Wednesday, May 14, 2014

Evolution Professor: Biological Designs Fall Into a Nested Hierarchy

Fact Checking the Evolutionists

To support their high claim that the spontaneous origin of the species is a fact, evolutionists enlist all kinds of scientific evidence. But inevitably their scientific evidence isn’t quite right. One problem that surprised me when I first began studying evolution is the downright misrepresentation of the evidence. Sometimes these misrepresentations are exaggerations that convert otherwise ambiguous evidence into supporting evidence. Other times the misrepresentations are starker. In any case, to marshal evidence for the fact of evolution misrepresentation is required. And so it was not too surprising that in his recent debate against Paul Nelson, evolutionist Joel Velasco continued this unfortunate tradition.

One of Velasco’s themes in the debate was that biological designs fall into a nested hierarchy. The idea is that the common ancestry model predicts and requires such a pattern and that the finding of this hierarchy in biology is an extremely powerful proof text for evolution. But if this were true then evolution would be false by modus tollens, for the actual scientific evidence, as we have discussed many times here, is not so simple. And so we will repeat once again, phylogenetic incongruence is rampant in evolutionary studies. Conflicts exist at all levels of the evolutionary tree and throughout both morphological and molecular traits.

This paper reports on incongruent gene trees in bats. That is one example of many. These incongruences are caused by just about every kind of contradiction possible. Molecular sequences in one or a few species may be out of place amongst similar species. Or sequences in distant species may be strangely similar. As one paper admitted, there is “no known mechanism or function that would account for this level of conservation at the observed evolutionary distances.” Or as another evolutionist admitted, the many examples of nearly identical molecular sequences of totally unrelated animals are “astonishing.”

An even more severe problem is that in many cases no comparison is even possible. The molecular sequence is found in one species but not its neighbors. When this problem first became apparent evolutionists thought it would be resolved as the genomes of more species were decoded. No such luck—the problem just became worse. Not surprisingly evolutionists carefully prefilter their data. As one paper explained, “data are routinely filtered in order to satisfy stringent criteria so as to eliminate the possibility of incongruence.”

Short genes that produce what are known as microRNA also contradict Dawkins’ high claim. In fact one evolutionist, who has studied thousands of microRNA genes, explained that he has not found “a single example that would support the traditional tree.” It is, another evolutionist admitted, “a very serious incongruence.”

Another paper admits that “the more molecular data is analysed, the more difficult it is to interpret straightforwardly the evolutionary histories of those molecules.”

And yet in public presentations of their theory, evolutionists present a very different story. Velasco’s claim is typical. For example, Richard Dawkins explained that gene comparisons “fall in a perfect hierarchy, a perfect family tree.” This statement is so false it isn’t even wrong—it is absurd.

128 comments:

  1. “Science seeks the truth. And it does not discriminate. For better or worse it finds things out. Science is humble. It knows what it knows and it knows what it doesn’t know. It bases its conclusions and beliefs on hard evidence -­- evidence that is constantly updated and upgraded. It doesn’t get offended when new facts come along. It embraces the body of knowledge. It doesn’t hold on to medieval practices because they are tradition.”
    Ricky Gervais - British comedian - Why I’m an Atheist," WSJ, 2010
    http://blogs.wsj.com/speakeasy/2010/12/19/a-holiday-message-from-ricky-gervais-why-im-an-atheist/

    And I would hold that science itself, in the long run, is like that. But scientists, as hard core Darwinists have made abundantly clear to me, are very different than science itself:

    “Scientists have thick skins. They do not abandon a theory [merely] because facts contradict it. They normally either invent some rescue hypothesis to explain what they then call a mere anomaly and if they cannot explain the anomaly, they ignore it, and direct their attention to other problems. Note that scientists talk about anomalies, [recalcitrant instances,] and not refutations. History of science, of course, is full of accounts of how crucial experiments allegedly killed theories. But all such accounts are fabricated long after the theory has been abandoned.”
    Imre Lakatos, Science and Pseudoscience

    Indeed, because of Darwinists, I’m now more inclined to take Planck’s pessimistic view, i.e. science ‘advances one grave at a time’ :

    “A new scientific truth does not triumph by convincing its opponents and making them see the light, but rather because its opponents eventually die, and a new generation grows up that is familiar with it.”
    Max Planck

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  2. Linnean classification is the observed nested hierarchy and it doesn't have anything to do with common ancestry. Also gradual evolution would expect a smooth blending of defining characteristics which would ruin any objective nested hierarchy.

    The problem comes from evos not understanding nested hierarchies and thinking that any tree pattern is a nested hierarchy. Just because a nested hierarchy can be represented as a tree pattern does NOT mean all tree patterns are therefor nested hierarchies. Yet that is what evos think.

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  3. Can organisms be arranged in a tree? Sure. Any group of objects can be. But can they be arranged in a whole UCA tree using the same criteria for the whole branching pattern? No. If and when that becomes possible, the next questions will be:

    1) are the tree arranging criteria even remotely related to the known effects or statistical effects of historical mutations?

    and

    2) are the ghost ranges posited to render the tree consistent with inferred fossil succession (which requires a lot of interpretation in the first place) posited arbitrarily or based on plausible geological, taphonomic, ecological inferences?

    Almost assuredly, the answer to the first question will be "no," and the answer to the second will be "arbitrarily." And never mind that We're nowhere near generating such a whole UCA tree. Currently, there is no way to even articulate enough assumptions to imply such a tree models historical genealogical relationships. That number (of assumptions) would be mind-boggingly large.

    There is NO inductive evidence for a UCA-style genealogical history of biological origins.

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  4. "As one paper explained, 'data are routinely filtered in order to satisfy stringent criteria so as to eliminate the possibility of incongruence.'"

    So go ahead and come up with all the additional criteria needed to eliminate the need to "routinely" filter out data. Then we'll see how much those criteria look like something that has ANYTHING to do with the effects of historical mutations, etc.

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  5. Cornelius Hunter: The idea is that the common ancestry model predicts and requires such a pattern and that the finding of this hierarchy in biology is an extremely powerful proof text for evolution.

    For common descent.

    Cornelius Hunter: But if this were true then evolution would be false by modus tollens, for the actual scientific evidence, as we have discussed many times here, is not so simple.

    The nested hierarchy doesn't have to be perfect to be observed as an objective pattern; and we can point to specific mechanisms where the nested hierarchy varies from the simple model, such as hybridization. But life is full of surprises, and evolutionary theory has and will bend to the evidence.

