Thursday, December 30, 2010

It Didn’t Begin (or End) With Darwin

By far the most amazing aspect of evolution is not its idea that all things just happened to arise spontaneously but—even more eyebrow raising—its claim that all of this is a scientific fact. It would be irrational and perverse to deny it, insist evolutionists. Evolution is, they say, beyond any shadow of a doubt, as certain as gravity, nay even more certain. This claim is so obviously false that it begs the question: what are evolutionists thinking?

Evolutionists say their idea is an obvious scientific fact and they have explained why over and over. In fact, the reasoning was already well established when Charles Darwin wrote Origin a hundred fifty years ago.

For instance, Darwin agreed that the perfection of the eye reminds us of the telescope which resulted from the highest of human intellect. Was it not right to conclude that the eye was also the product of a great intellect? This may seem the obvious answer but Darwin warned against it, for we should not “assume that the Creator works by intellectual powers like those of man.” Better to imagine the eye as the result of natural selection’s perfecting powers rather than having god too much involved in the world.

This warning against anthropomorphizing god came right out of the Enlightenment philosopher David Hume whose writings Darwin was well familiar with. It was a reaction to English natural theology that argued the world looks designed by god. Hume argued this made god out to be too much like His human creatures. For example, the natural theologians were fond of comparing the human body with machines such as clocks. No one doubts that a clock was designed, so why not the body as well? Hume used the problem of evil to negate this argument. Better to view god as distant and unknowable, and a creation that somehow arose on its own. Hume had no problem with god being infinitely powerful and wise, but he must also be transcendent and incomprehensible:

But as all perfection is entirely relative, we ought never to imagine that we comprehend the attributes of this divine being, or to suppose that his perfections have any analogy or likeness to the perfections of a human creature. Wisdom, thought, design, knowledge; these we justly ascribe to him; because these words are honorable among men, and we have no other language or other conceptions by which we can express our adoration of him. But let us beware, lest we think that our ideas anywise correspond to his perfections, or that his attributes have any resemblance to these qualities among men. He is infinitely superior to our limited view and comprehension; and is more the object of worship in the temple, than of disputation in the schools.

Far more lasting and influential than this anthropomorphic warning argument were the various arguments from evil, inefficiency and dysteleology. God would never have created this gritty world. These arguments had been developed and tested in the seventeenth and eighteenth centuries, and by Darwin’s day a foundation had been laid.

The predation and bloodshed in nature was an obvious example of a creation that seemed unbefitting of a loving god. But Darwin added a great many examples of nature’s designs that seemed to be better explained as a consequence of the blind interplay of natural laws than intelligent design.

Darwin presented these arguments throughout his book, with great conviction that they made his theory compelling. The first one appears at the end of the second chapter.

The first two chapters of Origin are on the topic of biological variation. In the first chapter Darwin discusses what breeders had learned (Variation Under Domestication) and in the second chapter he discusses biological variability in the wild (Variation Under Nature). The two chapters serve as a good summary of what was known at the time.

Darwin ends Chapter 2 with a section entitled Summary, but here he introduces a new, important idea. Yes, he summarizes what he has been discussing, but he provides a new, powerful interpretation:

In genera having more than the average number of species in any country, the species of these genera have more than the average number of varieties. In large genera the species are apt to be closely, but unequally, allied together, forming little clusters round other species. Species very closely allied to other species apparently have restricted ranges. In all these respects the species of large genera present a strong analogy with varieties. And we can clearly understand these analogies, if species once existed as varieties, and thus originated; whereas, these analogies are utterly inexplicable if species are independent creations.

Earlier in the chapter Darwin had made a few comments in passing about creationism, but nothing too significant. But here Darwin introduces the reader to the power behind his long argument. The pattern will repeat many times: long tedious passages followed by the powerful conclusion that nature’s evidence falsifies divine creation.

Don’t worry if you don’t completely follow the observations Darwin discusses in the above quote. Here’s what you need to understand. The take home message for evolutionists is that, as usual, there are no viable explanations other than evolution’s. The observations may not be fully understood under evolution, but under creation or design the story becomes downright impossible. As one of the twentieth century’s leading evolutionist Ernst Mayr wrote:

The greatest triumph of Darwinism is that the theory of natural selection, for 80 years after 1859 a minority opinion, is now the prevailing explanation of evolutionary change. It must be admitted, however, that it has achieved this position less by the amount of irrefutable proofs it has been able to present than by the default of all the opposing theories.

