bacteria, which may not be realistic for all organisms. Furthermore, growth rates of microorganisms in nature may, in some cases, be measured on time scales of centuries or longer, as illustrated by Parkes et al. (2000) for bacteria isolated from subseafloor sediments. Such long generation times might explain the similarities in 16S ribosomal DNA of Virgibacillus strain 2-9-3 and its contemporary relatives (Maughan et al., 2002)."

      However the point remains - if something 250 MYA remains so strikingly similar to a modern day version, the automatic response seemed to reject based almost purely on that finding. Why? Because it disagrees with what is non-falsifiable in evolution, gradual change over time must happen, especially if that time is 1/16th of the whole time that life has apparently been on this planet.

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    10. Dr JDD: However the point remains - if something 250 MYA remains so strikingly similar to a modern day version, the automatic response seemed to reject based almost purely on that finding. Why?

      The criticisms of Vreeland are substantial and well-supported. It is more likely that Vreeland's results are in error than the huge volume of other evidence that it contradicts.

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    11. Zachriel you have just proved the point.

      The point being, if a rabbit was found in the Pre-Cambrian it would be rejected because it was a rabbit in the pre-Cambrian and the result must be in error given the "huge volume of other evidence it contradicts."

      Therefore your statement that a "rabbit in the Pre-Cambrian would falsify evolution" is invalid, false, and a misnomer, as alluded to by Blas above. You would reject it despite how vigorous or attentive the researchers were, because in your opinion it must be in error as it contradicts so much other evidence.

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    12. Dr JDD: The point being, if a rabbit was found in the Pre-Cambrian it would be rejected because it was a rabbit in the pre-Cambrian and the result must be in error given the "huge volume of other evidence it contradicts."

      A purported find is not the same as an actual find. Any purported find would certainly be subject to scrutiny.

      Dr JDD: Therefore your statement that a "rabbit in the Pre-Cambrian would falsify evolution" is invalid, false, and a misnomer, as alluded to by Blas above.

      You are confusing a purported find with an actual demonstration of a rabbit in the Precambrian.
      I
      If someone said they had evidence they could transmit information faster than light, it would violate Relativity, but merely reporting that one has evidence, and actually confirming the fact are not the same thing.
      http://newsfeed.time.com/2012/02/22/einstein-was-right-all-along-faster-than-light-neutrino-was-product-of-error/

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    13. Zachriel - it was confirmed by the scientific method that the organism was 250 MYA. The rejection is not the scientific method, the rejection is based upon not fitting in with other evidence which is my point that you fail to grasp. I.e. it is unfalsifiable.

      Please show me evidence that points to the 250MYA being the result of contamination separate to what they responded to in the response I posted above?

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    14. Dr JDD: it was confirmed by the scientific method that the organism was 250 MYA.

      So was faster than light neutrinos.

      The way to resolve the issue is by developing independent lines of evidence supporting the original finding.

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    15. Zachriel,

      Nic: It's just that nothing has so far, right?

      Zachriel: "That's correct, depending on how tightly you constrain what is meant by the Theory of Evolution. A theory is an amalgam of different claims, and one or another may be falsified or modified. So we have Darwin's original theory, Neodarwinism, Neutral Theory, Endosymbiotic Theory, all under the rubric of the Theory of Evolution as most of the postulates of Darwin's original theory remain intact."

      So how does this statement differ from the statement which claims all findings are simply spun to affirm the truth of evolution? Your statement may be more verbose, but the conclusion is the same. Whatever is discovered, it confirms evolution.

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    16. Nic: So how does this statement differ from the statement which claims all findings are simply spun to affirm the truth of evolution?

      If the evidence contradicts a theory, the theory is either modified or discarded. That's not spin, that's how science works.

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    17. Zachriel,

      "If the evidence contradicts a theory, the theory is either modified or discarded. That's not spin, that's how science works."

      Ever hear the story of the guy who refused to throw out an axe because it used to belong to his beloved grandfather? He used it often over the years since his grandfather died and had over that time replaced the head twice and bought three new handles. Such is the theory of evolution.

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    18. Nic: Ever hear the story of the guy who refused to throw out an axe because it used to belong to his beloved grandfather?

      It's a semantic question whether you call it the same axe or a different axe.

      The Theory of Evolution still includes the most important components of Darwin's original theory, including common descent and natural selection as the primary engine of adaptation.

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    19. Zachriel,

      "Were you asking this of velikovskys?"

      Yep, sorry.


      "In any case, there's no workable theory of abiogenesis at this point."

      But one will eventually arise, right? After all, it's inevitable because as we all know, evolution is a fact.

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    20. Zachriel,

      "It's a semantic question whether you call it the same axe or a different axe."

      You're completely missing the point. The point is not whether or not it is the same axe, obviously it is not. The point is the guy refuses to accept the fact it is not.

      In the same way evolutionists refuse to accept the facts which counter the theory of evolution and simply modify all contrary evidence in some manner which will allow them to continue to believe it is the same 'axe'.

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    21. Nic: But one will eventually arise, right?

      It's amazing humans have learned so much already. Imagine knowing the contents of stars without having to actually take a sample. In any case, there is no guarantee that science will be able to solve the origin of life. We're rooting for the humans!

      Nic: After all, it's inevitable because as we all know, evolution is a fact.

      Not sure that the issues are directly linked. If replicators appeared slowly, then perhaps evolution was part of the process. On the other hand, if life suddenly appeared for one reason or another (perhaps seeded by a Comic Gardener), then there would no transition: evolution would proceed apace.

      Nic: The point is not whether or not it is the same axe, obviously it is not.

      All your body's molecules have been replaced one-by-one over time. Is your body not the same body you had before? When did it become a new body? When 50% was replaced? When 90% was replaced?

      Nic: allow them to continue to believe it is the same 'axe'.

      Again, it's a semantic distinction. Theories are often an amalgam of claims, some more strongly supported than others. The biological Theory of Evolution even includes an historical aspect. As such, the theory is in a constant state of change, as various hypotheses compete to explain the evidence. Nevertheless, the basic principles of Darwin's original theory are still part of the modern theory, including common descent, and natural selection as a mechanism of adaptation.

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    22. Heh. That should be Cosmic Gardener. Or maybe it was right the first time.

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    23. Nic: In the same way evolutionists refuse to accept the facts which counter the theory of evolution and simply modify all contrary evidence in some manner which will allow them to continue to believe it is the same 'axe'.

      Are you suggesting that non ad-hoc modifications are problems for theories? If so, why?

      By non ad-hoc, I mean conjecturing testable theories as to why observations themselves might be wrong, rather than the underlying explanation behind the theory itself.

      For example, this is what happened in the CERN OPERA experiment that Zachriel referenced earlier.

      Or are you suggesting that wasn't scientific?

      Delete
    24. Zachriel,

      "It's amazing humans have learned so much already. Imagine knowing the contents of stars without having to actually take a sample. In any case, there is no guarantee that science will be able to solve the origin of life. We're rooting for the humans!"

      True, science may never know the origin of life, but it does know for sure it was not created by an intelligence, right?

      As for the content of stars and the origin of life, on what planet are those two questions scientifically related?

      "On the other hand, if life suddenly appeared for one reason or another (perhaps seeded by a Comic Gardener), then there would no transition: evolution would proceed apace."

      Not an answer. You're only pushing the problem into the corner and hoping no one sees it there.

      "All your body's molecules have been replaced one-by-one over time. Is your body not the same body you had before? When did it become a new body? When 50% was replaced? When 90% was replaced?"

      You're equivocating. Replication is not the same as replacing, The axe head did not replicate itself, it was a completely different set of axe head DNA. And no, the body I have now is not the body I had in my twenties. No points there.

      "Again, it's a semantic distinction. Theories are often an amalgam of claims, some more strongly supported than others. The biological Theory of Evolution even includes an historical aspect. As such, the theory is in a constant state of change, as various hypotheses compete to explain the evidence. Nevertheless, the basic principles of Darwin's original theory are still part of the modern theory, including common descent, and natural selection as a mechanism of adaptation."

      More verbosity stating the same thing as before, evolution cannot be found false as everything is made to fit the paradigm.

      Delete
    25. Nic: True, science may never know the origin of life, but it does know for sure it was not created by an intelligence, right?

      Nothing is known with certainty, but there is evidence that life originated through natural processes on Earth.

      Nic: As for the content of stars and the origin of life, on what planet are those two questions scientifically related?

      They're only related in the sense that understanding the composition of stars seemed impossible, that is, until humans figured it out. Abiogenesis seems intractable, it happened so long ago, and left so few traces. But you can't say humans will never figure it out. Perhaps when they explore the stars.

      Nic: You're only pushing the problem into the corner and hoping no one sees it there.

      Your claim was that a theory of abiogenesis is inevitable because evolution is strongly supported. That doesn't follow. The causes may be completely different, or there may be a transitional phase. No one knows.

      Nic: Replication is not the same as replacing,

      We weren't talking about replication, but that virtually every molecule in your body has been replaced. The canonical example is the Ship of Theseus.

      Nic: And no, the body I have now is not the body I had in my twenties. No points there.

      As we said, it's semantics, so there's no right answer. Many people would say your body grew old, not that it was a different body.

      Nic: evolution cannot be found false as everything is made to fit the paradigm.

      Of course evolution can be falsified. Not sure why you keep saying otherwise. For instance, if we show that birds descended from therapods, rather than some other branch of archosaurs, this changes the Theory of Evolution. We might say it falsifies a particular version of the Theory of Evolution. But we have replaced it with a new and improved version of the Theory of Evolution. Similarly with neutral theory or punctuated equilibrium or endosymbiotic theory.