    Nothing you've noted calls into question the basic idea of common descent, much less supports Intelligent Design.

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    Replies
    1. Common descent is questioned because it cannot be tested. And gradual evolution does not predict an objective nested hierarchy.

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    2. Joe G: Common descent is questioned because it cannot be tested.

      It's hypothetico-deduction, as mentioned in the original post. Common descent predicts a nested hierarchy. A nested hierarchy is observed supporting the hypothesis. Fossil succession and the prediction of transitionals eliminates most other plausible hypotheses.

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    3. Zachriel:
      It's hypothetico-deduction, as mentioned in the original post.

      Common design is hypothetico-deduction and supported via observation and experience.

      Common descent predicts a nested hierarchy

      Liar. A family tree is an example of common descent yet a family tree does not form a nested hierarchy based on defining characteristics.

      You are obviously just spewing nonsense, as usual.

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    4. Joe G: Common design is hypothetico-deduction and supported via observation and experience.

      We've read your "common design" hypothesis, and the predictions are ad hoc.

      Joe G: A family tree is an example of common descent yet a family tree does not form a nested hierarchy based on defining characteristics.

      The human family tree is a different topology in that it crosses in every generation (sexual mating). However, the paternal and maternal lines each form nested hierarchies, and those lines are often used in genealogical research to determine direct ancestry.

      Delete
    5. Zachriel:
      We've read your "common design" hypothesis, and the predictions are ad hoc.

      That is your opinion and it is incorrect.

      However, the paternal and maternal lines each form nested hierarchies,

      No, they do not. You are sadly misinformed or uneducated.
      Just how can a patrilineage form a nested hierarchy based on defining characteristics? Please be specific.

      Delete
    6. Joe G: That is your opinion and it is incorrect.

      Did the Design Hypothesis predict a fishapod, or hominids with brain sizes between humans and other extant apes, or whales with hindlimbs, or transitional mammalian ossicles?

      Joe G: Just how can a patrilineage form a nested hierarchy based on defining characteristics?

      In modern times, by genetics. A father and son will share most of the y-chromosome, except for the occasional mutation. These mutations will also be transmitted down the paternal line. After many generations, this will result in a nested hierarchy, so we might tell if you are a descendant of Neill the Nail, or of a close male relative of Genghis Khan.

      Delete
    7. ZAchriel:
      Did the Design Hypothesis predict a fishapod, or hominids with brain sizes between humans and other extant apes, or whales with hindlimbs, or transitional mammalian ossicles?

      Unguided evolution definitely didn't predict any of those.

      Just how can a patrilineage form a nested hierarchy based on defining characteristics?

      In modern times, by genetics.

      Nice try at bluffing. A father's Y chromosome does NOT consist of nor contain his male descendants' Y chromosome.

      Again Zachriel proves that it is clueless wrt nested hierarchies.

      Delete
    8. Joe G: Unguided evolution definitely didn't predict any of those.

      They're predictions from Common Descent. There's additional evidence concerning the mechanisms of adaptation.

      Joe G: A father's Y chromosome does NOT consist of nor contain his male descendants' Y chromosome.

      The nested hierarchy is based on clades. It's not all that complicated.
      http://evolution.berkeley.edu/evosite/evo101/IIBPhylogeniesp2.shtml

      Delete
    9. Zachriel:
      They're predictions from Common Descent.

      Liar.

      A father's Y chromosome does NOT consist of nor contain his male descendants' Y chromosome.

      The nested hierarchy is based on clades.

      Yet a patrilineage does NOT form a clade. And clades are formed based on shared characteristics. And if one includes all of the alleged members of the clade the nested hierarchy disappears.

      Delete
    10. Did common descent predict fish-> tetrapods-> fishapods? That is what we see in the fossil record.

      Delete
    11. Common descent is consistent with fishapods existing after tetrapods, just as it is consistent with fish existing after tetrapods. Common descent doesn't constrain when a lineage ends, only when it begins.

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    12. Joe G: Yet a patrilineage does NOT form a clade.

      The nested hierarchy is formed of the ancestor and all of his descendants.

      Joe G: And clades are formed based on shared characteristics.

      The shared characteristics are the genetic mutations.

      Delete
    13. Zachriel:
      Common descent is consistent with fishapods existing after tetrapods,

      Nice try. The evidence has tetrapods existing before fishapods.

      Delete
    14. Zachriel:
      The nested hierarchy is formed of the ancestor and all of his descendants.

      Only if you are ignorant of nested hierarchies.

      The shared characteristics are the genetic mutations.

      Yet genetic mutations can revert back to the original state. Meaning a great grandson could have the exact same Y chromosome as his great grandfather even though his father's Y chromosome is different.

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    15. Joe G: The evidence has tetrapods existing before fishapods.

      Well, before Tiktaalik. As we said, common descent doesn't predict the end of a lineage, only its beginning. The existence of a fishapod is strong support for a transitional process.

      Joe G: Only if you are ignorant of nested hierarchies.

      This is from the University of California Museum of Paleontology with support provided by the National Science Foundation and the Howard Hughes Medical Institute.

      "Clades are nested within one another—they form a nested hierarchy."
      http://evolution.berkeley.edu/evosite/evo101/IIBPhylogeniesp2.shtml

      Pay particular attention to the diagrams they provide.

      Joe G: Yet genetic mutations can revert back to the original state.

      Sure, but we can look across multiple mutations to determine the pattern.


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    16. Please name one fishapod found before tetrapods and then tell us how it was determined to be before tetarpods.

      Zachriel:
      This is from the University of California Museum of Paleontology with support provided by the National Science Foundation and the Howard Hughes Medical Institute.

      And yet they never define what a nested hierarchy is. Also it does NOT support your claim about Y chromosomes.

      And their diagrams are meaningless without definitions and especially without demonstrating summativity.

      And genetic patterns can be explained by other mechanisms than common descent.

      Meaning a great grandson could have the exact same Y chromosome as his great grandfather even though his father's Y chromosome is different.

      Delete
    17. Joe G: Please name one fishapod found before tetrapods and then tell us how it was determined to be before tetarpods.

      Actually, Tiktaalik is older than any known tetrapod fossil organism, but there are apparent tetrapod tracks that predate Tiktaalik by a few million years.