Or as Stephen Jay Gould put it:

Odd arrangements and funny solutions are the proof of evolution—paths that a sensible God would never tread but that a natural process, constrained by history, follows perforce. No one understood this better than Darwin. Ernst Mayr has shown how Darwin, in defending evolution, consistently turned to organic parts and geographic distributions that make the least sense.

Designs that make the least sense. They are one of the keys to understanding evolutionary thinking. In addition to the other arguments for why evolution is a fact, I examined this argument from dysteleology ten years ago in my book Darwin’s God: Evolution and the Problem of Evil, and others such as Paul Nelson had discussed it earlier. And so I was delighted to see this key evolutionary argument for the fact of evolution elaborated in the prestigious science journal, Proceedings of the National Academy of Sciences, a year ago.

The paper was written by philosopher Elliot Sober who for years had been analyzing evolution’s arguments in great detail. In that paper Sober points out that while one of the main objections to evolution, both when Origin was published and in the minds of many present-day Creationists, is the idea that species are separated from each other by walls. Darwin, Sober explains, overcame this with those designs that make the least sense:

Darwin thought he had strong evidence for common ancestry. This is enough to show that insuperable species boundaries (and insuperable boundaries between “kinds”) are a myth; if different species have a common ancestor, the lineages involved faced no such walls in their evolution. …

Adaptive similarities provide almost no evidence for common ancestry while similarities that are useless or deleterious provide strong evidence for common ancestry.

And why are useless or deleterious similarities so helpful? It is not because they raise the probability of common ancestry, but rather because they lower the probability of separate ancestry. In other words, the reason common descent is a no-brainer is that the alternative, separate ancestry, is extremely unlikely. Sober call this Darwin’s Principle.

I referred to this analysis and Sober’s paper in my previous posting and several evolutionists commented that I had misrepresented Sober. Here are some of their comments:

False. Sober said no such thing in that book. In fact, he said the opposite.

Darwin’s principle refers to the notion that traits that are not selectively advantageous are better evidence for common descent than are traits that are selectively advantageous. He says this in the context of comparing common descent to separate ancestry.

You are quite fond of misunderstanding Sober, aren’t you?

But in fact Sober did say such a thing. In the paper Sober clearly explains that Darwin’s Principle, which demonstrates species are not separated by insuperable boundaries, is based on the ratio of (i) the probability of evidence on common ancestry divided by (ii) the probability of evidence on separate ancestry. The key is that the argument is compelling not because of the former being high, but because of the latter being low. It is not a direct argument for common ancestry, but rather an argument against separate ancestry.

As Mayr and Gould explain above, evolution is a fact because design or creation is false, as demonstrated by so many inefficiencies and bad designs that make the least sense. Over and over, Darwin made arguments against divine creation as his proofs for evolution.

Sober explains this argument in great detail in his book Evidence and Evolution. Here is how he summarizes the paradox that common descent can be found to be a fact though the evidence is unlikely:

This last result provides a reminder of how important the contrastive framework is for evaluating evidence. It seems to offend against common sense to say that E is stronger evidence for the common-ancestry hypothesis the lower the value is of [the probability of E given the common-ancestry hypothesis]. This seems tantamount to saying that the evidence better supports a hypothesis the more miraculous the evidence would be if the hypothesis were true. Have we entered a Lewis Carroll world in which down is up? No, the point is that, in the models we have examined, the ratio [the probability of E given the common-ancestry hypothesis divided by the probability of E given the separate-ancestry hypothesis] goes up as [the probability of E given the common-ancestry hypothesis] goes down. … When the likelihoods of the two hypotheses are linked in this way, it is a point in favor of the common-ancestry hypothesis that it says that the evidence is very improbable. [Sober, Evidence and Evolution, p. 314]

In other words, it doesn’t matter that common descent is not a good theory. It must be true because the alternative is even worse.

