Sunday, May 25, 2014

Evolution Professor: The Same Infection, In the Same Place, In the Same Gene

The Proofs of Evolution

In recent posts I have reviewed several problems with evolutionary thinking as evident in the Nelson-Velasco debate, including non scientific claims that only evolution can explain biology, arguments from authority, appeals to unknown or unlikely evolutionary mechanisms and pathways such as in the hypothetical evolution of the recurrent laryngeal nerve and ALUs, false claims about the empirical scientific evidence, such as with the ORFans and the so-called nested hierarchy, and appeals to a fictional track record of success of the theory of evolution. All of these problems are typical but if you stop there then you don’t really understand evolution. For while these may seem to be serious problems, they are dwarfed by the proofs of evolution.

In his debate with Paul Nelson, Joel Velasco argued that the recurrent laryngeal nerve is a powerful evidence for common descent and evolution. As Velasco explained, it is “one of my favorite examples,” but in fact it is quite challenging to figure out how evolution possibly could have evolved the nerve, whether in the fish or in the giraffe.

But that misses the point. The point is that its design, in giraffes for example, makes no sense. Therefore it would not have been created or designed. As Velasco explained:

[40:35] Now this is one of my favorite examples, this is a great picture here, this laryngeal nerve. There is a nerve that goes from your brain to your larynx. And if you look at a human it goes all the way down and wraps around the aorta, and then back up to the larynx. You might think, “Boy, that’s kind of weird.” Yes, it’s not that big of a deal. It seems like it’s kind of weird, it goes out of place. Now if you were a giraffe and that was 15 feet long you would really care.

In other words, in the giraffe this nerve is not a good design. Another popular example is the pentadactyl pattern found in so many species. Velasco explains that this design is not a useful trait:

[28:16] How do you predict this nested hierarchical structure? What does this have to do with evolution? Well only an evolutionary process—only descent with modification can possibly explain why when you look at different traits you get the same classification, over and over and over again. It’s not that having five fingers is a useful trait so the designer wanted a lot of things to have five fingers.

According to evolutionists, the pentadactyl pattern is not a rational design, for why would the same design be used for so many different purposes? It would not have been intended by a creator or designer. As Darwin had put it:

What can be more curious than that the hand of a man, formed for grasping, that of a mole for digging, the leg of the horse, the paddle of the porpoise, and the wing of the bat, should all be constructed on the same pattern, and should include similar bones, in the same relative positions?

Then there is the human tail which makes no sense, as Velasco explains:

[38:56] We have a tailbone. Now, it’s true, the tailbone is useful, you need it, you don’t want to lose it, but some people’s tailbone still have the tail muscle attached. The muscle to what? There’s no tail. Now that’s not quite right, many embryos do have tails. Usually it gets sucked back in and absorbed. It comes out in the babies first, you know the merconium it comes out, but actually some humans are born with tails. But the rest of us don’t have a tail, but we have a muscle that could move it if we had one. What’s that all about?

Here Velasco uses a rhetorical question to convey the hopelessness of rationalizing the design. The use of rhetorical questions is a common technique in the evolution genre. This is because evolutionists cannot actually demonstrate why any of these claims are true. Velasco has never been a giraffe so he doesn’t know how they feel about their 15 foot long laryngeal nerve.

Likewise Velasco has never created a pentadactyl pattern, much less an entire organism that has this design. Nor has he created tails or humans. In fact evolutionists would have a difficult time explaining just why these are such bad designs. So they shift the burden of proof to the creationist, using the rhetorical question.

And of course these cannot be extremely bad designs, because in that case they would never have evolved. Evolutionists are sure these are bad designs, but not real bad. And they offend our common sense. They may function, but they are not rational. No designer or creator would have done it that way. As Richard Dawkins explains, “it is the principle of the thing”:

Like any nerve, the optic nerve is a trunk cable, a bundle of separate “insulated” wires, in this case about three million of them. Each of the three million wires leads from one cell in the retina to the brain. You can think of them as the wires leading from a bank of three million photocells (actually three million relay stations gathering information from an even larger number of photocells) to the computer that is to process the information in the brain. They are gathered together from all over the retina into a single bundle, which is the optic nerve for the eye.

Any engineer would naturally assume that the photocells would point towards the light, with their wires leading backwards towards the brain. He would laugh at any suggestion that the photocells might point away from the light, with their wires departing on the side nearest the light. Yet this is exactly what happens in all vertebrate retinas. Each photocell is, in effect, wired in backwards, with its write sticking out on the side nearest the light. The wire has to travel over the surface of the retina, to a point where it dives through a hole in the retina (the so-called “blind spot”) to join the optic nerve. This means that the light , instead of being granted an unrestricted passage to the photocells, has to pass through a forest of connecting wires, presumably suffering at least some attenuation and distortion (actually probably not much but, still, it is the principle of the thing that would offend any tidy-minded engineer!).