      In any case, there could be fishapods alive today, so the end date is not at issue. The mere existence of the fishapod is a confirmation of the transitional form, even if the fishapod was found living today.

      Joe G: And yet they never define what a nested hierarchy is.

      They do saying the clades are nested, and they provide a helpful diagram.

      Joe G: And their diagrams are meaningless without definitions and especially without demonstrating summativity.

      Just think of them as semi-nested hierarchies, if that makes it easier for you.

      Joe G: And genetic patterns can be explained by other mechanisms than common descent.

      In the case of paternal lines, we can often draw on other evidence for confirmation.


      Joe G: Meaning a great grandson could have the exact same Y chromosome as his great grandfather even though his father's Y chromosome is different.

      That's very unlikely, but such convergence is one reason why the nested hierarchy may be imperfect in cases.

      Delete
    18. Oh look, it's Zachriel bluffing about his mythical nested hierarchy of common descent again, as usual. I think he believes if he just keeps asserting its existence enough times then it will become true.

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    19. lifepsy: mythical nested hierarchy of common descent again, as usual

      Perhaps Jeff can explain it to you. He seemed surprised the existence of an objective nested hierarchy was subject to question.

      Delete
    20. Zachriel:
      Actually, Tiktaalik is older than any known tetrapod fossil organism, but there are apparent tetrapod tracks that predate Tiktaalik by a few million years.

      The tracks are real, not apparent.

      So nothing with fishapods appearing before tetrapods. Got it.

      In any case, there could be fishapods alive today, so the end date is not at issue.

      Actually you have made it an issue with your nonsensical "extant organisms form an objective nested hierarchy". If the transitionals were alive there wouldn't be an objective nested hierarchy.

      And yet they never define what a nested hierarchy is.

      They do saying the clades are nested, and they provide a helpful diagram.

      Nope, you obviously don't know anything about nested hierarchies even though I have provided references explaining them to you.

      And their diagrams are meaningless without definitions and especially without demonstrating summativity.

      Just think of them as semi-nested hierarchies, if that makes it easier for you.

      I can't even say that about them. Not without those definitions.

      Meaning a great grandson could have the exact same Y chromosome as his great grandfather even though his father's Y chromosome is different.

      That's very unlikely,

      No it isn't. And it is as likely as any other change in the chromosome.

      but such convergence is one reason why the nested hierarchy may be imperfect in cases.

      What nested hierarchy? The one that exists only in your imagination that use your imagined rules?

      What are you, a high school drop-out?

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    21. Joe G: So nothing with fishapods appearing before tetrapods.

      Nevertheless, Tiktaalik represents a predicted transitional form.

      Joe G: No it isn't.

      Yes, it's unlikely. There are about 58 million bases on the Y-chromosome. You're suggesting the same base is mutated in two succeeding generations, with a measured mutation rate of about 3.0 x 10^-8 mutations per nucleotide per generation.

      Joe G: What nested hierarchy?

      Perhaps Jeff could explain it to you. He was unaware that anyone doubted the existence of the objective nested hierarchy.

      Delete
    22. Zachriel:
      Nevertheless, Tiktaalik represents a predicted transitional form.

      Only because it "looks like" a transitional form. And said form is predicted to be found between the arrival of fish and the arrival of tetrapods. Yet that prediction is unfulfilled.

      There are about 58 million bases on the Y-chromosome.

      So what? Each base has the same probability of mutating as any of the others.

      He was unaware that anyone doubted the existence of the objective nested hierarchy.

      He made no such claim in this thread. And given a common design no one should doubt the existence of an objective nested hierarchy. After all Linnean classification is based on a common design that uses shared characteristics to determine just how common the design is.

      Delete
    23. Joe G: Only because it "looks like" a transitional form.

      Meaning it has the features predicted of a transitional between fish and land vertebrates.

      Joe G: And said form is predicted to be found between the arrival of fish and the arrival of tetrapods.

      No. A transitional form doesn't have to be in a direct line of descent, and there's nothing in evolutionary theory that says fishapods can't coexist with tetrapods.

      Joe G: Each base has the same probability of mutating as any of the others.

      That's right. So what are the odds that the same base will be mutated in directly succeeding generations?

      Delete
    24. Zachriel:
      Meaning it has the features predicted of a transitional between fish and land vertebrates.

      Looking like a transitional does not make it one.

      And said form is predicted to be found between the arrival of fish and the arrival of tetrapods.

      No.

      It does too. Only a moron would think that a transitional form is not predicted between those two points.

      Each base has the same probability of mutating as any of the others.

      That's right.

      OK case closed. Thank you.

      Delete
    25. Joe G: Looking like a transitional does not make it one.

      Concentrate on the word predicted. It has the features predicted of a transitional between fish and land vertebrates.

      Joe G: Only a moron would think that a transitional form is not predicted between those two points.

      A common ancestor is predicted for fish and tetrapod, but the term transitional refers to any organism that exhibits traits common to both the ancestor and descendant; in this case, a fishapod.

      Joe G: OK case closed.

      You might want to learn some probability. The chance of two successive mutations occurring on the same base would then be one chance in 58 million. That would be rather rare.

      Delete
    26. Looking like a transitional does not make it one- period. And mutations happen and all positions have the same probability. So YOU might want to learn some probability.

      Delete
    27. Joe G: Looking like a transitional does not make it one

      Yes, you already said that, and we responded.

      Joe G: And mutations happen and all positions have the same probability.

      That's right, so the chance of two consecutive mutations hitting the same base when there are 58 million bases, is one in 58 million.

      Delete
    28. Zachriel:
      Yes, you already said that, and we responded.

      With what?

      That's right, so the chance of two consecutive mutations hitting the same base when there are 58 million bases, is one in 58 million.

      So what? Your entire position relies on improbabilities that are less than that, so do you have a point?

      Delete
  6. Jeff: 1) are the tree arranging criteria even remotely related to the known effects or statistical effects of historical mutations?

    While we can't observed historical mutations, we can show that observed rates of evolution are greater than the historical rates of evolution.

    Jeff: 2) are the ghost ranges posited to render the tree consistent with inferred fossil succession (which requires a lot of interpretation in the first place) posited arbitrarily or based on plausible geological, taphonomic, ecological inferences?

    Generally yes. Of course there are going to be anomalies, especially at the limits of observational resolution.

    Jeff: And never mind that We're nowhere near generating such a whole UCA tree.