As Sober explains his PNAS paper, the key is designs that are have low probability on separate ancestry. He gives examples such as gill slits in the human embryo and our tail bone, but Darwin used dozens of examples in addition to the Chapter 2 example above. These are classic examples used by evolutionists to show how compelling is evolution. The probability on common descent may be weak, but it must be true because the probability on design or creation is zero. Here are representative embryology and gill slit quotes from leading evolutionists:

How does God’s plan for humans and sharks require them to have almost identical embryos? [Douglas Futuyma, Science on Trial: The Case for Evolution, p. 48]

The passage through a fishlike stage by the embryos of the higher vertebrates is not explained by creation, but is readily accounted for as an evolutionary relic. [Tim Berra, Evolution and the Myth of Creationism, p. 22]

Now, we’re not absolutely sure why some species retain much of their evolutionary history during development. The “adding new stuff onto old” principle is just a hypothesis—and explanation for the facts of embryology. It’s hard to prove that it was easier for a developmental program to evolve one way rather than another. But the facts of embryology remain, and make sense only in light of evolution. [Jerry Coyne, Why Evolution is True, p. 78-9]

These evolutionary arguments certainly are powerful, but their power comes from their metaphysics. If the evolutionists are correct in their theological and philosophical premises then of course evolution is correct. Its likelihood would be a number divided by zero. And that is infinity. Granted the numerator may be small, but the denominator is zero. So it does not matter how ridiculous evolutionary theory is—it must be a fact.

All arguments for the fact of evolution are metaphysical. From the seventeenth century to today, evolutionists gain their tremendous confidence from their religious convictions. That doesn’t mean they are wrong, but it does place a tremendous burden on their metaphysics.

Sober does not approve of such metaphysics. Do they not make objective analysis impossible? In his book he first levels this criticism at creation and design. As I wrote in my review of his book:

Sober next presents what he takes to be a “devastating objection” to the design argument, first raised by David Hume in the eighteenth century. Sober argues that evolutionists should not make theological claims in proving evolution. Likewise, Sober finds the same defect in the design argument. For when Paley argued that the complexity of the eye implies a designer, was he not assuming knowledge of what God would design? [126, 141-147] Ultimately Sober concludes that creation and ID cannot even follow basic scientific protocol. [356]

And Sober agrees that evolutionists should not use such metaphysics as well. But Sober’s disapproval does not remedy the problem. As Gould and Mayr document, Darwin’s argument rested on the low probability of the alternative. This has not changed since Darwin and today, though evolutionists insist their idea is a scientific fact, it would be better characterized as a religious mandate. Every argument for why evolution is a fact is metaphysical. That doesn’t mean it is false, but it should not be thought of as a scientific fact.

222 comments:

  1. Hunter:

    Every argument for why evolution is a fact is metaphysical.

    I don't see a logical connection between the (questionable) claim that contrastive reasoning is metaphysical and the above sweeping claim. Here's an opportunity for Professor Hunter to clarify his thinking. What other arguments for why evolution is a fact are metaphysical?

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  2. Another clarification that is overdue is the Professor's definition of "metaphysical."

    Does that word mean hypothetical, or not testable empirically, or what?

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  3. Cornelius Hunter, you really need to contact your blogspot support to find out why comments keep disappearing.

    ReplyDelete
  4. Zachriel,

    Try posting without any embedded links, leaving websites as plain text to be copied and pasted.

    ReplyDelete
  5. Cornelius Hunter:

    No one doubts that a clock was designed, so why not the body as well?

    No one doubts this because we have seen humans design and build clocks.

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  6. Cornelius Hunter: Evolution is, they say, beyond any shadow of a doubt, as certain as gravity, nay even more certain. This claim is so obviously false that it begs the question: what are evolutionists thinking?

    Evolution is a fact; it is observed.
    Evolutionary theory is an entangled set of hypotheses and observations.
    Common descent is one of those hypotheses; when creationists say evolution is false, they generally mean they do not accept the validity of common descent.

    The hypothesis of common descent is not beyond the shadow of doubt (since there are plenty of people who doubt it), but it is beyond reasonable doubt given the information that we have from genetics, embryology, morphology, ethology, and paleontology. Scientists consider it absurd that anyone conversant with this data would deny common descent. It is telling that the major voices speaking out against it have a religious axe to grind.

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  7. Apologies to all for double posting. I seem to lack the ability to delete my own posts.