      Now let's say we can show that all the various 'kinds' don't have common ancestry, then there would be no viable replacement evolutionary theory. It would require an entirely new theory; the Cosmic Gardener, or frogs from mud, or something.

      Delete
    26. Zachriel,

      "Nothing is known with certainty,..."

      Are you certain?

      "but there is evidence that life originated through natural processes on Earth."

      And that evidence would be?

      "Abiogenesis seems intractable, it happened so long ago, and left so few traces. But you can't say humans will never figure it out. Perhaps when they explore the stars."

      As it is not known that abiogenesis occurred at all, as such it certainly is not known that it happened so long ago, and that is therefore the reason it is so intractable. . Do you not comprehend the fallacious nature of this argument?

      "Your claim was that a theory of abiogenesis is inevitable because evolution is strongly supported."

      What ever gave you that idea?

      "We weren't talking about replication,..."

      You were.

      "Of course evolution can be falsified."

      I know it can, and it has been, long ago.

      "But we have replaced it with a new and improved version of the Theory of Evolution."

      And I suppose you typed that sentence with a straight face?

      Delete
    27. Nic: Are you certain?

      Reasonably so.

      Nic: And that evidence would be?

      The discovery that all of life's processes are chemical in nature, that all life shares a common ancestry, that life appeared on Earth shortly after liquid water formed, that chemicals can act as catalysts and information carriers, that membranes can spontaneously form and divide.
      http://molbio.mgh.harvard.edu/szostakweb/

      Without a greater understanding of the process, though, there is still some uncertainty.

      Nic: As it is not known that abiogenesis occurred at all, as such it certainly is not known that it happened so long ago, and that is therefore the reason it is so intractable.

      Let's put it this way, the first life on Earth appeared long ago.

      Zachriel: Your claim was that a theory of abiogenesis is inevitable because evolution is strongly supported.

      Nic: What ever gave you that idea?

      Z: In any case, there's no workable theory of abiogenesis at this point.

      N: But one will eventually arise, right? After all, it's inevitable because as we all know, evolution is a fact.

      Just because evolution is strongly supported doesn't mean we'll ever have a theory of abiogenesis.

      Nic: You were.

      No we were not. We were talking about replacement of molecules, the Ship of Theseus.

      Nic: I know it can {be falsified}, and it has been, long ago.

      Interesting that biologists are unaware of this falsification. What is that falsification?

      Nic: And I suppose you typed that sentence with a straight face?

      (Not sure why you went from having a reasonable discussion to handwaving, but whatever.) We provided an example of how one aspect or another of a theory may be modified while leaving the overall theory intact.

      Delete
    28. How life evolved depends on how it arose. If materialistic processes produced life then we can infer it produced the diversity. OTOH if the OoL was designed then we infer the diversity also arose by design.

      Also there still isn't any evidence that natural selection can produce adaptions. So that would be an issue.

      Delete
    29. Joe G: How life evolved depends on how it arose.

      The Theory of Evolution, including common descent, is strongly supported regardless of life's origin.

      Delete
    30. Zachriel:
      The Theory of Evolution, including common descent, is strongly supported regardless of life's origin.

      That is your opinion and only an opinion. Universal common descent cannot be tested so how can it be supported?

      Delete
    31. BTW there still isn't any support for Darwin's claim that natural selection is a designer mimic.

      Delete
    32. Joe G: Universal common descent cannot be tested so how can it be supported?

      Common Descent is a tree topology, so is predicted to leave a specific pattern. When we group the leaves of the tree (extant species) in the most parsimonious way, they will naturally group together such that each subset is contained within a superset. Furthermore, the branching process will occur over time. Based on this, we might be able to discover transitional organisms, those that exhibit both primitive and derived traits of the group in question.

      Delete
    33. People can make tree patterns out of just about anything. The Army is a tree pattern. It also has subsets contained within supersets. And guess what? It was designed that way

      You have no idea what makes an organism what it is. And that means you have no way to test your claim

      Delete
    34. Joe G: People can make tree patterns out of just about anything.

      However, when we group artifacts, they don't naturally group together such that each subset is contained within a superset.

      Delete
    35. If one includes all of the alleged organisms that ever lived they could not be grouped together in subsets and supersets. You lose.

      Delete
    36. Joe G: If one includes all of the alleged organisms that ever lived they could not be grouped together in subsets and supersets.

      We said, "When we group the leaves of the tree (extant species) in the most parsimonious way, they will naturally group together such that each subset is contained within a superset." And that is what we observe.

      Delete
    37. If we cherry-picked artifacts, as you do with organisms, we could get them to fit an objective nested hierarchy.

      Delete
    38. Joe G: If we cherry-picked artifacts, as you do with organisms, we could get them to fit an objective nested hierarchy.

      If you cherry-pick artifacts, that is correct. However, with extant organisms you don't have to cherry-pick. The vast majority naturally group together such that each subset is contained within a superset.

      Delete
    39. Zachriel:
      When we group the leaves of the tree (extant species) in the most parsimonious way, they will naturally group together such that each subset is contained within a superset."

      That isn't a prediction of unguided evolution. And it has nothing to do with universal common descent.

      Delete
    40. Joe G: That isn't a prediction of unguided evolution.

      It's a prediction of common descent. See Darwin 1859.

      Delete
    41. Choosing only extant organisms is cherry-picking. Obviously you don't know what you are talking about.

      Delete
    42. No Zachriel. Darwin never said anything about nested hierarchies nor having extant organisms for one. You are sadly mistaken.

      Delete
    43. The Army is a tree pattern. It also has subsets contained within supersets. And guess what? It was designed that way

      You have no idea what makes an organism what it is. And that means you have no way to test your claim.

      Delete
    44. Joe G: Choosing only extant organisms is cherry-picking.

      It's the prediction from theory.

      Joe G: Darwin never said anything about nested hierarchies nor having extant organisms for one.

      We're not discussing your notion of nested hierarchies, but whether extant organisms naturally group such that each subset is contained within a superset.

      Delete
    45. Choosing only extant organisms is cherry-picking.

      Zachriel:
      It's the prediction from theory.

      Cherry-picking is a prediction of the theory? Are you mad?

      Darwin never said anything about nested hierarchies nor having extant organisms for one.

      We're not discussing your notion of nested hierarchies

      My notion is fully supported by peer-review. IOW it isn't my notion. It is the only notion that counts.

      OTOH you have no idea what a nested hierarchy entails.

      but whether extant organisms naturally group such that each subset is contained within a superset.

      That is Linnean taxonomy which gas nothing to do with common descent.

      Delete
    46. typo alert:

      That is Linnean taxonomy which has nothing to do with common descent.

      Delete
    47. Joe G: Cherry-picking is a prediction of the theory?

      It's not cherry-picking to look at all the leaves on a tree.

      Joe G: My notion is fully supported by peer-review.

      We're not concerned with your notions. We're discussing a specific pattern, a grouping such that each subset is contained within a superset.

      Joe G: That is Linnean taxonomy which gas nothing to do with common descent.

      Common descent provides a parsimonious explanation of Linnaean taxonomy, and makes specific empirical predictions.

      Delete
    48. OK so Zachriel concedes the point that design can indeed produce a nested hierarchy as evidenced by the structure of the US Army.

      Delete
    49. Zachriel:
      It's not cherry-picking to look at all the leaves on a tree.

      Of course it is as you are leaving out all of the other organisms that make up the twigs, branches and trunk,

      We're not concerned with your notions.

      It isn't my notion. And I have supported my claims and you haven't. Go figure.

      We're discussing a specific pattern, a grouping such that each subset is contained within a superset.

      In what way are they subsets contained within a superset?

      Common descent provides a parsimonious explanation of Linnaean taxonomy,

      That is your opinion and an opinion only.

      and makes specific empirical predictions.

      And more opinion. Where's the science?

      Delete
    50. Joe G: Zachriel concedes the point that design can indeed produce a nested hierarchy as evidenced by the structure of the US Army.

      Army formations are grouped such that each subset is contained within a superset. That's a single artifact.

      However, when classifying an array of artifacts, they generally do not naturally group such that each subset is contained within a superset.

      Delete
    51. BTW Zachriel, no one cares about your notion of nested hierarchies.

      Delete
    52. ZAchriel:
      Army formations are grouped such that each subset is contained within a superset.

      Just as I said.

      However, when classifying an array of artifacts, they generally do not naturally group such that each subset is contained within a superset.

      It all depends on the artifacts. And if we use all organisms then common descent does not produce an objective nested hierarchy.

      Delete
    53. Joe G: Of course it is as you are leaving out all of the other organisms that make up the twigs, branches and trunk

      We're discussing the leaves on the tree, and how they naturally group.

      Joe G: It isn't my notion.

      We're discussing a specific pattern such that each subset is contained within a superset.

      Joe G: In what way are they subsets contained within a superset?

      Are you referring to the pattern, or the taxonomy? The pattern is defined as subsets contained within supersets. The taxonomy refers to how we group organisms according to trait.

      Joe G: That is your opinion and an opinion only.

      It's not merely an opinion, but a direct deduction from the postulate of common descent.

      Joe G: Where's the science?

      The science occurs when you test those predictions.

      Delete
    54. Joe G: It all depends on the artifacts.

      Try vehicles. Or artwork. Or containers. Or buildings. Or all of them!