    The good news is that science allows us to reach some reasonable, albeit tenative, conclusions, with less than complete knowledge.

    Jeff: Currently, there is no way to even articulate enough assumptions to imply such a tree models historical genealogical relationships.

    The only necessary assumptions are gradual evolution and the process of speciation, for which there is direct observational evidence.

    ReplyDelete
    Replies
    1. Gradual evolution precludes an objective nested hierarchy.

      Delete
    2. Um, no. Gradual evolution predicts that extant organisms will form a nested hierarchy.

      Delete
    3. Zachriel:
      Gradual evolution predicts that extant organisms will form a nested hierarchy.

      Liar.

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

      Delete
    5. This comment has been removed by the author. Because Zachriel doesn't have anything to counter the accusation that he is lying wrt nested hierarchies.

      Delete
    6. Jeff: 1) are the tree arranging criteria even remotely related to the known effects or statistical effects of historical mutations?

      Z: While we can't observed historical mutations, we can show that observed rates of evolution are greater than the historical rates of evolution.

      J: That assumes what you're supposed to provide evidence for. You're confused.

      Jeff: 2) are the ghost ranges posited to render the tree consistent with inferred fossil succession (which requires a lot of interpretation in the first place) posited arbitrarily or based on plausible geological, taphonomic, ecological inferences?

      Z: Generally yes. Of course there are going to be anomalies, especially at the limits of observational resolution.

      J: On the contrary, stratigraphic correlation is done on the utterly over-simplistic assumption that

      1) locally observed fossil succession corresponds with actual fossil succession and

      2) actual fossil succession corresponds with existential succession.

      It's circular reasoning all the way down. Even Last Thursdayism fares well that way.

      Z: The good news is that science allows us to reach some reasonable, albeit tenative, conclusions, with less than complete knowledge.

      J: There's nothing "reasonable" about a hypothesis for which there is no inductive evidence.

      Z: The only necessary assumptions are gradual evolution and the process of speciation, for which there is direct observational evidence.

      J: Evolution can be gradual and causal of speciation and still be cyclical and/or otherwise limited in "vertical" extent.

      Moreover, there are tons of hypothetical histories consistent with your assumptions. Otherwise, you wouldn't arbitrarily posit contingent branchings in terms of the effects of contingencies like asteriod impacts, etc.

      Once you say one can speculate on historical branching patterns, you've already rendered the probability (as calculable by current knowledge) of any one such tree VERY small.

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    7. Jeff: That assumes what you're supposed to provide evidence for.

      You mean it's hypothetico-deduction. We assume the premise, deduce the implications, then test them. That's called the scientific method.

      Jeff: 1) locally observed fossil succession corresponds with actual fossil succession and

      Geological succession can be determined without regard to fossils.

      Jeff: Evolution can be gradual and causal of speciation and still be cyclical and/or otherwise limited in "vertical" extent.

      The evidence indicates otherwise.


      Delete
  7. Zach:

    Don't you need gradual evolution plus the extinction of species near the edges, and only near the edges to get a nested hierarchy?

    ReplyDelete
    Replies
    1. natschuster- evolutionism only tries to explain the observed, ie Linnean, nested hierarchy. It does not expect it and can live quite fine without it.

      Zachriel is an infant wrt nested hierarchies.

      Delete
    2. Joe G: evolutionism only tries to explain the observed, ie Linnean, nested hierarchy.

      Linnaean classification is similar in many respects to a modern cladogram.

      Delete
    3. Zachriel:
      Linnaean classification is similar in many respects to a modern cladogram.

      It is dissimilar in many ways too.

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    4. Joe G: It is dissimilar in many ways too.

      Sure. A lots been learned since then.

      Delete
  8. natschuster: Don't you need gradual evolution plus the extinction of species near the edges, and only near the edges to get a nested hierarchy?

    To have clearly delineated sets, you would have to have something which pushes the branches apart. With trees, it's competition for light. It evolution, it's competition for resources.

    However, even if every organism that ever lived were still alive, it would still arrange into a natural order. The sets would have chaotic edges, but there would still be strong correlations due to the natural order. For instance, having mammaries would still correlate with having three ossicles.

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    Replies
    1. Zachriel:
      However, even if every organism that ever lived were still alive, it would still arrange into a natural order.

      And what natural order would that be?

      Delete
  9. But there would be something that had some sort of protomammaries that looked a lot like a reptile. In fact, there would be a whole continuum of animals with things ranging from something like, I don't know, warts to fully functioning mammaries.

    ReplyDelete
    Replies
    1. natschuster: But there would be something that had some sort of protomammaries that looked a lot like a reptile.

      Sure, which is why the edges would be chaotic. However, you would still find a correlation between having mammaries and having three ossicles. You might want to look at the negative space. There would still be no centaurs or griffins.

      Delete
    2. Zachriel:
      However, you would still find a correlation between having mammaries and having three ossicles.

      Why? Evolutionism does not require such a thing.

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    3. Inheritance means the transmission of traits from one generation to the next.

      Delete
    4. Nice cowardly non-response. Evolutionism does not require there be a correlation between having mammaries and having three ossicles.

      Delete
  10. Finding nests is no evidence, anyways, if its also evidence for a non evolutionary origin.
    If a creator made life on basic blueprints and just tweeked things at the beginning it ALSO would look like a nest on basic things!
    Evolutions evidence is is not evidence but only a option based on a line of reasoning.
    where am i wrong here?

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  11. Robert Byers: If a creator made life on basic blueprints and just tweeked things at the beginning it ALSO would look like a nest on basic things!

    No. You would expect more mixing-and-matching. When humans invent they come up with centaurs and griffins. Nor would that explain the fossil succession.

    ReplyDelete
    Replies
    1. Yes, If a creator made life on basic blueprints and just tweeked things at the beginning it ALSO would look like a nest on basic things! That is juts a fact of life and one that Linne picked up on and produced his nested hierarchy.

      Delete
    2. Zach:

      The fossil record looks a lot like a museum collection of the evolution of technology. If the designer built on previous designs, like humans do, I would expect the fossil record to look like it does. And if, by invent, you mean thought of then humans dod make griffons and centaurs, If you mean actually made, then that is a different story,

      And just how much mixing and matching would you expect to see? It looks like organism do display a lot of mixing and matching,especially at the genetic level.

      Delete
    3. natschuster: The fossil record looks a lot like a museum collection of the evolution of technology.