    Cornelius, feel free to remove my first comment in this thread.

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  8. anaxyrus:

    "Apologies to all for double posting. I seem to lack the ability to delete my own posts."
    ===

    You can actually do this yourself by clicking on the garbage can symbol at the bottom of your post next to the Date/Time post link at the bottom. The trash icon will remain for some time(not sure how long) and it will only be seen by you when logged in to post. Hope that helps. Others have helped me here, but even still the software program at times remains a bit of a mystery even for the oldies.

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  9. anaxyrus: Try posting without any embedded links, leaving websites as plain text to be copied and pasted.

    We'll try that. You also conveniently posted most of our response.

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  10. Eocene,

    Thanks for trying to help, but there is no trashcan symbol visible on my previous posts. When I go to comment, I log in. After the comment is posted, it immediately logs me back out again.

    I'll try to be careful with my posts, but the error in my first post had to be corrected because it changes the meaning of the sentence entirely.

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  11. Pedant:

    "Another clarification that is overdue is the Professor's definition of "metaphysical."

    Does that word mean hypothetical, or not testable empirically, or what?"
    ===

    This has never been tough to define or understand. I believe most people understand what he means and he has defined this in the past. Science is supposed to fascillitate the explanations of things not understood by "LAYMAN"(gasp) through NATURALISTIC or PHYSICAL explanation so that physical material beings such as ourselves can relate to. Unfortunately this is almost totally difficult for both sides of the Creos vrs Evos debate.

    I look at the term as I remember it used years ago when I first heard it with regards New Age healing as opposed to conventional healing. Someone claiming to healing by means of unexplained power through their healing hands as opposed to any physical conventional medicine. Hence New Age healing through spiritualistic or metaphysical meaning spiritualistic or non-physical. So "metaphysical healing" means healing by means of remedies that are not physical as we understand is the case with conventional medicine.

    Meta meaning "beyond" and Physics a root word of "physical". So think in terms of an explanation beyond the realms of physical understanding of life as we know and relate to it. That's why both sides incorporate faith-based statements for things that cannot be explain in purely physical terms. Many of the stories of assumed events and life from the past are often presented as fact when in fact no one was actually there and the readers are expected to take it on faith that the story teller has it right. Become skeptical of the story telling(especially in an atmosphere of ideology promotion) and you become demonized by the other side. Again this can go both ways and many on both sides will deny this is the case.

    But I believe you and others do understand what he means, you simply don't like it.

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  12. anaxyrus:

    Evolution is a fact; it is observed.

    Is this a fair statement? What Creationists call micro-evolution is surely observed. But they object that macro-evolution - the appearance of new body parts, such as lungs - has not been directly observed; it is an inference.

    Can such inferences be regarded as facts, even if not directly observed? I think they can, if adequately supported by observations (which are facts, by the way.)

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  13. Ernst Mayr: The greatest triumph of Darwinism is that the theory of natural selection, for 80 years after 1859 a minority opinion, is now the prevailing explanation of evolutionary change. It must be admitted, however, that it has achieved this position less by the amount of irrefutable proofs it has been able to present than by the default of all the opposing theories.

    Here Mayr is talking about something completely different from Hunter's argument. Common descent became the majority opinion less than two decades after 1859. It is the dominance of natural selection as the agent of evolutionary change that remained a minority opinion until the 1940s (as many scientists favored orthogenesis or some flavor of saltationism). Mayr couldn't replay the tape of life, so he couldn't prove natural selection's prominent role in history. But to paraphrase A.C. Doyle, when all other possibilities are extinguished, the probability that the sole remaining explanation is correct approaches unity.

    Ironically, this conclusion can be rejected today; most aspects of evolution are explicable by genetic drift rather than necessitating natural selection. Natural selection remains the preferred explanation of adaptation (and has been proven in field studies to yield adaptation), it's just that most of evolution is not adaptation.

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  14. Pedant: Is this a fair statement? What Creationists call micro-evolution is surely observed. But they object that macro-evolution - the appearance of new body parts, such as lungs - has not been directly observed; it is an inference.