      Delete
    55. A family tree is an example of descent with modification, ie common descent, yet it does NOT form a nested hierarchy.

      We're discussing the leaves on the tree, and how they naturally group.

      What criteria are using to "group them naturally"?

      We're discussing a specific pattern such that each subset is contained within a superset.

      With nested hierarchies there are specific definitions for each set.

      It's not merely an opinion, but a direct deduction from the postulate of common descent.

      And yet we would not observe one if we included every organism that allegedly existed. And we do not observe one with family trees. IOW you pulled that deduction from your arse, as usual.

      BTW, vehicles have been done in "Evolution: A Theory in Crisis". The over-riding superset would be "Transportation", from there you have air, land, water and any hybrids.

      Buildings you would go by the materials used. Geez Zach, it isn't that difficult. Nested hierarchies are purely an man-made construct, after all.

      Delete
    56. Correction- buildings would be type of structure, and then materials, architecture (framing), etc.

      Delete
    57. But anyway, whether or not evolution is guided or unguided depends on whether or not the OoL was guided or unguided. How life originated determines how it evolved.

      Delete
    58. Joe G: A family tree is an example of descent with modification, ie common descent, yet it does NOT form a nested hierarchy.

      We're discussing a specific pattern such that each subset is contained within a superset. However, human family trees do not form this pattern as there is extensive crossings.

      Joe G: What criteria are using to "group them naturally"?

      Traits. For instance, of cats, dogs and frogs, cat and dogs have more traits in common, and few differences, so we would have {frog, {cat, dog}}.

      Joe G: And yet we would not observe one if we included every organism that allegedly existed.

      One what? A set pattern such that each subset is contained within a superset?

      If we group each organism with all of its descendants (forming clades), then yes, we would have a set pattern such that each subset is contained within its superset. That's due to the tree-like structure. The obvious deduction is that the traits of the leaves, given descent with modification, would naturally group together such that each subset is contained within a superset. The set patterns would closely match.

      Joe G: BTW, vehicles have been done in "Evolution: A Theory in Crisis". The over-riding superset would be "Transportation", from there you have air, land, water and any hybrids.

      Keep going. What comes next in your taxonomy of vehicles?

      Joe G: buildings would be type of structure, and then materials, architecture (framing), etc.

      What do you mean by "type of structure"? Do you mean the use of the structure?

      Delete
    59. We're discussing a specific pattern such that each subset is contained within a superset.

      Actually you were trying to say that common descent produces such a pattern. Obviously it doesn't

      For instance, of cats, dogs and frogs, cat and dogs have more traits in common,

      Due to a common design.

      A set pattern such that each subset is contained within a superset?

      Gone if all alleged transitionals were included.

      If we group each organism with all of its descendants (forming clades), then yes, we would have a set pattern such that each subset is contained within its superset.

      A family tree forms a clade. Yet it does not form a nested hierarchy.

      Keep going. What comes next in your taxonomy of vehicles?

      Figure it out for yourself or pay me. I don't work for free.

      Delete
    60. Joe G: Actually you were trying to say that common descent produces such a pattern. Obviously it doesn't

      Of course it does. Consider a simple case:

      Big --> BigGreen, BigRed

      BigGreen --> BigGreenHairy, BigGreenBald
      BigRed --> BigRedDimpled, BigRedSmooth

      BigGreenHairy --> BigGreenHairyFast, BigGreenHairySlow
      BigGreenBald --> BigGreenBaldStrong, BigGreenBaldWeak
      BigRedDimpled --> BigRedDimpledStripes, BigRedDimpledPlaid
      BigRedSmooth --> BigRedSmoothSweet, BigRedSmoothSour

      After a few generations, these are the leaves on the tree:

      BigGreenHairyFast
      BigGreenHairySlow
      BigGreenBaldStrong
      BigGreenBaldWeak
      BigRedDimpledStripes
      BigRedDimpledPlaid
      BigRedSmoothSweet
      BigRedSmoothSour

      The most parsimonious grouping is obvious, and it matches our pattern of each subset being contained with a superset.

      Joe G: Gone if all alleged transitionals were included.

      Nope. The sets are still there.


      Big

      BigGreen
      BigGreenHairy
      BigGreenHairyFast
      BigGreenHairySlow
      BigGreenBald
      BigGreenBaldStrong
      BigGreenBaldWeak

      BigRed
      BigRedDimpled
      BigRedDimpledStripes
      BigRedDimpledPlaid
      BigRedSmooth
      BigRedSmoothSweet
      BigRedSmoothSour

      Joe G: Figure it out for yourself or pay me. I don't work for free.

      In other words, you made a claim you can't support.

      Delete
    61. Actually you were trying to say that common descent produces such a pattern. Obviously it doesn't

      Zachriel:
      Of course it does.

      AGAIN- a family tree does not produce a nested hierarchy and a family tree is common descent.

      n other words, you made a claim you can't support.

      Nice projection as that is all you have been doing. OTOH I can support my claim- anyone who is educated can do it- so what is your problem? As I said it is in the book "Evolution:A Theory in Crisis".

      Delete
    62. Zachriel:
      If we group each organism with all of its descendants (forming clades), then yes, we would have a set pattern such that each subset is contained within its superset.

      A family tree forms a clade. Yet it does not form a nested hierarchy.

      You lose.

      Delete
    63. Joe G: a family tree does not produce a nested hierarchy and a family tree is common descent.

      A family tree is not common descent, that is, unless you have a habit of marrying your cousins. In most cases, mating is between families, not within families.

      Joe G: The over-riding superset would be "Transportation", from there you have air, land, water and any hybrids.

      Keep going. What comes next in your taxonomy of vehicles?

      Delete
    64. Phylogenetic trees are hypothesised evolutionary relationships (common ancestry) USED to inform modern taxonomy (i.e.naming of things in nested hierarchies). The evolutionary inference (common ancestry) remains, regardless of how well these evolutionary relationships allow us to create natural groupings and nested hierarchies for the reasons we do that.

      These trees can be made using extant species only (most common), but can also use fossil species, though this is more difficult.

      Delete
    65. Zachriel:
      A family tree is not common descent, that is, unless you have a habit of marrying your cousins.

      So my offspring are not my descendants? I have to marry my cousin in order to have descendants? Really?

      In most cases, mating is between families, not within families.

      So what? What does that have to do with common descent?

      If we group each organism with all of its descendants (forming clades), then yes, we would have a set pattern such that each subset is contained within its superset.

      Right, a family tree forms a clade. Yet it does not form a nested hierarchy.

      What comes next in your taxonomy of vehicles?

      Denton 1985 ;)

      Delete
    66. Joe G: So my offspring are not my descendants?

      Your family tree includes the wife of your brother, and the husband of your daughter. Are they your descendants?


      Delete
    67. Zachriel:
      Your family tree includes the wife of your brother, and the husband of your daughter.

      True, but a non-sequitur.

      Are they your descendants?

      No. How is that relevant?

      I have descendants and I did not mate with my cousin. Most people have descendants without mating with their cousins.

      Obviously you have no idea how common descent works.

      Parents have offspring that are slightly modified versions of themselves. These offspring then have offspring that are slightly modified versions of them. And so on until the offspring no longer resemble the original parents, and it keeps going and possibly diverging and converging.

      That is how the tree pattern is formed.

      Delete
    68. Joe G: True, but a non-sequitur.

      Your wife is probably not your recent common ancestor. Your family tree includes members who are neither your ancestor nor your descendants, hence some members do not share any recent common descent with other members of the tree.

      You could restrict your tree to only the paternal or maternal lines, or exclude mates, then everyone on the tree would share common descent. Generally, a family tree includes crossings, so does not have the topology of a plant tree, which is the basic model of evolutionary divergence.

      Delete
    69. Zachriel:
      Your wife is probably not your recent common ancestor.

      So what? And elephant is not a descendant of humans yet elephants are on the same tree as humans.

      Your family tree includes members who are neither your ancestor nor your descendants, hence some members do not share any recent common descent with other members of the tree.

      So does the alleged tree of life.

      A family tree is an example of common descent. Anyone who doubts that is ignorant or on an agenda.

      Generally, a family tree includes crossings,

      So you think humans mate with other species? LoL!

      so does not have the topology of a plant tree, which is the basic model of evolutionary divergence.

      Which plant tree? There are many and they have differing topologies.

      Obviously you have no idea how common descent works.

      Parents have offspring that are slightly modified versions of themselves. These offspring then have offspring that are slightly modified versions of them. And so on until the offspring no longer resemble the original parents, and it keeps going and possibly diverging and converging.

      That is how the tree pattern is formed.

      Delete
    70. Joe G: And elephant is not a descendant of humans yet elephants are on the same tree as humans.

      The phylogenetic tree shows elephants and humans sharing a common ancestor. Your family tree probably does not show a common ancestor for you and your wife.

      Joe G: So does the alleged tree of life.

      A phylogenetic tree shows all organisms sharing common ancestors (other than the trunk, of course).

      Joe G: Which plant tree? There are many and they have differing topologies.

      Oh, choose a nice maple, — or an ornamental cherry.

      Delete
    71. Zachriel:
      The phylogenetic tree shows elephants and humans sharing a common ancestor.

      Common POPULATION, maybe. But all of that happened without inbreeding

      Obviously you have no idea how common descent works.

      Parents have offspring that are slightly modified versions of themselves. These offspring then have offspring that are slightly modified versions of them. And so on until the offspring no longer resemble the original parents, and it keeps going and possibly diverging and converging.