      No. Artifacts don't naturally form a single nested hierarchy.

      natschuster: And just how much mixing and matching would you expect to see?

      When one automaker introduces a car radio, they all end up with car radios. When flight is introduced in mammals, it's as if the designer never saw a bird.

      Delete
    4. I'm not talking about the nested hierarchy, I'm talking about the fossil record. It looks a lot like a museum collection of the evolution of technology. In fact it looks more like a museum collection than something where one species actually changed into another thing. That didn't get caught.

      And mammals and pterosuars used a similar technique of stretching skin over long fingers to make an airfoil. FIsh and dolphins have fins. SO did icthyosaurs. Eyes are kinda the same in a number of different groups. Lotta mixing and matching there. They even use the same pax gene. And there a lto of mixing at the gene level. There's tose bugs with fungus genes. Slugs that make chlorophyll. How much mixing and matching do you expect?

      Delete
    5. natschuster: I'm not talking about the nested hierarchy, I'm talking about the fossil record.

      Fossil form a nested hierarchy.

      natschuster: It looks a lot like a museum collection of the evolution of technology.

      Sure, superficially at least. So now you would want to look more closely.

      natschuster: In fact it looks more like a museum collection than something where one species actually changed into another thing.

      Well, no.

      natschuster: And mammals and pterosuars used a similar technique of stretching skin over long fingers to make an airfoil.

      natschuster: And mammals and pterosuars used a similar technique of stretching skin over long fingers to make an airfoil.

      Bats stretch skin between their fingers and metacarpels. Pterosaurs stretch skin primarily from a single finger. Notably, they are modifications of the same basic pattern, humerus, radius, ulna, carpus, metacarpus, phalanges. It's as if they started with the same pattern, then stumbled on different solutions to the problem of flight.

      natschuster: FIsh and dolphins have fins.

      Sure, but look at the bones in the fins. Once you look with a critical eye, you will quickly determine that a dolphin is closer to a dog than a dogfish.

      natschuster: There's tose bugs with fungus genes. Slugs that make chlorophyll.

      Sure, and if you look at your own genome, you will see snippets of DNA that look like viruses. These are the exceptions to the overall pattern, and we have mechanisms that explain these exceptions. We know that viruses can infect genomes. HIV is a retrovirus.

      Sequence some retroviruses within the primate family, and they too form a nested hierarchy, just what they would look like if they had infected a primitive primate ancestor.

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    6. So there is some mixing and matching. Exactly how much mixing and matching do you expect if life was designed?

      And just like in a museum collection of artifacts we see change over time, but we don't see one artifacts turning into another, the fossil record doesn't show one species actually turning into another, just change over time, just like artifacts.

      I understand that if you sequence some erv's we get different trees. For example, some of our erv's are closer to monkey's than to chimps. So we got some mixing and matching.

      Delete
    7. And I for one , would not expect the fossil record to form a nested hierrtchy, I would expect the fossil record to have all, or at least some, of the transitionals that sit near the borders of the groups.

      Delete
    8. natschuster: So there is some mixing and matching.

      Yes, hybridization, for instance. There's also convergence, such as the hydrodynamic shapes of fish and cetaceans.

      natschuster: Exactly how much mixing and matching do you expect if life was designed?

      You would have to make some suppositions about the designer, but if the designer was at least as intelligent as humans, then it would be rampant.

      natschuster: I understand that if you sequence some erv's we get different trees.For example, some of our erv's are closer to monkey's than to chimps.

      You might want to be specific. You might even want to be somewhat skeptical and think about whether there is a plausible explanation.

      Delete
    9. natschuster: And I for one , would not expect the fossil record to form a nested hierrtchy

      And yet it does, so the presumptions or your reasoning that led to your expectations must be viewed with skepticism.

      natschuster: I would expect the fossil record to have all, or at least some, of the transitionals that sit near the borders of the groups.

      And some such fossil records exists, such as for long stretches of fossil Cirripedia. However, fossilization is happenstance, many organisms don't fossilize well, either because of their structure, or because of their environment. In addition, population genetics suggests that a lot of evolutionary change will occur in small, isolated populations.

      Delete
    10. ""natschuster: And I for one , would not expect the fossil record to form a nested hierrtchy

      And yet it does, so the presumptions or your reasoning that led to your expectations must be viewed with skepticism.""

      Thats the problem. I would exoect to see smotth transitions and continuum between groups because that is what really happened.




      ""However, fossilization is happenstance, many organisms don't fossilize well, either because of their structure, or because of their environment. In addition, population genetics suggests that a lot of evolutionary change will occur in small, isolated populations.""

      So the fossil record does not show what actually happened. We need all kinds of apologetics to make it fit evoltution. Just like we need all kinds of stuff to explain the anomalies in the nested hierarchy.e.g. the parallel evolution of eyes acroos groups. It hardly seems parsimonious. Why not just take the fossil record at face value and say yhat it shows what really happened, different species living at different times.

      Delete
    11. natschuster: So the fossil record does not show what actually happened.

      Of course it does, but it only shows snapshots at irregular intervals.

      natschuster: the parallel evolution of eyes acroos groups.

      Again, try to be specific.

      natschuster: say yhat it shows what really happened, different species living at different times.

      As we pointed out above, there are series of fossils showing clear transitions. More important, we can predict and confirm the existence of transitional forms. How did Shubin know to look for a fishapod? Lucky guess?

      Delete
    12. Shubin found the fishapod in the wrong place. According to his own logic, had he known of the Polish tetrapod tracks he wouldn't have even been looking where he did.

      Delete
    13. Joe G: Shubin found the fishapod in the wrong place.

      A transitional may be found at any place after the divergence.

      Delete
    14. CORRECTION:

      Something that looks like a transitional may be found at any place after the divergence.

      And according to Shubin's own logic, had he known of the Polish tetrapod tracks he wouldn't have even been looking where he did.

      Delete
    15. Joe G: And according to Shubin's own logic, had he known of the Polish tetrapod tracks he wouldn't have even been looking where he did.

      Did you bother to read what we wrote? He could look anywhere after the posited divergence. The closer to the point of divergence, the more primitive the characters will likely be, and the more likely any such transitional may have yet avoided extinction.

      Delete
    16. Zachriel:
      Did you bother to read what we wrote?

      Yes, but obviously you didn't bother to read what we wrote. Or you are too stupid to grasp what we wrote.