Then there are those irrational designs that repeatedly appear in neighboring species, such as broken genes. It is the so-called “shared-error argument”:

[42:10] Why don’t we smell very well. Well if you know something about biology you might think, “well we don’t have enough genes that get expressed as olifactory receptors,” you know we have about 400, but mice have a thousand. Four hundred is actually not that much. But actually we have 800 olifactory receptor genes, 400 are just broken. That is, we still have the genes inside our body, but there is just some mutation that has turned it off or messed with it. In fact, all the primates have the same broken genes, in the same place, broken in the same way. That’s why primates don’t smell as well as dogs. Dogs have the same genes we do, ours are just broken. [42:50] Most mammals don’t need to eat fruit. They can make their own Vitamin C. They can metabolize it. But actually the primates can’t. Now here, interestingly, there’s one other group—the fruit bats can’t. That’s not a result of common descent. That’s a separate break. In fact when you look at the details, it’s broken in a different place. But all the primates have the gene for making Vitamin C broken in exactly the same way. In exactly the same place. Why? Because it was broken in the ancestor mammals, and just got passed on.

And retro viruses:

[45:50] Now normally this wouldn’t get passed on, but every once in awhile, it inserts itself into a sperm or an egg cell, that gets passed on. So there is a record of viral DNA. When we look at your DNA, here’s a string, maybe a hundred base pairs, from a virus. You’re like, wow, that’s weird. You have 30,000 of them. It’s about 1% of your genome, is viral DNA, from retro viruses. And in fact, when we look, we share the retro virus infection—so there are some that all humans have. But actually there are some that the great apes have—humans, chimps, gorillas. You think, why do the three of us have the same infection, in the same place, in the same gene? Answer: Because actually the thing that was infected is the ancestor of the great apes.

And useless genetic markers:

[~48:00] We share lots of things in common, but when you look at the molecules, you look at the molecular markers inside, the case is overwhelming. We have markers that serve no purpose, they come from viruses.

Of course the similarities between species are many. One could make a long, long list of all the similarities between different species. So why do evolutionists focus on those similarities that don’t look right? Why does Velasco list off the similarities that are inefficient and broken?

Indeed these make evolution less likely. If Velasco was trying to explain why the evidence makes evolution more probable then he chose the wrong set of data. But evolution is all about contrastive thinking. The point is not to prove evolution but to disprove the competition. Evolution is more probable not because these broken designs raise its probability, but because they lower the probability of the alternatives.

From a scientific perspective the idea that the species arose spontaneously is absurd. Evolutionists do not have anything close to a scientific explanation for their ridiculous idea. Indeed, science flatly refutes evolutionary theory. Evolution can’t even create a single protein, much less millions upon millions of species.

But this isn’t about science. It never was. Evolution is no different from ancient Epicureanism. It is a non scientific belief system that mandates a strictly naturalistic origins theory.

Religion drives science and it matters.

53 comments:

  1. atheists have their theology, which is basically: "God, if he existed, wouldn't do it this way (because) if I were God, I wouldn't (do it that way)."
    http://www.evolutionnews.org/2014/05/creationists_th085691.html

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    1. BA77:

      Not atheists, but evolutionists. The distinction between atheist and theist is not really very meaningful. They all hold the same religious beliefs.

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    2. Can you point out the religious beliefs in my comment below? Please be specific.

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    3. bornagain77 atheists have their theology, which is basically: "God, if he existed, wouldn't do it this way (because) if I were God, I wouldn't (do it that way)."

      http://www.evolutionnews.org/2014/05/creationists_th085691.html


      Klinghoffer, as usual, fields one of his army of strawmen.

      The argument, correctly stated, is that we see structures in biology which ID proponents tell us bear the hallmarks of design. We point out that, from the perspective of human design, we can see a way or ways in which it could have been done better. If ID proponents want to make the case for design, therefore, they must not only provide evidence for the existence of a more advanced alien designer but also explain why the structure is not the inferior design it appears to be.

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    4. Cornelius Hunter Not atheists, but evolutionists. The distinction between atheist and theist is not really very meaningful. They all hold the same religious beliefs.

      So believing a god exists is the same as not believing a god exists? A proposition is the same as its negation? Not collecting stamps is as much a hobby as collecting stamps?

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    5. Ian:

      Not collecting stamps versus collecting stamps makes little difference in a soccer game. When atheists such as Richard Dawkins, PZ Myers, etc., claim god wouldn't create X, and theists such as Francis Collins also claim god wouldn't create X, it is the metaphysical claim that counts, not their belief in God, or lack thereof.