      That is how the tree pattern is formed.


      By ignoring that you are proving that you would rather obfuscate then educate.

      Delete
    72. Joe G: Common POPULATION, maybe.

      The nodes on phylogenetic trees are taxonomic units, typically species.

      Your family tree probably does not show a common ancestor for you and your wife.

      Delete
    73. How is it possible that elephants and humans can share a common ancestor but two humans cannot?

      Obviously you have no idea how common descent works.

      Parents have offspring that are slightly modified versions of themselves. These offspring then have offspring that are slightly modified versions of them. And so on until the offspring no longer resemble the original parents, and it keeps going and possibly diverging and converging.

      That is how the tree pattern is formed.


      Ignorance it is then.

      Delete
    74. Joe G: How is it possible that elephants and humans can share a common ancestor but two humans cannot?

      You introduced the typical family tree. Your family tree probably does not show a common ancestor for you and your wife. Is that correct?

      In any case, humans do share common descent, and there is certainly a lot of crossings involved. This is not posited topology of phylogenetics, which is largely uncrossed descent.

      Delete
    75. Zachriel:
      You introduced the typical family tree.

      That is a small sample of the over-all tree of life. If nested hierarchies are to exist they have to exist at all levels. It's stupid to think a process that doesn't produce a nested hierarchy on a small scale would magically produce one on a large scale.

      Oh, that's right, gradual evolution doesn't produce a nested hierarchy. So it does follow what happens at a small scale.

      But anyway, you don't seem to understand the concept of common descent.

      Delete
    76. Joe G: That is a small sample of the over-all tree of life.

      Phylogenetic trees only include posited furcations, so the topology is different from a family tree.

      Delete
    77. Phylogenetic trees are not nested hierarchies.

      If nested hierarchies are to exist they have to exist at all levels. It's stupid to think a process that doesn't produce a nested hierarchy on a small scale would magically produce one on a large scale.

      Oh, that's right, gradual evolution doesn't produce a nested hierarchy. So it does follow what happens at a small scale.

      But anyway, you don't seem to understand the concept of common descent.

      Delete
    78. Joe G: Phylogenetic trees are not nested hierarchies.

      We're not discussing "nested hierarchies". You're still stuck on the difference between a typical family tree, which involves constant crossings, with a phylogenetic tree, a connected and ordered graph wherein any two vertices are connected by just a single simple path.

      Delete
    79. Zachriel:
      We're not discussing "nested hierarchies".

      Of course we are. That is all we have been discussing. Well, then you demonstrated that you don't understand the concept of common descent.

      Did your parents ever have that "talk" with you? Do you find dates at family reunions?

      Once you figure out how common descent works come back and we can have a discussion.

      Delete
    80. Joe G: Of course we are. That is all we have been discussing.

      No, we had been discussing a set pattern such that each subset is contained with a superset. Then you were apparently confused by the graph differences between the typical family tree and a phylogenetic tree. If you refuse to learn, then, well, you'll never learn.

      Here's a simple phylogenetic tree. Please note that there is exactly one simple path from any branch to the root, and that there are no crosses between branches.
      http://img.docstoccdn.com/thumb/orig/132618390.png

      Delete
    81. Zachriel, Until you figure how common descent works we cannot have a discussion about what patterns it will produce.

      If your parents won't explain things to you perhaps you can take some time and google it.

      Delete
  6. Nic,

    Demonstrating life arising spontaneously from non-life might be a good place to start. Care to make an attempt?


    Really? The supernatural can be ruled out?

    ReplyDelete
    Replies
    1. Design can be ruled out in that scenario.

      Delete
    2. Zachriel,

      Nic: Are you certain?

      Zachriel: "Reasonably so."

      That qualifies as a no.

      "The discovery that all of life's processes are chemical in nature,..."

      And that is only evidence for evolution how?

      " that all life shares a common ancestry,..."

      That is something you do not know but simply believe as an evolutionist.

      "that life appeared on Earth shortly after liquid water formed, that chemicals can act as catalysts and information carriers, that membranes can spontaneously form and divide."

      Again, this is only evidence for evolution how?

      "Let's put it this way, the first life on Earth appeared long ago.

      When life appeared does not do much to help your argument as to how and why it appeared, does it?

      Zachriel: Your claim was that a theory of abiogenesis is inevitable because evolution is strongly supported.

      Nic: What ever gave you that idea?

      Z: In any case, there's no workable theory of abiogenesis at this point.

      N: But one will eventually arise, right? After all, it's inevitable because as we all know, evolution is a fact.

      Z:Just because evolution is strongly supported doesn't mean we'll ever have a theory of abiogenesis.

      You obviously don't catch on to sarcasm quickly.

      Zachriel: "Interesting that biologists are unaware of this falsification."

      I would assume they are to busy thinking up ways to adapt the falsifications into new arguments supporting evolution.

      Nic: And I suppose you typed that sentence with a straight face?

      Zachriel: "(Not sure why you went from having a reasonable discussion to handwaving, but whatever.)"

      That's not hand waving, I'm quite serious. Arguing that all that is happening with the theory of evolution is that it's becoming new and improved is like arguing the Space Shuttle is the result of a long series of new and improved toasters. It is, to be blunt, a completely ridiculous statement. It's the kind of argument which can only be presented by someone who is willfully blinded himself to any other way of thinking.

      Delete
    3. Nic: And that is only evidence for evolution how?

      Huh? You asked about abiogenesis.

      Nic: That is something you do not know but simply believe as an evolutionist.

      It's something strongly supported by the evidence.

      Nic: Again, this is only evidence for evolution how?

      Huh? You asked about abiogenesis.

      Nic: When life appeared does not do much to help your argument as to how and why it appeared, does it?

      Of course it does. It eliminates alternatives, such as Young Earth Creationism.

      Nic: I would assume they are to busy thinking up ways to adapt the falsifications into new arguments supporting evolution.

      You forgot to answer. What is that falsification?

      Nic: Arguing that all that is happening with the theory of evolution is that it's becoming new and improved is like arguing the Space Shuttle is the result of a long series of new and improved toasters.

      When provided an example, you absentmindedly waved your hands. We have a Theory of Evolution which includes a history. If we change the theory to put birds as descendants of therapods rather than some more primitive archosaur, then that is an example of a theory being modified. It's not that difficult a concept, even if you reject the particular example.

      If the evidence contradicts a theory, the theory is either modified or discarded. That's not spin, that's how science works.

      Delete
    4. A theory requires supporting evidence and to date there isn't any evidence that we can get design without a designer (Darwin's dangerous idea).

      Delete
    5. Zachriel,

      "It's something strongly supported by the evidence."

      One particular interpretation of the evidence only.

      Nic: When life appeared does not do much to help your argument as to how and why it appeared, does it?

      Zachriel: "Of course it does. It eliminates alternatives, such as Young Earth Creationism."

      Wow! That's a big help.

      "You forgot to answer. What is that falsification?"

      Epigentics is one, as is the dramatic fall of junk DNA. The complete failure of phylogentic trees. Is that enough for now?


      "If the evidence contradicts a theory, the theory is either modified or discarded. That's not spin, that's how science works."

      But it just so happens that when it comes to evolution all that is ever necessary is modification. Funny how that works.

      Delete
    6. Nic: One particular interpretation of the evidence only.

      When we say supported by the evidence, we mean it makes specific and distinguishing predictions that have been verified.

      Nic: Wow! That's a big help.

      Of course it is.

      Nic: Epigentics is one

      How does epigenetics falsify evolution?

      Nic: as is the dramatic fall of junk DNA

      Not sure "junk DNA" has fallen, but how does that falsify evolution?

      Nic: The complete failure of phylogentic trees.

      Um, no. While there are some anomalies at the root of the tree, the overall tree structure remains strongly supported.

      Nic: But it just so happens that when it comes to evolution all that is ever necessary is modification.

      That's because life has evolved over millions of years. Any theory has to explain this fact.

      Delete
    7. Zachriel:
      When we say supported by the evidence, we mean it makes specific and distinguishing predictions that have been verified.

      And what predictions are borne from differing accumulations of genetic accidents? Please be specific.

      Delete
    8. Joe G: And what predictions are borne from differing accumulations of genetic accidents?

      We were discussing common descent.

      However, you might check out Lederberg & Lederberg 1952. They show that mutations are random with respect to antibiotic resistance in bacteria.

      Delete
    9. Zachriel,

      "When we say supported by the evidence, we mean it makes specific and distinguishing predictions that have been verified."

      Making a correct prediction does not in and of itself verify your theory. It is completely possible to make a correct prediction based on a false theory.

      "Of course it is."

      How?

      "How does epigenetics falsify evolution?"

      As the major base of evolution is the occurrence of natural selection working on random mutations the discovery that such adaptations occur via built in, designed features is completely counter to that belief and demonstrates the false nature of that belief. That's painfully obvious to any enquirer with an open mind.

      "Not sure "junk DNA" has fallen, but how does that falsify evolution?"

      Let it go, it's over. Your precious little argument that DNA was full of junk because of the long ages of mutations changing a common ancestor into the variety of life we see is dead. If you can't figure out how that falsifies evolution you really need to spend less time here and more time reading.

      "Um, no. While there are some anomalies at the root of the tree, the overall tree structure remains strongly supported."

      Thank you for supplying another example of how evolution is supported no matter what the facts say.

      "That's because life has evolved over millions of years. Any theory has to explain this fact."

      I'm guessing you're completely oblivious the circuitous nature inherent in that statement.