      He could look anywhere after the posited divergence.

      Obviously you never read what Shubin wrote and you think your ignorance means something.

      Delete
    17. Joe G: you never read what Shubin wrote

      Wrong again, Joe G.

      Delete
    18. Then you are just ignorant, stupid or dishonest.

      Delete
    19. According to Shubin's own logic, had he known of the Polish tetrapod tracks he wouldn't have even been looking where he did.

      That is a fact which Zachriel would have known had it read and understood what Shubin wrote.

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

      Delete
    21. Your area of confusion is thinking that because the oldest evidence of tetrapods is, say, 365 million years old, that this means that scientists think that there were not tetrapods before 365 million years ago.

      The Fram formation is just part of the Devonian found on South Ellesmere Island. Not only did they want a date close to the divergence, but they also needed one associated with a semi-aquatic environment. They still would have probably ended up looking about where they did.

      Delete
    22. Zachriel:
      Your area of confusion is thinking that because the oldest evidence of tetrapods is, say, 365 million years old, that this means that scientists think that there were not tetrapods before 365 million years ago.

      Liar- I never even thought of such a thing.

      However Shubin made a point and the tetrapod tracks found in Poland ruined that point. Shubin thought he was looking in the strata between fish and the appearance of tetrapods- he was wrong.

      Delete
    23. First, the set-up:

      "In a nutshell, the 'fish–tetrapod transition' usually refers to the origin, from their fishy ancestors, of creatures with four legs bearing digits (fingers and toes), and with joints that permit the animals to walk on land. This event took place between about 385 and 360 million years ago toward the end of the period of time known as the Devonian. The Devonian is often referred to as the 'Age of Fishes,' as fish form the bulk of the vertebrate fossil record for this time."- Jennifer Clack, The Fish–Tetrapod Transition: New Fossils and Interpretations; "Evolution: Education and Outreach", 2009, Volume 2, Number 2, Pages 213-223

      Got that- "the transition" refers to an event, a specific event that occurred between two specified time periods, a time when there were fish and no tetrapods and the time when there were fish and tetrapods.

      With that now firmly established we return to "Your Inner Fish" chapter 1 where Shubin discusses what he was looking for- hint: evidence for the transition, ie the event:

      Let's return to our problem of how to find relatives of the first fish to walk on land. In our grouping scheme, these creatures are somewhere between the "Everythings" and the "Everythings with limbs". Map this to what we know of the rocks, and there is strong geological evidence that the period from 380 million to 365 million years ago is the critical time. The younger rocks in that range, those about 360 million years old, include diverse kinds of fossilized animals that we would recognize as amphibians or reptiles. My colleague Jenny Clark at Cambridge University and others have uncovered amphibians from rocks in Greenland that are about 365 million years old. With their necks, their ears, and their four legs, they do not look like fish. But in rocks that are about 385 million years old, we find whole fish that look like, well, fish. They have fins. conical heads, and scales; and they have no necks. Given this, it is probably no great surprise that we should focus on rocks about 375 million years old to find evidence of the transition between fish and land-living animals.- Neil Subin pages 9-10

      OK he did it just exactly as described, bracketed the dates. However his dates were wrong, which means he did not find evidence for the transition, which occurred many millions of years earlier.

      In order to find what he was looking for, evidence of the transition, he needed to focus on rocks 400 million years old, as the new data puts terapods in existence about 395 million years ago.

      Zachriel loses again, as usual.

      Delete
    24. Yet, he found a fishapod. Did you find a fishapod? How lucky can you be?!

      Delete
    25. So what? He didn't find what he was looking for- that is according to his logic.

      It isn't my fault that you are too dim to follow along.

      Delete
    26. Joe G: First, the set-up

      You are conflating transition with transitional. The latter term refers to an organism which exhibits traits common to both the ancestor and descendant.

      Joe G: OK he did it just exactly as described, bracketed the dates.

      Sure, but the dates don't have to be exact. He wanted to look close to the time of divergence, and in a semi-aquatic environment. He was looking just about where he needed to look, within a few percent of the age of the actual transition.

      Delete
    27. Zachriel:
      You are conflating transition with transitional.

      Talk to the scientists.

      Zachriel:
      The latter term refers to an organism which exhibits traits common to both the ancestor and descendant.

      Something that looks like it could be a transitional. Got it.

      According to Shubin's own logic, had he known of the Polish tetrapod tracks he wouldn't have even been looking where he did.

      That is a fact which Zachriel would have known had it read and understood what Shubin wrote.

      Delete
    28. Joe G: He didn't find what he was looking for

      He found exactly what he was looking for, something never seen by human before.

      Delete
    29. Again- Shubin was NOT looking for just a transitional form. He was looking for evidence of the transition.

      Shubin's own words make that very clear.

      Delete
    30. Joe G: Talk to the scientists.

      Your first quote concerns transition, not transitional fossil.

      Transitional forms
      http://evolution.berkeley.edu/evolibrary/article/lines_03

      Delete
    31. Zachriel:
      He found exactly what he was looking for,

      Not according to Shubin. I will go with what he said over your ignorant spewage.

      Delete
    32. Joe G: Shubin was NOT looking for just a transitional form. He was looking for evidence of the transition.

      A transitional form is evidence of the transition.

      Delete
    33. Zachriel:
      Your first quote concerns transition, not transitional fossil.

      Yes, I know. Shubin said he was looking for evidence of the TRANSITION.

      Delete
    34. Zachriel:
      A transitional form is evidence of the transition.

      Only if found in the proper place and time. Otherwise it just looks like a transitional form which is not evidence for the transition.

      Delete
    35. Joe G: Shubin said he was looking for evidence of the TRANSITION.

      That's right. A transitional form, an organism that exhibits traits common to both the posited ancestor and descendant, is evidence of the transition.

      Delete
    36. Joe G: Only if found in the proper place and time. Otherwise it just looks like a transitional form which is not evidence for the transition.

      That is incorrect. A transitional form might be found at any time after the divergence.

      Delete
    37. Zachriel:
      A transitional form, an organism that exhibits traits common to both the posited ancestor and descendant, is evidence of the transition.

      That is incorrect. The transitional form has to be in the right place and time before it can be considered as evidence for the transition.

      Again I will go with what Shubin wrote over an ignorant ass such as yourself.

      Delete
    38. Zachriel:
      A transitional form might be found at any time after the divergence.