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  2. CH: but in fact it is quite challenging to figure out how evolution possibly could have evolved the nerve, whether in the fish or in the giraffe.

    Fortunately, we're not limited to what you can "figure out".

    CH: But that misses the point. The point is that its design, in giraffes for example, makes no sense. Therefore it would not have been created or designed. As Velasco explained:

    [...] Now if you were a giraffe and that was 15 feet long you would really care.

    You seemed to be taking a more reasonable approach in previous articles. Apparently, I have to spell it out for you.

    If you were a giraffe that was also a person, who can comprehend and create explanatory theories about how the world works, you would care. You wouldn't be you if you were a giraffe. That's because only people can conceive of problems and propose explanatory theories speciously targeted at solving them.

    CH: In other words, in the giraffe this nerve is not a good design.

    Like good explanations, very good designs are hard to vary without significantly reducing their ability to solve a problem.

    For example, based on explanatory theories, such as signal propagation, the length and placement of the nerve in the giraffe could be routed somewhere else significantly out of the way and work just as well. It's current placement also greatly exposes the nerve to potential damage along the entire neck. However, a more directly route would reduce the time the signal takes to travel from the brain to the larynx and reduce exposure to damage.

    When building modern day CPUs, we use complex computer programs to layout the path of each signal to keep distance to a minimum. This increases performance and reduces power consumption. Automating the process also allows us to completely re-layout significant areas or even a CPU's entire signal path when even small changes are made to the processor. IOW, improvements in CPU speed and efficiency are, in part, explained to us having created explanatory knowledge of how to more efficiently layout signal paths on a chip. Again, there are many different layouts that are equally, significantly less efficient and take much longer for signals to propagate.

    So, the design of the nerve makes sense from an non-explantory perspective, because non-explanatory knowledge has limited reach. However, it doesn't make sense from an explanatory perspective because explanatory knowledge has significantly greater reach. For example, If we take ID seriously, in that the designer routed the nerve in the first place using explanatory knowledge, re-routing just that nerve again would be trivial.

    CH: According to evolutionists, the pentadactyl pattern is not a rational design, for why would the same design be used for so many different purposes?

    Again, see above. Humans are good explanations for human designed things precisely because of our limitations. However, ID's designer is abstract and has no defined limitations. There is no limit on what it knows or when it knew it. This is by design.

    CH: In fact evolutionists would have a difficult time explaining just why these are such bad designs. So they shift the burden of proof to the creationist, using the rhetorical question.

    Given that I didn't have problems explaining why these designs do not make sense in the context of explanatory knowledge, does that mean I'm not an "evolutionist"?

    CH: And of course these cannot be extremely bad designs, because in that case they would never have evolved.

    I've never suggested that useful rules of thumb are, well, not useful. Rather, they have limited reach.

    Design isn't a black box that we cannot make progress explaining. The idea that we know absolutely nothing unless we explain something exhaustively is bad philosophy.

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  3. Cornelius Hunter: Of course the similarities between species are many.

    Not just similarities, but a family resemblance (nested hierarchy).

    Cornelius Hunter: Indeed these make evolution less likely.

    Why would a nested hierarchy of mutations in endogenous retroviruses make evolution less likely?

    Cornelius Hunter: The point is not to prove evolution but to disprove the competition.

    There are several ways to approach the question. We can test hypotheses with high surprisal, we can attempt to falsify hypotheses, and we can compare the hypothesis with other hypotheses attempting to explain the same phenomenon. Generally, all three are done, and in most cases, using different types of data and methodologies in order to add confidence in the conclusion.

    Cornelius Hunter: From a scientific perspective the idea that the species arose spontaneously is absurd.

    Not sure why you say that. The evidence seems conclusive. Do you have an alternative hypothesis to propose?

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    1. Zachriel:

      Not sure why you say that. The evidence seems conclusive.

      For instance, as I mentioned in the OP, evolution can’t even create a single protein. It falls ~27 orders of magnitude short, and even that is according to the unrealistic calculations of evolutionists. For instance, the number of tries available to evolution was calculated assuming the pre existence of bacteria, and therefore proteins. So the number of tries available to evolve a protein entails the pre existence of proteins! And even with that circular logic, even with every advantage, evolution falls astronomically short.

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    2. Zachriel:

      Not just similarities, but a family resemblance (nested hierarchy).

      First off, there are many examples of non-nested hierarchy in living organisms. Why lie? Second, why should a nested hierarchy (or common descent) be evidence against intelligent design? As a software designer, I use a nested hierarchy to design my C++ and C# classes all the time. Reusing previous designs is a time-honored tradition and the intelligent thing to do. It automatically creates a mostly nested hierarchy with a few instances of horizontal (multiple) inheritance. Most object oriented computer languages enforce a strictly nested hierarchy. There is certainly an evolution in software development but it is not Darwinian evolution.