      Delete
    10. And what predictions are borne from differing accumulations of genetic accidents?

      Zachriel:
      We were discussing common descent.

      So the proks with flagella didn't have any ancestors? Really?

      However, you might check out Lederberg & Lederberg 1952. They show that mutations are random with respect to antibiotic resistance in bacteria.

      They have no idea what caused the variation. Your notion is meaningless.

      Delete
    11. Nic: Are you certain?

      Zachriel: "Reasonably so."

      That qualifies as a no.

      Nic, I thought Zach was going to redefine 'nothing' for the class. :)

      Delete
    12. Nic: Making a correct prediction does not in and of itself verify your theory. It is completely possible to make a correct prediction based on a false theory.

      Of course it is. However, support for common descent includes everything from biological evidence to molecular evidence to geological evidence. The wide variety of evidence and methods give us confidence in the theory. Furthermore, any alternative theory must explain this close fit to the existing theory, while Intelligent Design merely engages in handwaving.

      Nic: How?

      Eliminating a myriad of possible histories is certainly a big help in understanding what happened.

      Nic: As the major base of evolution is the occurrence of natural selection working on random mutations the discovery that such adaptations occur via built in, designed features is completely counter to that belief and demonstrates the false nature of that belief.

      Unless you show that epigenetics can cause a permanent change in heredity, then it's just another type of phenotype.

      Nic: Your precious little argument that DNA was full of junk because of the long ages of mutations changing a common ancestor into the variety of life we see is dead.

      It's hardly precious as a strict darwinist would reject the idea of large amounts of vestigial DNA. Can you explain why?

      Nic: Thank you for supplying another example of how evolution is supported no matter what the facts say.

      Darwin actually considered the possibility of multiple origins for life, so it's not clear why you think that would be a problem for evolutionary theory.

      Nic: I'm guessing you're completely oblivious the circuitous nature inherent in that statement.

      We're merely stating that the Earth moves. Sure, it's a tentative conclusion, but "confirmed to such a degree that it would be perverse to withhold provisional assent." If you prefer, any replacement theory has to explain why the world has all the appearance of that life has evolved over millions of years.

      Joe G: They have no idea what caused the variation.

      What they showed was that the mutations were random with respect to fitness.

      Delete
    13. Zachriel:
      What they showed was that the mutations were random with respect to fitness.

      Not really and that is irrelevant to whether or not the mutations were chance events.

      And until we know what makes an organism what it is, there isn't any support for Common Descent.

      Delete
    14. Joe G: that is irrelevant to whether or not the mutations were chance events.

      Um, showing the mutations are random to fitness is irrelevant to whether they are chance events? How so?

      Delete
    15. Zachriel,

      "Darwin actually considered the possibility of multiple origins for life, so it's not clear why you think that would be a problem for evolutionary theory."

      That's the point, NOTHING is a problem for evolutionary theory because everything is made to fit the theory. it's science with a rubber ruler.

      "If you prefer, any replacement theory has to explain why the world has all the appearance of that life has evolved over millions of years."

      Not everyone believes the world 'has all the appearance of life has evolved over millions of years'. Tell us, what would a world that was only 50,000 years old look like?

      Delete
    16. Nic: NOTHING is a problem for evolutionary theory because everything is made to fit the theory.

      Make up your mind. Earlier you said evolution was falsified. Now you say it's not falsifiable.

      In any case, just because some aspects of a theory change doesn't mean the theory is not falsifiable.

      Darwin: There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved.

      Think about it. You're saying the unifying theory of biology for the last 150 years, years that have seen profound advances in biology, is not even a valid scientific theory. Does that make any sense?

      Nic: Tell us, what would a world that was only 50,000 years old look like?

      Oh, my Goodness. All sorts of things are wrong, from deposits of sedimentary rock, decay of radioactive minerals, plate tectonics, geomagnetic reversals, human y-chromosome studies, ice layers, lunar retreat, coral reefs, evidence from past cosmic rays, astronomical science concerning how stars and planets form, not to mention the fossil evidence of evolution.

      Delete
    17. Zachriel:
      Um, showing the mutations are random to fitness is irrelevant to whether they are chance events?

      They didn't show the mutations were random wrt fitness.

      How so?

      Because it doesn't say what caused the mutations. The resistance was there but no one knows what caused the change. It could have been communication. It could have been via other sensing of the environment.

      Delete
    18. Joe G: It could have been communication. It could have been via other sensing of the environment.

      No. They eliminated the possibility of communication or sensing the environment. You may also want to look at the Luria–Delbrück experiment.

      Delete
    19. No, they didn't eliminate that. They didn't even know such mechanisms existed. The resistant bacteria existed amongst non-resistant bacteria. And in that scenario there is plenty of communicating and sensing going on.

      Delete
    20. Joe G: No, they didn't eliminate that.

      Please explain the Lederbergs results, and how communication was involved.

      Delete
    21. Zachriel- YOU explain how "They eliminated the possibility of communication or sensing the environment".

      We have been over this many times already. And all you did was wave your hands each and every time.

      With a colony of bacteria on a plate, how can the scientists, who didn't know that bacteria can and do communicate, eliminate the possibility of sensing and communicating?

      They took stamp plates and exposed them to an anti-biotic. Some bacteria survived. This means the variation was already present. Did you not understand that when I posted it earlier?

      Delete
    22. Joe G: With a colony of bacteria on a plate, how can the scientists, who didn't know that bacteria can and do communicate, eliminate the possibility of sensing and communicating?

      What did they communicate?

      Joe G: This means the variation was already present.

      That's right. The variation occurred before the bacteria were exposed. They may or may not have ever been exposed. The variation is random with respect to fitness.

      Delete
    23. Zachriel:
      What did they communicate?

      Their biochemistry. And by doing that the population can tell what each has and what the population needs to survive.

      The anti-biotic used wasn't synthetic and it is easily possible that bacteria have been exposed to it some time in the past.

      The variation is random with respect to fitness.

      The variation ensured fitness. The variation appeared without any apparent foresight the anti-biotic was coming, but that doesn't point to a chance nature for the variation.

      You are confusing two different things, as usual.

      Delete
    24. Joe G: And by doing that the population can tell what each has and what the population needs to survive.

      How do they know they need antibiotic resistance?

      The Luria–Delbrück experiment implies a constant rate of random mutation. The variation may help the population survive, but it's not due to any intercellular communication.

      Delete
    25. How do they know they need antibiotic resistance?

      The lack of a biochemical signal that variation would produce.

      The Luria–Delbrück experiment implies a constant rate of random mutation.

      Cuz you say so?

      The variation may help the population survive, but it's not due to any intercellular communication.

      And more say-so.

      All science so far- not.

      Delete
    26. Joe G: Cuz you say so?

      No, because that's what the experiment shows.

      Joe G: And more say-so.

      That's funny. What support do you have that bacterial cells communicate in order to have antibiotic resistance?

      Delete
    27. Zachriel- YOU explain how "They eliminated the possibility of communication or sensing the environment".

      We have been waiting and waiting- stop being a little weasel.

      What support do you have that bacterial cells communicate in order to have antibiotic resistance?

      Not my claim. Stop being a little child.

      Delete
    28. Marcus,

      "Nic, I thought Zach was going to redefine 'nothing' for the class. :)"

      I imagine he got scared off after watching Hawking and Krauss make such absolute fools of themselves.

      Delete
    29. Zachriel,

      Nic: NOTHING is a problem for evolutionary theory because everything is made to fit the theory.

      Zachriel: "Make up your mind. Earlier you said evolution was falsified. Now you say it's not falsifiable."

      Seriously, where did you get your education? I can't believe you have such a poor grasp of my argument. Certainly evolution is falsifiable, and it has been falsified, several times. I have never argued otherwise. My statement saying evolution is not allowed to be falsified is not a claim to it being unfalsifiable, it's a claim to the fact evolutionists will not allow anything to falsify it. Can you not grasp the difference between those two statements?

      "Think about it. You're saying the unifying theory of biology for the last 150 years, years that have seen profound advances in biology, is not even a valid scientific theory. Does that make any sense?"

      Sure does.

      Nic: Tell us, what would a world that was only 50,000 years old look like?

      Zachriel: "Oh, my Goodness. All sorts of things are wrong, from deposits of sedimentary rock, decay of radioactive minerals, plate tectonics, geomagnetic reversals, human y-chromosome studies, ice layers, lunar retreat, coral reefs, evidence from past cosmic rays, astronomical science concerning how stars and planets form, not to mention the fossil evidence of evolution."

      I like how you always mange to get back to the fossil record. It's not your ally my friend. It's time you learned that fact.

      As for everything else you mentioned what demands millions of years to occur?

      Also, you failed to describe how a world only 50,000 years old would look.

      Delete
    30. Zachriel: What support do you have that bacterial cells communicate in order to have antibiotic resistance?

      Joe G: Not my claim.

      In other words, you have no such evidence.

      Nic:evolutionists will not allow anything to falsify it.

      So you're saying biologists have the evidence, but don't recognize it for what it is?

      Nic:I like how you always mange to get back to the fossil record.

      It's only one of many lines of evidence that we mentioned.

      Nic: As for everything else you mentioned what demands millions of years to occur?

      They all require more than 50,000 years.

      Zachriel: Also, you failed to describe how a world only 50,000 years old would look.

      We answered that.

      Delete
  7. velikovskys,

    Nic: Demonstrating life arising spontaneously from non-life might be a good place to start. Care to make an attempt?

    velikovskys: "Really? The supernatural can be ruled out?"