      True, but Shubin wasn't looking for just a transitional form. Also no one knows how long after the alleged divergence transitional forms will last. Making yours an emotional plea lacking scientific rigor.

      Delete
    39. Joe G: Again I will go with what Shubin wrote

      Shubin never said that a transitional form has to be in an exact place and time, only that it was a reasonable place to look.

      "organisms that show the intermediate states between an ancestral form and that of its descendants are referred to as transitional forms."
      http://evolution.berkeley.edu/evolibrary/article/lines_03

      Delete
    40. Zachriel:
      A transitional form might be found at any time after the divergence.

      And yet we don't see Tiktaalik around today. You must be lying, again.

      Delete
    41. What Shubin said was he was looking for "relatives of the first fish to walk on land". That does not imply a direct line of descent.

      Delete
    42. Joe G: And yet we don't see Tiktaalik around today.

      Add "might" to the words you don't seem to understand. As fishapods don't exist today, how did Shubin know they once existed?

      Delete
    43. Zachriel:
      Shubin never said that a transitional form has to be in an exact place and time, only that it was a reasonable place to look.

      He said that his transitional form would be found before tetrapods. He was wrong.

      Delete
    44. According to Shubin's own logic, had he known of the Polish tetrapod tracks he wouldn't have even been looking where he did.

      That is a fact which Zachriel would have known had it read and understood what Shubin wrote.

      Deal with that or admit that you are an ignorant ass on an agenda.

      Delete
    45. OK he did it just exactly as described, bracketed the dates. However his dates were wrong, which means he did not find evidence for the transition, which occurred many millions of years earlier.

      In order to find what he was looking for, evidence of the transition, he needed to focus on rocks 400 million years old, as the new data puts terapods in existence about 395 million years ago.

      Zachriel loses again, as usual.

      Delete
    46. Joe G: He said that his transitional form would be found before tetrapods.

      No, he didn't say that. He said that strata before the oldest known tetrapods would be a good place to look. The oldest known tetrapods doesn't necessarily mean the oldest tetrapods.

      Joe G: According to Shubin's own logic, had he known of the Polish tetrapod tracks he wouldn't have even been looking where he did.

      As we pointed out, the Fram formation is just part of the Devonian found on South Ellesmere Island. Not only did they want a date close to the divergence, but they also needed one associated with a semi-aquatic environment. They still would have probably ended up looking about where they did.

      Joe G: However his dates were wrong, which means he did not find evidence for the transition, which occurred many millions of years earlier.

      That is incorrect. Shubin found a transitional form, which is evidence of the transition. He didn't say a direct ancestor of land vertebrates, but a "relative of the first fish to walk on land".

      As fishapods don't exist today, how did Shubin know they once existed?

      Delete
    47. He said that his transitional form would be found before tetrapods.

      No, he didn't say that

      Yes, he did. No one goes looking for transitional forms millions of years after the transition. Only retards do something like that.

      Shubin found a transitional form,

      In the wrong place- that is according to Shubin.

      Again no one goes looking for transional forms millions of years after the transition. That is a retards' errand

      Delete
    48. And is common descent the only explanation for fishapods? Nope, not by a long shot.

      Delete
    49. Joe G: No one goes looking for transitional forms millions of years after the transition.

      Darwin pointed out that transitional forms can be extant. However, the most interesting forms, ones with the most primitive traits, are going to be near the point of divergence.

      As fishapods don't exist today, how did Shubin know they once existed?

      Delete
    50. No one goes looking for a transitional form millions of years AFTER the alleged transition. That is because no one knows how long they will last.

      And that is why Shubin wrote what he did and that is also why he didn't find what he was looking for. What he was looking for occurred millions of years earlier than Tiktaalik.

      Delete
    51. Zachriel:
      As fishapods don't exist today, how did Shubin know they once existed?

      He didn't. However that they existed is not evidence for common descent.

      Delete
    52. Joe G: He didn't.

      Just a really odd coincidence, that he would be wondering an Arctic wilderness looking for a never before seen fishapod, and just stumble across one. Lucky?

      Delete
    53. Zach:

      How many transitionals exited that have not been found, Each and every transitional that has not been found can count as a failed prediction of evolution. So the half dozen or so times that evolution got it right compared to the hundreds of failed predictions, may very well be just lucky guesses,

      Delete
    54. natschuster: How many transitionals exited that have not been found

      For every transitional found, there's two more gaps!

      Delete
    55. That makes the problem worse. Where are all the transitionals, if they really existed? And I would only give half credit for Tiktaalik, since it isn't the real ancestor. That's still missing.

      Delete
    56. natschuster: That makes the problem worse.

      Heh. So you say you grew up, that your adult form developed from a baby, then toddler, then teen, then adult. So you show a picture when you're 10 and when you're 18. The skeptic asks, where's the inbetweens to show that you actually grew up. So you show a picture when you were 15. Ah, says the skeptic, now there's two gaps!

      The number of fossils is only the tiniest fraction of the total organisms that have ever lived. All they provide is a snapshot. But we can predict the existence of transitional fossils. Keep in mind that transitionals don't have to be direct ancestors, but finding hominids with brains intermediate between humans and chimpanzees is important confirmation of a transitional process.

      Delete
  12. CH: To support their high claim that the spontaneous origin of the species is a fact, evolutionists enlist all kinds of scientific evidence.

    You still haven't explained what you mean by "some kind of assistance", even when given the opportunity to point out exactly where said assistance would have occurred. As such, it's unclear how you can distinguish anyone's view from "spontaneous", including your own.

    CH: But inevitably their scientific evidence isn’t quite right.

    Can you contrast this statement with a theory for with the scientific evidence that is "quite right"?

    CH: The idea is that the common ancestry model predicts and requires such a pattern and that the finding of this hierarchy in biology is an extremely powerful proof text for evolution. But if this were true then evolution would be false by modus tollens, for the actual scientific evidence, as we have discussed many times here, is not so simple.

    First, is there a particular reason why you think it would be "simple", as opposed to no more simple than need be to explain what we observe? Why should our theories be exhaustive and not contain errors to some degree?

    Second, here's an example of modus tollens.

    If I am the axe murderer, then I can use an axe.
    I cannot use an axe.
    Therefore, I am not the axe murderer.

    Note, this is a process of criticism, not positive confirmation.