      So again, I ask. Why do you present the existence of a nested hierarchy in living organisms as evidence against intelligent design when the exact opposite is the truth? What are you, a wise guy?

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    3. Cornelius Hunter: For instance, as I mentioned in the OP, evolution can’t even create a single protein.

      You may have mentioned it, but it's not accurate. Not only are proteins found in random sequences, but exon shuffling can create new proteins, and we have evidence of their historical evolution from the nested hierarchy.

      Louis Savain: First off, there are many examples of non-nested hierarchy in living organisms.

      You're not being specific enough. If you mean we can detect anomalies against the background nested hierarchy, then yes. Of course that grants there is a background pattern with which to notice the anomalies.

      Louis Savain: As a software designer, I use a nested hierarchy to design my C++ and C# classes all the time. Reusing previous designs is a time-honored tradition and the intelligent thing to do.

      And for that reason, when we categorize many different software programs, there are many equally rational categorizations. With biology, there is only one categorization that makes sense for the vast majority of organisms.

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    4. Zachriel:

      Louis Savain: First off, there are many examples of non-nested hierarchy in living organisms.

      You're not being specific enough. If you mean we can detect anomalies against the background nested hierarchy, then yes. Of course that grants there is a background pattern with which to notice the anomalies.


      This is not about probability. Only one exception breaks the rule. A single example of horizontal gene sharing is enough. Conjuring up laughable scenarios like convergent evolution to explain horizontal gene sharing is not a scientific explanation. It's superstition of the voodoo kind.

      Louis Savain: As a software designer, I use a nested hierarchy to design my C++ and C# classes all the time. Reusing previous designs is a time-honored tradition and the intelligent thing to do.

      And for that reason, when we categorize many different software programs, there are many equally rational categorizations. With biology, there is only one categorization that makes sense for the vast majority of organisms.


      This is nonsense. First off, all modern object-oriented software use strictly nested class design. Only a few C++ programs use multiple inheritance. Why? Because it makes logical sense. It's not something that was adopted on a whim. Second, we see both nested and non-nested designs in nature. The fact that the vast majority is nested is powerful evidence for intelligent design. Why? Because this is what intelligent designers do.

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    5. LS: As a software designer, I use a nested hierarchy to design my C++ and C# classes all the time. Reusing previous designs is a time-honored tradition and the intelligent thing to do.

      A software developer, you know we currently cannot simply rewrite an entire application overnight to migrate from, say, Win32 to C#. It's simply not practical due to our limitations.

      However, ID's designer is abstract and has no defined limitations. As such it's not limited by what it knows, when it knew it, what resources or time has at it's disposal, etc. As such, it's not limited from rewriting an application, in it's entirety, for every single customer, to meet their specific needs. And the same could be said about designing computers. Entire one-off operating systems could be written for each one-off computer built for each customer, along with one-off versions off each application to run on them.

      Nor is ID's designer limited from creating one-off programming languages for each customer's application.

      To use another example, we currently do not design entirely new automobiles every year because doing so is simply too resource intensive, expensive, etc. It's simply not practical. Even then, new models often rely on the same power train because next gen engines need to be long term tested on the track, etc. However, ID's designer would not be limited from designing an entirely new model, from the ground up, for every single customer. This is because it has no limitations on what it knows, such as if a design is crash worthy, if it has long term engineering issues, etc. Nor is it limited from designing automobiles in the order of most complex to least, or even all at once.

      At some point in the future, assuming we create the necessary knowledge in time to prevent ourselves from going extinct, we'll use exponentially more powerful computers that we have now to create one off systems and products for each customer, in conjunction with vastly more capable manufacturing systems which make 3D printing look like child's play. Heck, customers will do it in their own homes and garages. So will their *children*.

      IOW, you greatly underestimate the role that knowledge, or the lack there off, plays in design. Human beings are good explanations for human deigned things, precisely because of our current limitations.

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    6. Zachriel,

      I think CH was referring to the origin of the first protein on the planet.

      Of course, science has no plausible explanation of how it arose. But neither does "creation." Creation is just another placeholder for what we don't know.

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    7. Scott: However, ID's designer is abstract and has no defined limitations.

      J: There's way more than one "ID designer" conception, Scott. And they're not all equally explanatory or coherent in what they posit of the designer and what they think they're explaining. If you can't conceive of how to explain a way to distinguish warranted HUMAN belief from non-warranted HUMAN belief, you can't explain anything else with any discernible plausibility that is relevant to HUMAN communication.

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    8. Scott: However, ID's designer is abstract and has no defined limitations.