    And that is stated or implied where?

    ReplyDelete
  8. velikovskys: "Really? The supernatural can be ruled out?"

    Nic:And that is stated or implied where?



    Is that a no? If so, no experimental result can eliminate supernatural intervention. Therefore no experimental results could contradict that hypothesis.

    ReplyDelete
  9. velikovskys,

    "Is that a no? If so, no experimental result can eliminate supernatural intervention. Therefore no experimental results could contradict that hypothesis."

    Excuse me, are you operating under the naive assumption that physical sciences are the only way of determining truth? That everything MUST be subject to scientific investigation to be considered true?

    ReplyDelete
    Replies
    1. Of course not. Philosophy is an important perspective.

      But that's not what velikovskys asked. He asked about the supernatural, which itself would be subject to philosophical criticism.

      "That's just what God must have wanted" is a bad explanation. It's bad philosophy.

      Delete
    2. Nic:
      Excuse me, are you operating under the naive assumption that physical sciences are the only way of determining truth?


      Not at all, science is limited in its reach. It can only describe the physical in physical terms to the best of our present knowledge with our present tools, it is at best an approximation of a truth.

      Which truth are you talking about?

      That everything MUST be subject to scientific investigation to be considered true?

      Not everything, just things that can be measured objectively.

      But that is beside the point, that a supernatural hypothesis is not even possibly falsifiable, so the question remains what can contradict the design hypothesis?

      Or do you only require evolution to have to ability to be falsified?

      Delete
    3. Intelligent Design can be tested and potentially falsified. OTOH unguided evolution can't even be tested.

      For example how can we test the claim the unguided evolution produced a bacterial flagellum?

      Delete
    4. Joe,
      Intelligent Design can be tested and potentially falsified.


      Not without some knowledge of the capabilities of the designer.

      OTOH unguided evolution can't even be tested.

      Since the scales of evolution exceed historical human society, how do you know?

      For example how can we test the claim the unguided evolution produced a bacterial flagellum?

      Are you asking whether we can guide unguided evolution to create a specific outcome? Perhaps it would be helpful to know how design created one.

      Delete
    5. Not without some knowledge of the capabilities of the designer.

      Don't pin your limitations on us. How do we know ancient people had the capability to design and build the Antikythera Mechanism? The Antikythera Mechanism.

      Since the scales of evolution exceed historical human society, how do you know?

      Because all you have is to hide behind father time.

      Are you asking whether we can guide unguided evolution to create a specific outcome?

      That doesn't make any sense, so no. However we can design things to evolve such that they evolve by design. Evolutionary and genetic algorithms are great examples of evolution by design.

      Perhaps it would be helpful to know how design created one.

      That is an "after" question. First design is determined and studied. Only then can we have any chance of answering the other questions, in order of relevance, of course.

      Delete
    6. velikovskys,

      "But that is beside the point, that a supernatural hypothesis is not even possibly falsifiable, so the question remains what can contradict the design hypothesis?"

      If something was found to be truly unfalsifiable would it then be considered unscientific?

      Delete
    7. Joe,
      Don't pin your limitations on us. How do we know ancient people had the capability to design and build the Antikythera Mechanism? The Antikythera Mechanism.


      joe,
      Don't pin your limitations on us. How do we know ancient people had the capability to design and build the Antikythera Mechanism? The Antikythera Mechanism.


      Exactly we judge using other lines of evidence to judge technical ability of a human designer with regard to a particular artifact.

      But that is not falsifying ID that is falsifying a particular designer.

      The problem is with even if nature is capable of X, a designer of unknown ability could be manipulating those same natural processes, ID would be unfalsifiable

      Because all you have is to hide behind father time.

      It is part of the theory, just like geology. But go ahead, design and produce a flagellum in real time


      That doesn't make any sense, so no.


      Then your demand is illogical

      However we can design things to evolve such that they evolve by design.

      Exactly, how can you tell the difference?

      Evolutionary and genetic algorithms are great examples of evolution by design.

      If the model reflects a non teleological process the result is non teleological.

      That is an "after" question. First design is determined and studied.

      Now who is hiding behind time? But wait, I thought IC proved design seems time to move on to step two.

      Only then can we have any chance of answering the other questions, in order of relevance, of course.

      Without knowledge of the capabilities of the designer, how can you do that?




      Delete
    8. Knowledge of cause and effect relationships- that is how we determine design in the absence of direct observation or designer input.

      If, say, Dr Behe designed a flagellum in the lab do you think that would be evidence for ID? If so I give yo the work of Venter et al.

      And my demand is illogical because your position is untestable?

      Evolutionary and genetic algorithms reflect telic processes. That is the point. They solve the problems they are designed to solve.

      Also you obviously don't know how scientific investigations proceed nor what each position posits. YOURS is the position that posits gradual step-by-step processes yet it cannot demonstrate such. OTOH archaeology and forensic science make it very clear that the only possible way to the designer (absent designer input or direct observation) is by studying the design and all relevant evidence.

      As for the capability of the designer, we know that by the design they leave behind. That is how it works with science.

      Delete
    9. Joe G: If, say, Dr Behe designed a flagellum in the lab do you think that would be evidence for ID?

      Sort of like a kid piling up rocks and saying that's evidence for the intelligent design of mountains.



      Delete
    10. Well Zachriel talk to vel. He seems to think that would be evidence for ID. I do not.

      Delete
    11. Joe,
      And my demand is illogical because your position is untestable?


      No Joe because it is a bogus demand, you are asking an unguided process to produce a specific outcome.

      Evolutionary and genetic algorithms reflect telic processes.

      Not if they are modeled after non telic processes.

      Zach:Sort of like a kid piling up rocks and saying that's evidence for the intelligent design of mountains.

      Joe:Well Zachriel talk to vel. He seems to think that would be evidence for ID. I do not.

      Not exactly, I think ID thinks it is evidence for ID. With no knowledge of a designer, anything could be intelligently designed, therefore anything can be evidence for ID. Which makes it equivalent to a supernatural hypothesis

      Delete
  10. Scott,

    "But that's not what velikovskys asked."

    Why don't we let velikovskys answer my question instead of presuming what he meant?

    ReplyDelete
  11. Nic: Why don't we let velikovskys answer my question instead of presuming what he meant?

    Regardless of what he meant, why don't you address the rest of my comment.

    To rephrase as a question, are you operating under the assumption that there are only two options of determining truth: science and the supernatural?

    ReplyDelete
    Replies
    1. Scott,

      "are you operating under the assumption that there are only two options of determining truth: science and the supernatural?"

      I'm operating under no such assumptions. I asked velikovskys a question and I will wait until he answers it before proceeding.

      Delete
  12. Unguided/ blind watchmaker evolution doesn't have any explanation for the spliceosome

    ReplyDelete
  13. So Zachriel appears to be ignorant of how the concept of Common Descent works.

    Parents have offspring that are slightly modified versions of themselves. These offspring then have offspring that are slightly modified versions of them. And so on until the offspring no longer resemble the original parents, and it keeps going and possibly diverging and converging.

    That is how the tree pattern is formed.

    But how stupid does an evolutionist have to be to not understand that? Or is it that Zachriel sees that it has stepped on its own little brain and will say anything to distract from that fact?

    Can't lose the nested hierarchy debate to us so Zachriel goes into full denial mode.

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

    ReplyDelete
  15. Joe, I *think* your original question was about whether common descent would be supported if, instead of "cherry picking" living taxa, you examined extinct taxa as well. Perhaps I was too indirect before:

    YES, IT WOULD. And it is.

    Interestingly, in many cases, phylogenies based on non-coding DNA match phylogenies based on morphological structures, and match older taxonomic distinctions. IOW, common descent is supported by both "nested hierarchies" of traditional taxonomy, and genetic evidence.

    Branching patterns are indeed produced in a variety of systems, both biological and non-biological. And nested hierarchies can be made of all sorts of things, it's true. Doesn't say much about the probability of a designer, unless you're not willing to acknowledge naturalistic processes for ANYTHING.

    ReplyDelete
    Replies
    1. Hi Stuart- Yes, your previous post was vague.

      How can common descent be supported if we don't know what makes an organism what it is?

      BTW a common design, ie a design based on a set of standards, explains your evidence.

      And I am more than willing to acknowledge naturalistic processes can produce things. No designer required to "litter" my yard with leaves.

      Delete
    2. It did require reading...but the point that nested, taxonomic hierarchies are informed by phylogeny (not vice versa) is fairly clear.

      I gave you two ways in which we know what an organism is: molecular and morphological. What more do you want?

      I don't know what "standards" you are referring to. Whose standards?

      Delete
  16. Stuart, we know what an organism is but we do not know what makes an organism what it is.

    What makes a human a human? Is it the sum of our genome? If so how can we test that claim?

    All we know is that a human baby comes from the successful mating of two humans.

    Standards are used in construction and engineering. There are reasons why houses built to the same building codes have a lot in common.

    ReplyDelete
  17. J: Is it the sum of our genome?

    That, and our developmental and post-developmental environment, yes. Do you REALLY want evidence for the significance of DNA?


    J: All we know is that a human baby comes from the successful mating of two humans. -

    Umm, we know an AWFUL lot more than this.

    Re: Standards:
    Do beavers have standards? Is that why when they build dams and lodges they look so similar? Do honey bees have design standards? Is that why the architecture of their nests is so uniform?

    Or did you mean something less tangible in the way of standards?