    For example, this doesn't falsify theory that someone else was the axe murderer or that the victim was murdered by an axe. Rather we (provisionally) discard the individual who cannot use the axe as the murderer, change our theory to another suspect, repeat, etc.

    CH: As one paper admitted, there is “no known mechanism or function that would account for this level of conservation at the observed evolutionary distances.” Or as another evolutionist admitted, the many examples of nearly identical molecular sequences of totally unrelated animals are “astonishing.”

    Can you express his as modus tollens? For example...

    If common descent is true, there will be conserved gene sequences and we will have exhaustive explanations for each conserved sequence
    There are conserved gene sequences for which we have no explanation
    Common descent is not true?

    But, this doesn't follow. Care to provide one that does?

    CH: An even more severe problem is that in many cases no comparison is even possible.

    Again, can you express this as modus tollens? For example...

    If common decent is true we will devise a way to compensate for every event which prevents comparison.
    We have not devised a way to compensate for at least three known events
    Common decent is not true?

    But, this doesn't follow, either. Our inability to compensate for these events means they do not tell us anything, one way or the other. Care to provide one that does?

    ReplyDelete
  13. CH: Short genes that produce what are known as microRNA also contradict Dawkins’ high claim.

    First, what is Dawkins' "high claim"? Why is it "high"?

    Second, we're not sure which tree is wrong. Any replacement theory would not only explain the same data just as well, but also explain the discrepancy between trees.

    To quote the article....

    “It looks like either the mammal microRNAs evolved in a totally different way or the traditional topology is wrong. We don't know yet.

    For example, take the OPERA experiment, in which neutrinos were "observed" going faster than the speed of light. This was a serious discrepancy as well. But did this result in discarding Einstein's theory? No, it did not. A replacement theory would not only have to explain the same observations just as well, but also explain why neutrinos obeyed the speed limit in every other experiment, except OPERA.

    Eventually, an explanation for the discrepancy between experiments was found: a loose cable and timer running at the wrong speed.

    AFAIK, no such replacement theory exists for the discrepancy between trees WRT microRNA. "Some designer must have wanted it to appear that way" doesn't explain anything.

    ReplyDelete
    Replies
    1. Scott, yours doesn't have a theory for explaining anything. We don't need a replacement theory for that.

      Delete
    2. BTW common design explains the similarities and the differences- the similarities are due to a common design and the differences are due to different final configurations involving a common design core.

      Delete
    3. Joe: Scott, yours doesn't have a theory for explaining anything.

      I don't think we're in agreement about what problem evolutionary theory addresses, or even what an explanation is. For example....

      Scott: Any theory about improvement raises the following question: how is the knowledge of how to make that improvement created? If it was already present at the outset, that theory is a form creationism. If it 'just happened', that theory is spontaneous generation.

      Distinct from either of these, biological Darwinism is the theory that the knowledge of how to make improvements in biological adaptations in nature was genuinely created over time through a process of variation that is random *to any specific problem to solve* and criticism in the form of natural selection. It genuinely did not exist before then.


      So, why don't you start out by providing an alternate explanation for the growth of this knowledge, then point out how biological Darwinism doesn't fit that explanation. In other words, AFAIK, if anyone lacks a theory, it's you.

      But, by all means, feel free to indicate otherwise.

      Delete
    4. Scott, you don't even have an explanation, so I don't need an alternate explanation.

      Delete
  14. Scott:
    If common descent is true, there will be conserved gene sequences and we will have exhaustive explanations for each conserved sequence

    Why is that? Why does common descent expect conserved gene sequences?

    ReplyDelete
    Replies
    1. Joe: Why is that? Why does common descent expect conserved gene sequences?

      Knowledge is information that tends to remain when instantiated in a storage medium. This includes brains, books and genomes. It is knowledge because it plays a causal role in being retained.

      For example, we still use Newton's laws of motion when launching space craft because it's an accurate enough approximation. However, it's not accurate enough in the case of global positioning systems. So, in those "environments" it is superseded by GR.

      In the case of genes being retained means being copied into the next generation.

      Good ideas are good regardless of what their source is. Adding a deigned to the mix doesn't add to the explanation.

      Delete
    2. Joe G: Why does common descent expect conserved gene sequences?

      Because you share most of your genes with your ancestors.

      Delete
    3. And all of my ancestors were human.

      Delete
    4. Really?

      Do muslims also track their ancestry from Adam and Eve? I never knew that. So Hitchens was right that Mohammed plagiarized the Old (and New) Testament to come up with the Koran and Islam.

      Delete
    5. Alan Fox: So Hitchens was right that Mohammed plagiarized the Old (and New) Testament to come up with the Koran and Islam.

      It wasn't plagiarism per se, but explicit incorporation.
      http://en.wikipedia.org/wiki/Islamic_view_of_the_Christian_Bible

      Delete
  15. Zachriel
    Why should a created blueprint not logically flow between different creatures?
    The nest is just showing what one would see from basic design. why not?

    The fossil record is not related since we are talking about a claimed nest. anyways it only shows depositions of life. the connections are not shown by the depositions but by interpretation of them by men. The wrong men to date!

    ReplyDelete
    Replies
    1. Robert Byers: The nest is just showing what one would see from basic design. why not?

      No. It would as if a designer of a Ford never saw a Chevy, or for that matter, the designer of a 1966 Mustang never saw a 1965 Mustang. Every new car seems to have a new blind and deaf designer. Sometimes the designers stumble across similar solutions, but most of the time they go off in different directions, trying to adapt existing systems to new environments. This is very unlike human engineers who rapidly adopt other design ideas.

      Furthermore, the designer never seems able to rethink anything. If a wire loops around something in a small car, even if the car is stretched, it continues to loop around it, even though a human engineer would just reroute it.

      Robert Byers: The fossil record is not related since we are talking about a claimed nest.

      There a many ways to arrange vehicles into nested hierarchies, but there is only one reasonable way to organize organisms by traits. That's because vehicle designers rampantly borrow across lineages, while organisms rarely do. Even then, we can often determine the natural mechanism involved.

      One other thing. Organisms reproduce, cars don't.

      Delete
    2. And your position can't explain reproduction, it has to start with it. Also gradual evolution does not expect a nested hierarchy as it would produce a smooth blending of defining characteristics.

      Perhaps Zachriel should grow up and get an real education.

      Delete
    3. Hey Chubs!

      Congrats on coming third in the elections for library monitor.

      Delete