      Jeff: There's way more than one "ID designer" conception, Scott. And they're not all equally explanatory or coherent in what they posit of the designer and what they think they're explaining.

      Jeff, the necessity of God as your foundation is arbitrary for reasons I've outlined elsewhere. For example, why doesn't God need a foundation?

      Even if, for the sake of argument, we assume the necessity of finality of explanation, God need not be that foundation. Furthermore, I've presented an epistemology by which the finality of explanation necessary.

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  4. Louis Savain: Only one exception breaks the rule.

    Hybridization breaks the "rule", though it's not a rule, but a pattern. There is a pattern, even if it is not perfect.

    Does the Earth follow an elliptical orbit around the Sun?

    Louis Savain: Conjuring up laughable scenarios like convergent evolution to explain horizontal gene sharing is not a scientific explanation.

    Um, those are two separate mechanisms.

    Louis Savain: First off, all modern object-oriented software use strictly nested class design.

    Within a program, it may be strictly nested, but between programs, there is more than one valid classification.

    Louis Savain: Second, we see both nested and non-nested designs in nature.

    You're not being specific enough. If you mean we can detect anomalies against the background nested hierarchy, then yes. Of course that grants there is a background pattern with which to notice the anomalies.

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  5. Dr. Hunter, I actually have found many of the arguments you present above, genes broken in the same place, retroviruses in the same place, disease producing point mutations in the same place, as compelling evidence for universal common descent. It is in fact these very arguments that cause me to hold to UCD.

    You have made many arguments over the years that seriously challenge neo-Darwinism. Some of these arguments are doing exactly what you are accusing the Darwinists of doing, making a case against the other point of view. Such logic is absolutely reasonable whether you use it, or they do.

    What you have done for me with your "this can't be explained with Darwinism" arguments is to bolster my agreement with you.

    I hold that UCD is correct, as supported by the evidence above. I hold that neo-Darwinism is incorrect as supported by the many challenges you have made.

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    1. Thanks bFast for the thoughtful comment (and while I'm at it, thanks to all the others--evolutionists and skeptics--for their good comments). One problem is that while there are some similarities and shared "errors," there are myriad contradictions--comparisons that violate common ancestry and are way outside evolution's noise level.

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  6. Dr. Hunter, interesting that you mention pentadactylism. I find pentadactylism to make a compelling case against neo-Darwinism.

    It appears from rare mutations, that polydactylism is very easily achieved genetically. Many quadrupeds have developed oversized appendages, yet not a one of them has done so by adding an extra digit. Why would nature avoid using this obviously handy method of getting greater breadth? Natural selection should not select out such an obvious solution to an oft repeated problem.

    My view only seems to be respected by the late Stephen Gould who, in "8 Little Piggies" seriously puzzled why nature held so tenaciously to 5 digits.

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  7. Once again common design is a option for likeness in biology. What would you do??
    Why would a creator make each kind of creature different in its innate structure? why not a common design and then tweek it?
    Its a option.
    For YEC the giraffe was not created but a post flood later adaptation from some small creature.
    I say bats were not created but a post flood adaptation for a rat to fly.
    Moles were originally not made to burrow in the ground.
    Creationists can and must accept great changes in biology by unknown mechanisms.
    People are at least a little bit changed from Noahs family.

    All this istill evolutionism using lines of reasoning beside mere raw data.
    Its not biological scientific evidence. Its just putting two and two together.
    Thats math and not science.
    And its still wrong.

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  8. Robert Byers: Why would a creator make each kind of creature different in its innate structure? why not a common design and then tweek it? Its a option.

    Given an ordinary designer, if each organism were an individual creation, like a vehicle design, then they would not form a specific nested hierarchy due to rampant mixing-and-matching. However, if the designer worked by tweeking common descendants then it might still form a nested hierarchy. Think of a tree that has been trimmed to form a particular shape or grow in a particular direction. The tree topology is the natural component, but the overall shape is not. To determine whether that is a possibility, we would have to look at other evidence.

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    1. If I understand. I mean the creator tweeks KINDS of creatures. Not at a species level.
      So having common design/DNA would be reasonable and a option at atomic or basic levels.
      Its less likely a creator would make kINDS different enough like he was thinking it over.
      It would be a equation or a computer output from a simple original equation.
      I expect and desire to find biology all related at basic DNA levels and creatures all having hearts and butts and bones as if off the same rack.
      My arm bones should be like a rats or a elephants if common design was the equation.
      Its an option and so JUST because of this option its not oNLY the option that like looks equals common descent.
      Common deswcent is not shown by biological scientific evidence but only by a line of reasoning that eliminates any other option(s).
      Common design as a option eliminates common descent as true by mere reasoning from like looking data.

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    2. Robert Byers: I mean the creator tweeks KINDS of creatures.