    ReplyDelete
  18. J: "we know what an organism is but we do not know what makes an organism what it is"

    This is a meaningless distinction in this context - we know the biological features of organisms, and from these can infer evolutionary relationships (e.g., common descent).

    In fact, I am not sure in what context this distinction WOULD be meaningful.

    ReplyDelete
    Replies
    1. In his book (English title) “Why is a Fly not a Horse?”, the prominent Italian geneticist Giuseppe Sermonti, tells us the following:

      Chapter VI “Why is a Fly not a horse?” (same as the book’s title)

      ”The scientist enjoys a privilege denied the theologian. To any question, even one central to his theories, he may reply “I’m sorry but I do not know.” This is the only honest answer to the question posed by the title of this chapter. We are fully aware of what makes a flower red rather than white, what it is that prevents a dwarf from growing taller, or what goes wrong in a paraplegic or a thalassemic. But the mystery of species eludes us, and we have made no progress beyond what we already have long known, namely, that a kitty is born because its mother was a she-cat that mated with a tom, and that a fly emerges as a fly larva from a fly egg.”

      Delete
    2. Yup, looks like he said that. But, we do know more. SInce you start by referring to him as a geneticist, I'll follow your suit and point out that this book is not genetics, it's spiritual.



      Delete
    3. LoL!@ Stuart- I have the book and there isn't anything spiritual about it. It does, however, discuss science and evidence.

      Delete
  19. Stuart,

    "we know the biological features of organisms, and from these can infer evolutionary relationships (e.g., common descent)."

    If one assumes the truth of evolution they would indeed infer common descent to be the cause of biological similarities. What if one does not assume evolution to be true and infers a different reason for biological similarities?

    ReplyDelete
    Replies
    1. Nic: If one assumes the truth of evolution they would indeed infer common descent to be the cause of biological similarities.

      If common descent then it will leave certain evidence (nested sets of traits, fossil succession, predictions of transitionals). Successful confirmation supports the hypothesis.

      Nic: What if one does not assume evolution to be true and infers a different reason for biological similarities?

      If it can make all the same *specific* predictions, or better yet, the same predictions, plus new *distinguishing* predictions we can test, then you may have a plausible replacement theory.

      Einstein's theory not only predicted everything Newton's did, but made new predictions that could distinguish his theory from all the other possible theories.

      Delete
    2. Gradual common descent would produce a smooth blending of traits that would cause overlapping of sets that would ruin any objective nested hierarchy.

      The alleged "predictions" of common descent are just based on someone's belief as no one knows what pattern such a long and arduous journey would leave behind.

      No one knows how many mutations it takes to get new body plans. No one knows what genes were involved. That makes it untestable- interesting, yes, science, no.

      Delete
    3. Zachriel,

      Nic: If one assumes the truth of evolution they would indeed infer common descent to be the cause of biological similarities.

      Zachriel: "If common descent then it will leave certain evidence (nested sets of traits, fossil succession, predictions of transitionals). Successful confirmation supports the hypothesis."

      You guys are like a puppy with a squeaky toy, you just don't let go. The nested hierarchy argument is not a knock down argument in favour of evolution. It fits a design scenario just as well, if not better. Widespread application of useful features is a hallmark of design, not so in blind, purposeless evolution.

      Also, the fossil record is no help when it comes to the idea of common descent. In fact it is probably your worst enemy for it simply does not display the gradual and continuous progression of traits you would need. That's beyond questioning.

      As for your 'transitionals'; those are clearly found only in the eyes and minds of evolutionists who require such creatures. The evidence again is just not there. And please, no claims for pakicetus, et al.

      Nic: What if one does not assume evolution to be true and infers a different reason for biological similarities?

      Zachriel: "If it can make all the same *specific* predictions, or better yet, the same predictions, plus new *distinguishing* predictions we can test, then you may have a plausible replacement theory."

      What specific predictions does evolution make which would be seen as unique to it only? And exactly how do you propose to test what has happened in the unobservable past?

      Delete
    4. This comment has been removed by the author.

      Delete
    5. Joe G: Gradual common descent would produce a smooth blending of traits that would cause overlapping of sets that would ruin any objective nested hierarchy.

      We're discussing a pattern such that each subset is contained within a superset. And they would still form into sets, though as you point out, the edges might be difficult to discern.

      Nic: Widespread application of useful features is a hallmark of design, not so in blind, purposeless evolution.

      Which is why artifacts rarely form into nested hierarchies! Human designers don't respect such boundaries.

      Nic: In fact it is probably your worst enemy for it simply does not display the gradual and continuous progression of traits you would need.

      There are lots of excellent fossil transitions, and substantial evidence for many other transitions. There's also the nested hierarchy in time.

      Nic: As for your 'transitionals'; those are clearly found only in the eyes and minds of evolutionists who require such creatures.

      If they can predict the traits of heretofore unknown organisms, then find those organisms, then that requires more of an explanation than a speck in their eye.

      Nic: What specific predictions does evolution make which would be seen as unique to it only?

      There are an infinitude of theories that could explain the evidence, however, the Theory of Evolution is the most parsimonious that is consistent with the evidence that also makes verifiable predictions. However, we would be happy to look at any competing theory.

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    6. Joe, Nic, read my comment below on the consistency of molecular sequence divergence with common descent REGARDLESS of whether you want to quibble about how traits arrange themsleves or about this or that branching pattern.

      Also, Joe says: "No one knows how many mutations it takes to get new body plans. No one knows what genes were involved. That makes it untestable- interesting, yes, science, no."

      This is dead wrong. We know some of the developmental genes, mutations in which create large differences in body organisation.

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    7. Stuart- mutations to developmental genes are detrimental- fruit flies with an extra set of useless wings or with legs for antennae.

      YOU don't have any idea if common descent would produce the pattern you observe.

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    8. Documented changes to these genes do produce variation among extant taxa. *e.g. gene duplications alter body segmentation oin arthropods. This would seem to be evidence they are not entirely detrimental. Some would be, sure - many mutations are detrimental.

      More closely related versions of these genes are found in taxa ALSO found to be more closely related based on independent sequence data.

      Descent with mods.

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    9. Common design Stuart. Do you really believe that differing accumulations of genetic accidents can produce developmental genes and a genetic toolkit?

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    10. Zachriel,

      Nic: Widespread application of useful features is a hallmark of design, not so in blind, purposeless evolution.

      Zachriel: "Which is why artifacts rarely form into nested hierarchies! Human designers don't respect such boundaries."

      You're kidding, please tell me you're kidding.

      Nic: In fact it is probably your worst enemy for it simply does not display the gradual and continuous progression of traits you would need.

      Zachriel; "There are lots of excellent fossil transitions, and substantial evidence for many other transitions. There's also the nested hierarchy in time."

      This story has been repeated so many times over the years I'm sure you truly believe it to be factual. Sorry, it simply is not. You can't produce one single indisputable example of one type of animal transitioning to another type. They are simply not there. You can extrapolate until you're blue in the face, but extrapolation helps you not one iota.

      Nic: As for your 'transitionals'; those are clearly found only in the eyes and minds of evolutionists who require such creatures.

      Zachriel: "If they can predict the traits of heretofore unknown organisms, then find those organisms, then that requires more of an explanation than a speck in their eye."

      And I suppose you're going to throw Tiktaaalik into the fray again? BORING!

      Nic: What specific predictions does evolution make which would be seen as unique to it only?

      Zachriel: "There are an infinitude of theories that could explain the evidence,..., However, we would be happy to look at any competing theory."

      Well if you would be happy to do so, please be my guest. There is, however, one necessary caveat. You MUST do so with an open mind. However, such minds are extremely rare among evolutionists.

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    11. Nic: You're kidding, please tell me you're kidding.

      That's easy to test. Arrange vehicles into a nested hierarchy. Or containers. Or buildings. Or all of them. And explain why yours is the only rational ordering based on trait.

      Nic: You can't produce one single indisputable example of one type of animal transitioning to another type.

      There are many excellent fossil series, such as for cirripedia.

      Nic: And I suppose you're going to throw Tiktaaalik into the fray again?

      The evidence doesn't go away because you find it boring. The reason Tiktaalik is often mentioned is because it represents one of the most profound transitions in evolutionary biology, and the scientists who predicted then discovered Tiktaalik had to work for years in an Arctic wasteland.

      Nic: You MUST do so with an open mind.

      Sure. What is the theory? We're particularly interested in how it explains all the specific evidence that most scientists believe supports evolutionary theory?



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    12. Zachriel,

      Nic: You're kidding, please tell me you're kidding.

      ZAchriel: "That's easy to test. Arrange vehicles into a nested hierarchy. Or containers. Or buildings. Or all of them."

      Do you understand the concept of a nested hierarchy?

      Nic: You can't produce one single indisputable example of one type of animal transitioning to another type.

      Zachriel: "There are many excellent fossil series, such as for cirripedia."

      So where in there is there an example of one type of creature becoming another type of creature? Where does a barnacle become Barney Rubble?

      Nic: And I suppose you're going to throw Tiktaaalik into the fray again?

      "The evidence doesn't go away because you find it boring. The reason Tiktaalik is often mentioned is because it represents one of the most profound transitions in evolutionary biology, and the scientists who predicted then discovered Tiktaalik had to work for years in an Arctic wasteland."

      Tiktaalik is a fish, in what way is that transitional?
      Because scientists worked for years in the Arctic wasteland is more than irrelevant.

      Nic: You MUST do so with an open mind.