      That doesn't explain why "kinds" form a nested hierarchy, much less the fossil succession.

      Robert Byers: It would be a equation or a computer output from a simple original equation.

      You have to contort the idea to make it work. That's just not how human designers work. The designer of the bat never saw a bird or even a feather.

      Robert Byers: My arm bones should be like a rats or a elephants if common design was the equation.

      We understand the idea of taking a basic design and modifying it, but human designers also rework the design, while borrowing rampantly across lineages. When Ford puts a radio in their cars, so does GM. When Apple puts windows in their operating system, so does Microsoft. But when mammals fly, they don't use feathers.

      That's why human artifacts don't form a single nested hierarchy, but can be classified in many different, equally rational, ways.

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    3. Zachriel:

      Could it be that feathers wouldn't work so well to accommodate a bat's lifestyle? Maybe feathered wings don't allow enough manuverability.

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    4. I keep on reading that the relationships among mammalian groups gets revised based on genetic data. For example, pangolins used to be considered close to anteaters and sloths, Now they are in the same clade as carnivores. This would seem to indicate that there is more than one way to classify organisms as well.

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    5. And there is plenty of mixing and matching among organisms. e.g. pangolins have scales that make them look like reptiles. Just how much do you expect?

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    6. natschustser: Could it be that feathers wouldn't work so well to accommodate a bat's lifestyle?

      Many birds hunt insects, but certainly bats are highly adapted to their own niche. That's expected of design and of evolution by natural selection. However, only evolution predicts the nested hierarchy.

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    7. natschuster: I keep on reading that the relationships among mammalian groups gets revised based on genetic data.

      The closer the relationship, the more distant in time, the less resolution we have; but the overall pattern remains. It's the genetic data that helped resolve the origins of pangolins.

      natschuster: Just how much do you expect?

      Something akin to human design, otherwise the posited designer is constrained in ways that mere humans are not.

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    8. The genetic data conflicts with the morphology, so we get mixed signals, or mixing and matching. So the nested hierarchy kinda breaks down when looking at orders. It can even be hard to sort out the relationships at the species level because of conflicting signals. It gets really hard to sort out relationships at the level of the kingdom and phylum. I'm finding it harder and harder to accept evolution as the best explanation for the nested hierarchy.

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    9. natschuster: The genetic data conflicts with the morphology, so we get mixed signals, or mixing and matching.

      More accurately the anatomical data is often not sufficient to reach a firm conclusion. In any case, the nested hierarchy is not perfect, nor was that ever a claim. You do realize that Darwin not only recognized the problem you described, but provided a consistent theoretical explanation.

      natschuster: I'm finding it harder and harder to accept evolution as the best explanation for the nested hierarchy.

      Well, at least your recognize that there is a nested hierarchy.

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    10. An aardvark looks more like a anteater than it does an elephant. But it is considered closer to the elephant. A tenrec looks more like an insectivore, yet it is considered a closer to the manatee. Whales don't look anything like cows , but they are considered members of sister groups. And I understand that sometimes you even get conflicting data from the genes as well.

      And I understand that Darwin's approach to the problem was to claim convergence. Does that explain why animals that are distantly related have similar DNA? Is there convergent DNA?

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    11. natschuster: An aardvark looks more like a anteater than it does an elephant.

      Sure, and a dolphin looks superficially like a fish.

      Does the aardvark have eukaryotic cells? Cell differentiation? Ingest food for nourishment? Bilateral symmetry? An alimentary tube? A nerve cord? A head with a brain and an array of sense organs? Bony vertebrae? Jaws? Teeth? Bony limbs with digits? An amniote? Mammary glands? Placenta? So they fit the nested hierarchy quite well. We're quibbling over details.

      There are notable anatomical differences between aardvarks and anteaters, such as the placement of their claws. Their separate origins was determined by anatomical differences before the genetic evidence provided confirmation.

      natschuster: And I understand that Darwin's approach to the problem was to claim convergence.

      Yes. It's evidence of natural selection, yet if we look closely, we can usually determine their separate origins—just as Darwin postulated.

      natschuster: Does that explain why animals that are distantly related have similar DNA?

      You might want to be specific, but molecular data supports the nested hierarchy.

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    12. The aardvark used to be put in the same family as anteaters because of the similarities. That means there is mixing and matching. So it can be hard to sort out the groups at every level.

      The tenrec look s more like a insectivore than an elephant. yet it is considered more closely related to the elephant. You have one big group of animals that are very different morphologically. Then you have another big group of animals hat are also all over the place morphologically. That's a lot of mixing and matching, just like in artifacts.

      And isn't saying that artifacts don't form one nested hierarchy quibbling over details as well?
      It all depends on your criteria.

      And does convergence explain why there distantly related organisms sometimes have similar DNA, and more closely related organism don't?

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    13. natschustser: The aardvark used to be put in the same family as anteaters because of the similarities. That means there is mixing and matching.

      Yes, and dolphins look superficially like fish. Some traits don't fit the overall nested hierarchy. Nevertheless, when you look at the majority traits, the classification becomes more clear.

      You ignored the overarching classification; eukaryote, metazoan, bilaterial, deuterostome, chordate, chordate, vertebrate, gnathostomes, tetrapod, aminote, mammal, eutheria. So do you agree that they classify quite well into the larger sets?

      natschuster: And isn't saying that artifacts don't form one nested hierarchy quibbling over details as well?

      No, because artifacts don't classify properly at any level, often especially at the highest level. There's no doubt how to classify anteaters and aardvarks as eukaryotes ... eutherians.

      natschustser: And does convergence explain why there distantly related organisms sometimes have similar DNA, and more closely related organism don't?

      We asked for specifics.

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    14. Even within the overarching classification, it can be hard to sort things out, like how things connect at the kingdom and phylum level.

      And why can't we classify things like vehicles into land vehicles, sea vehicles, and airships. Then land vehicles are cars, trains, bicycles. Cars into trucks SUV's and cars? Its all in the definitions,

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    15. "We asked for specifics."

      Sea slugs have plant DNA. Aphids have fungal DNA.
      Some of our genes are closer to the gorilla than the chimp.

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    16. natschuster: like how things connect at the kingdom and phylum level.

      You have trouble distinguishing most plants and animals, or sponges from chordata?

      natschuster: And why can't we classify things like vehicles into land vehicles, sea vehicles, and airships. Then land vehicles are cars, trains, bicycles. Cars into trucks SUV's and cars?

      Sure you can. Or you can classify first by maker, then by model. Or first by passenger or cargo, then number of wheels. And so on. There's no single rational way to classify vehicles. But with life, organisms fall naturally into a single pattern; eukaryote, chordate, amniote, eutheria, aardvark. This was determined before Darwin.

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    17. natschuster: Sea slugs have plant DNA. Aphids have fungal DNA.

      Those are obvious cases of endosymbiosis.

      natschuster: Some of our genes are closer to the gorilla than the chimp.

      That's due to incomplete lineage sorting, the basic arithmetic of population genetics.

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    18. There's stuff like this two:

      http://www.sciencedaily.com/releases/2007/10/071009212538.htm

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    19. "You have trouble distinguishing most plants and animals, or sponges from chordata?"

      I understand that it is hard to sort out how the various animal phyla are connected. Annelids, arthropods, things like that. It is also hard to determine how the kingdoms are connected. are we closer to bacteria or archeaobacteria? Things like that.

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    20. natschuster: There's stuff like this

      Yes, the explanation makes sense.

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    21. natschuster: I understand that it is hard to sort out how the various animal phyla are connected.

      Think about it? What does evolution say about how two lineages diverge? At the time of divergence, the two lines are very similar, so, of course the closer we get to that time, the more difficult it will be to determine the differences.

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    22. "Those are obvious cases of endosymbiosis."


      I was under the impression that the sea slugs didn't have algae living inside their cells, but rather had algae DNA in their genomes. Same thing with the aphids.

      Say, for example. annelids branched off first. That would mean that, for example, mollusks and arthropods are closer to each other than to annelids. It shouldn't be too hard to see that, somehow. It should actually be easier given all this time they have been evolving apart. And I'm not talking about going back in time. I'm talking about what we see now. It's hard to sort out things near the trunk.

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    23. If decided to sort organisms based on things like econiche, function, purpose,habitat, relationship to humans, ritually pure or impure, you would get different results, just liek with artifacts. It all depends on your criteria.

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    24. natschuster: I was under the impression that the sea slugs didn't have algae living inside their cells, but rather had algae DNA in their genomes. Same thing with the aphids.

      Yes, and eukatyores have remnants bacterial genomes in both their nucleus and in the cytoplasm in the form of mitochondria. Yes, we already said there is some mixing-and-matching, but is usually the exception, and we can often find evidence of what happened historically.

      natschuster: That would mean that, for example, mollusks and arthropods are closer to each other than to annelids. It shouldn't be too hard to see that, somehow. It should actually be easier given all this time they have been evolving apart.

      Evolving apart means we can tell them apart, but that doesn't mean we can easily tell the branching order. They started close together, so resolution is going to be poor. However, they all have eukaryotic cells, and they each form their own nested hierarchy. Again, it's like we see three branches on a tree from a distance, and can't quite see where they join. Maybe they're just floating there, but the rest of the tree looks joined in the standard topology. Meanwhile, genetic data has helped resolve some of these types of questions.

      natschuster: If decided to sort organisms based on things like econiche, function, purpose,habitat, relationship to humans, ritually pure or impure, you would get different results, just liek with artifacts.