      Zachriel: "Sure. What is the theory? We're particularly interested in how it explains all the specific evidence that most scientists believe supports evolutionary theory?"

      Grow up, seriously!

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    13. Nic: Do you understand the concept of a nested hierarchy?

      Yes. Now, are you going to arrange vehicles into a nested hierarchy. Or containers. Or buildings. Or all of them. And explain why yours is the only rational ordering based on trait.

      Nic: So where in there is there an example of one type of creature becoming another type of creature?

      What is a "type" of creature? Do you mean different species?

      Nic: Tiktaalik is a fish, in what way is that transitional?

      Because it exhibits both primitive and derived traits. In particular, it has a robust rib cage and lungs, functional wrist, intermediate ear structure, and mobile neck.

      Zachriel: What is the theory? We're particularly interested in how it explains all the specific evidence that most scientists believe supports evolutionary theory?"

      Nic: Grow up, seriously!

      In other words, you can't provide an alternative theory for consideration that explains the data.

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    14. Zachriel,

      Nic: Do you understand the concept of a nested hierarchy?

      "Yes. Now, are you going to arrange vehicles into a nested hierarchy. Or containers. Or buildings. Or all of them. And explain why yours is the only rational ordering based on trait."

      You really understand the concept and still claim you can't arrange vehicles into a hierarchy, or buildings? Why do I doubt you understand the concept?

      Nic: So where in there is there an example of one type of creature becoming another type of creature?

      What is a "type" of creature? Do you mean different species?

      Nic: Tiktaalik is a fish, in what way is that transitional?

      Zachriel: "Because it exhibits both primitive and derived traits. In particular, it has a robust rib cage and lungs, functional wrist, intermediate ear structure, and mobile neck."

      You're claims are in dispute, but to pursue the subject will only result in my presenting my case and you denying the accuracy of it. So for the sake of brevity why don't I accept your claims. Now, how is it no longer a fish? And please, no extrapolation based arguments.


      "In other words, you can't provide an alternative theory for consideration that explains the data."

      Seriously, it does nothing for your credibility, or integrity to feign ignorance as to the existence of alternate explanations.

      Delete
  20. Stuart- we don't know any more than that. I know what DNA does and it doesn't determine what type of organism will develop.

    And I explained standards- see also IEEE

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    1. Oh really? what does it do then?

      That gene I can manipulate add whole new organs to plants, what's up with that?

      I don't know what IEEE is...sorry. Still no clear on which biological standards we're aiming at. Once again - Do beavers have standards? Is that why when they build dams and lodges they look so similar? Do honey bees have design standards? Is that why the architecture of their nests is so uniform?
      What did you mean?

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    2. Dr Denton puts it this way in his article in "Uncommon Dissent":

      To understand the challenge to the “superwatch” model by the erosion of the gene-centric view of nature, it is necessary to recall August Weismann’s seminal insight more than a century ago regarding the need for genetic determinants to specify organic form. As Weismann saw so clearly, in order to account for the unerring transmission through time with precise reduplication, for each generation of “complex contingent assemblages of matter” (superwatches), it is necessary to propose the existence of stable abstract genetic blueprints or programs in the genes- he called them “determinants”- sequestered safely in the germ plasm, away from the ever varying and destabilizing influences of the extra-genetic environment.


      Such carefully isolated determinants would theoretically be capable of reliably transmitting contingent order through time and specifying it reliably each generation. Thus, the modern “gene-centric” view of life was born, and with it the heroic twentieth century effort to identify Weismann’s determinants, supposed to be capable of reliably specifying in precise detail all the contingent order of the phenotype. Weismann was correct in this: the contingent view of form and indeed the entire mechanistic conception of life- the superwatch model- is critically dependent on showing that all or at least the vast majority of organic form is specified in precise detail in the genes.


      Yet by the late 1980s it was becoming obvious to most genetic researchers, including myself, since my own main research interest in the ‘80s and ‘90s was human genetics, that the heroic effort to find information specifying life’s order in the genes had failed. There was no longer the slightest justification for believing there exists anything in the genome remotely resembling a program capable of specifying in detail all the complex order of the phenotype. The emerging picture made it increasingly difficult to see genes as Weismann’s “unambiguous bearers of information” or view them as the sole source of the durability and stability of organic form. It is true that genes influence every aspect of development, but influencing something is not the same as determining it. Only a small fraction of all known genes, such as the developmental fate switching genes, can be imputed to have any sort of directing or controlling influence on form generation. From being “isolated directors” of a one-way game of life, genes are now considered to be interactive players in a dynamic two-way dance of almost unfathomable complexity, as described by Keller in The Century of The Gene.


      And if you don't know what the IEEE is then I would say you don't know much about designing and engineering. Your not knowing is not a refutation.

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    3. Yup, it's complex stuff, and as he points out, there are probably very few real switch-like genes of large developmental effect. If you think about it, this makes sense given the likely sensitivity of such switches to the odd deleterious mutation. Makes evolutionary sense that is.

      Joe says: And if you don't know what the IEEE is then I would say you don't know much about designing and engineering.

      True! I'm an evolutionary biologist, and no engineer. Well spotted.


      Joe also says: Your not knowing is not a refutation.

      Also true - never said it was, I just said I didn't know. Curious, I see it is simply some electrical/engineering standards. But in your petulance, you have neglected to indicate how these matter to our biological discussion.

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    4. IEEE exemplifies a common design. If you employ standards then different designers can build different things that can play together- universal remotes for the TV, PC clones, PCs and smart phones, houses- my house has an addition that was built to the same code as the house. That means despite different designers and builders, the addition looks as if it came with the house.

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    5. So you're a polytheistic creationist? Cool. I knew one of those once - John Davison. Crazy dude.

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    6. Anyway, I gather from the lack of any statement to the contrary, you have no real connection to make to biology here. You're probably worried that if you do point out a biological "standard", I will point out numerous species or situations in which the standard is clearly not met.

      It's a legit worry, I grant you.

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  21. Yes, I never said anything about inferring X after assuming X.

    Studies of sequence divergence (millions of characters) are consistent with common ancestry, and are compelling because morphological traits may show convergence (are often functional), and fossils are very hard to find. We can also show that the rate of sequence divergence is related to whether the sequence is funtcional (or near a functional sequence), and that other genetic forces can modulate the rate of divergence in predictable ways.

    Nic, I'm sure your new theory will deal with all that.

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  22. Stuart,

    "Yes, I never said anything about inferring X after assuming X."

    But yet you do so, as does every evolutionist. In fact they do so so often they've become completely oblivious to the fact.

    "Nic, I'm sure your new theory will deal with all that."

    Well thanks for the credit, but it's not my theory, such beliefs have been around a very, very long time. And no, design theory has no problem explaining similarity among morphological traits. I'm surprised you would think it would. Wait, no, I'm not surprised. I'm sure, as with most evolutionists, you're completely beyond being able to even conceive of any other possibility.

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    1. Umm, no, I have repeatedly spelled out what I mean. I don't think you read the last comment carefully enough. Substance now.

      And I see you're conflating "theory" and "belief". I'd make some sweeping statement...something about "like all IDiots", but that would be stereotyping, and we refrain from that, right?

      Again, you need to use design to deal with explaining sequence variation that is robustly consistent with there being evolutionary relationships among taxa. Go on now.

      Delete
    2. Stuart,

      "And I see you're conflating "theory" and "belief". I'd make some sweeping statement...something about "like all IDiots", but that would be stereotyping, and we refrain from that, right?"

      Sorry, conflating theory with belief is a strong suit of evolutionists. If you get to the bottom line evolution does not even reach the standard of theory.

      As for stereotyping, I try to refrain, yes, however, you have been guilty of circuitous reasoning and assumption.

      "Again, you need to use design to deal with explaining sequence variation that is robustly consistent with there being evolutionary relationships among taxa."

      No one is arguing there are no sequence variations among taxa. What you fail to do is demonstrate these variations can be explained only via evolution.
      Another stereotypical trait of evolutionists. If you wish not to be stereotyped, break away from the herd mentality and quit trotting out the same tired old arguments.

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    3. Kind of amounts to a "no, YOU'RE a..." statement. You described your perspective clearly as both belief and theory in the same sentence. Don't be mad at me b/c you're embarrassed at what this slip likely says about the quality of your thinking as either belief OR theory.

      I am quite glad you have acknowledged sequence variation. Now, again - go back and read what I wrote about exactly WHAT type of variation i'm talking about and the pattern I describe. I make the case that this explainable by evolution. If you want to seriously dispute this (or have me take you seriously), you're going to have to do a little better than avoiding the topic!

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    4. Stuart,

      "I make the case that this explainable by evolution."

      So what? Because it is explainable by evolution does not mean it is the result of evolution or that it is not explainable under a different scenario. Again, typical evolutionist arrogance. Because you believe evolution is the explanation, in your thinking it then follows there is no question that is indeed the case.

      What you wrote in no way is explainable only via evolutionary actions. So I really have no idea why you think it's such a devastating argument. Because you believe evolution to be the only explanation does not make that belief a fact. There is a vast difference between you not believing, or not knowing of any other explanation and there in fact not being any other explanation. To make the claim there is no other way to explain this situation you would have to be aware of all possible explanations. As you cannot possibly possess such knowledge, you're simply blowing smoke. Yet another activity common to evolutionists.

      "have me take you seriously,..."

      Believe me, I couldn't care less whether or not you take me seriously. Who are you that I should worry about your opinion? Evolution is dead in the water and only the truly dedicated try to deny it any longer.

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