      You can force fit anything into any scheme, but there's only one reasonable classification. Consider this: If you have an organisms with mammary glands, we can reasonably predict it will have eukaryotic cells, cell differentiation, bilateral symmetry, an alimentary tube, a nerve cord, a head with an array of sense organs, vertebrae protecting the nerve cord, jaws with teeth probably heterodont, embryo with four limb buds, an amniote, four chambered heart, bellows lungs, hair follicles, auditory ossicles, etc. That's what the nested hierarchy means.

      Now with vehicles, it has a radio. What can you tell us about the vehicle? It has four wheels. What does that tell you? If has a four-cylinder engine. What does that correlate with?

      A cargo truck or passenger car may have a radio. A Ford or a Chrysler may have four wheels. And you may or may not consider a motorcycle to be impure, but you probably can't construct a consistent correlation with other traits.

      But when you compare a fish and a dolphin, you can look at just the fins, and tell which one has mammaries.

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    25. To the best of my knowledge, if you find an air speed indicator, then it is a pretty safe bet that it is an airplane, and it has wings. If you find a keel then it is a pretty safe bet it is a boat, and has a propellor. If you find a differential axle, then it is probably a car, and has wheels.

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    26. natschuster: if you find an air speed indicator, then it is a pretty safe bet that it is an airplane, and it has wings.

      Helicopter

      natschuster: If you find a keel then it is a pretty safe bet it is a boat, and has a propellor.

      Sail boat.

      natschuster: If you find a differential axle, then it is probably a car, and has wheels.

      Could say truck, but we'll go with equation clock.

      Now, you've just started. Try to do the same with more and more characteristics, and you'll find that there are just too many anomalies to make a consistent pattern.

      Think how many consistent levels are involved with organic taxonomy; eukaryotic cells, cell differentiation, bilateral symmetry, an alimentary tube, a nerve cord, a head with an array of sense organs, vertebrae protecting the nerve cord, limbs with digits, amniote, mammaries, placenta, and so on.

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  9. Zach:

    If I understand you correctly, you are saying that the best explanation for the nested hierarchy is evolution because a human like designer would have more mixing and matching at the species level. However, I understand that it gets really hard to sort out the relationships of the major groups at the kingdom and phylum level. If they descended via a bifurcation then we should be able to determine sister groups. But we keep on getting different signals, so people produce different arraignments.

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    1. natschuster: If I understand you correctly, you are saying that the best explanation for the nested hierarchy is evolution because a human like designer would have more mixing and matching at the species level.

      That, and all sorts of other evidence, including the fossil succession.

      natschuster: However, I understand that it gets really hard to sort out the relationships of the major groups at the kingdom and phylum level.

      The more distant the time, the more close the relationship, the more rapid the transition, the lower the resolution. This is the expected pattern. Even then, such difficulties don't call into question the overall pattern. It's like looking at a tree from a distance, and seeing the pattern of branches and limbs forming the nested topology, but not being able to resolve some branches that are farthest away.

      natschuster: If they descended via a bifurcation then we should be able to determine sister groups.

      Not necessarily due to limited data, and the nature of the data. It's the fact that hominids closely resemble other apes, and having to work with fragmentary remains, that we have trouble distinguishing the various taxon.

      natschuster: But we keep on getting different signals, so people produce different arraignments.

      The overall pattern remains, even if we have troubles determining whether birds are more closely related to theropods or to some more primitive archosaur.

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  10. Zachriel
    i don't see why you make a case that common design shouldn't predict, as a option, the very common design found in biology?
    its just as it would be if i was creating nature.
    one blueprint and tweeking.
    This YEC suspects bats were not designed but a post flood adaptation of a rat. no creator involved.
    its still just a line of reasoning your pushing here about like looks equals like descent. even if true its just deduction.
    Deduction is not science. it demands no other options or deduction is worthless to discover the fact.

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    1. Robert Byers: i don't see why you make a case that common design shouldn't predict, as a option, the very common design found in biology?

      Because,

      1. Human artifacts, our only example, don't form a single nested hierarchy.
      2. The fossil succession.

      Robert Byers: This YEC suspects bats were not designed but a post flood adaptation of a rat.

      Mice and bats are not that closely related, but they do have a common ancestor. Hence, they form a nested hierarchy. Now by the same logic, common descent explains the nested hierarchy of mice and bats with other mammals, and other vertebrates, and other eukaryotes.

      Robert Byers: Deduction is not science.

      Deduction is part of science, as in hypothetico-deduction. Confirmation is the other part. So positing common descent predicts transitional forms, and that is what the evidence supports.

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