    Microevolution is evolution. Macroevolution is also evolution. These terms describe the evolutionary process viewed at different scales of observation. Scientists use these terms too (creationists didn't invent the terms micro- and macroevolution), as well as the definition of scientific fact that you mentioned and Gould discussed. Microevolutionary adaptation and drift are observable facts; macroevolutionary universal common descent is an inferable fact.

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  15. anaxyrus,

    Good, we agree. I thought it might be helpful to have your clarification.

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  16. Cornelius,
    What a pathetic response. First, you do not even acknowledge that you were mistaken stating that Sober agreed that bad designs were evidence against Creationism/ID (in fact he said the opposite). Second, you do not acknowledge the significance of this point, i.e. that the bad design argument is completely dispensable as evidence for evolution. You seem to think it is the linchpin of evolutionary thought, but in fact it is just a silly piece of rhetoric. Third, you still do not seem to understand that what you term "contrastive reasoning" is the basis of most modern science. In any statistical test, you only support Hypothesis X by showing that the null hypothesis is extremely improbable (typically, p<0.05). In the case of common ancestry, Hypothesis X is common descent and the null is separate descent.

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  17. anaxyrus,
    nice catch on the Mayr distortion by CH. that's two in two days, but I'm sure he won't acknowledge this one either.

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  18. Pedant:

    "Evolution is a fact; it is observed."

    Is this a fair statement? What Creationists call micro-evolution is surely observed.
    ===

    The real truth here, is it even evolutionary in the first place ??? Or is it an example of an organism simply adapting and maintaining it's existance in the environment. Examples are the constant engineering of bacteria and other micro-organisms to consume and recycle the elements around the natural world. Especially is this important when bacteria's job is made more challenging by the pigs on the planet called Human Beings. Still it will always remain a major faith statement of belief that it nevertheless drives macro and if you don't believe it your a stupid and delusional for even questioning the Ecclesiastical Hierarchies running modern secularistic science.
    ---

    Pedant:

    "But they object that macro-evolution - the appearance of new body parts, such as lungs - has not been directly observed; it is an inference.
    ===

    Well of course. All the major philosophers(Dawkins, etc) even admit it is impossible to observe/test/prove without faith that it nevertheless is a fact. This observed process of the "micro" is always ASSUMED as the driver behind what makes the dogma of macro work. So faith-based statements are manufactured to prop up what cannot be physically or naturalistically proven/explained(MACRO) other than speculations, assertions and assumptions. Hence we come back full circle to custom of "metaphysics" insertion to word picture the unexplainable through story invention and have to deal with word gaming which makes the whole subject meaningless except to the faithful.

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  19. Pedant:

    "Can such inferences be regarded as facts, even if not directly observed?"
    ===

    If your heart(seat of what motivates you) wants it bad enough, sure.
    ---

    Pedant:

    "I think they can, if adequately supported by observations (which are facts, by the way.)"
    ===

    But then we're back to square one with just exactly what should be considered a hard core physically observable fact and what is purely nothing more than faith.

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  20. What Creationists call micro-evolution is surely observed.

    Eocene: The real truth here, is it even evolutionary in the first place ???

    Yes, it is certainly evolution. It is the change in heritable traits in a population. For instance, we can start with a single bacterium. Over time, we can show that some of its offspring are resistant to antibiotics, and that this resistance is heritable. We can also note that in the presence of antibiotics, there is a tendency for the population to be dominated by the resistant strain. That's biological evolution.

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  21. Cornelius Hunter: Ernst Mayr has shown how Darwin, in defending evolution, consistently turned to organic parts and geographic distributions that make the least sense.

    The geographic distributions, such as no frogs in distant volcanic island freshwater settings, made very little sense to Darwin and others who were willing to question it, under the model of special creation that held at the time. Their absence under that model had to be a quirk, a curiosity. But under the model of common descent, the difficulty of amphibian dispersal made this result a highly explicable and understandable outcome.

    The gross inefficiencies and the clumsy if adequate constructions seen in some parts of the natural world are improbable only if natural selection is operating with free reign to start from scratch in each species; understanding that natural selection is constrained by history, these quirks are probable results. Again, a god could have done this, or anything else. The observation becomes just a curiosity. Inasmuch as "a capricious god willed it that way" can be used to explain literally anything, it has no currency in science, having been recognized as an impediment to further understanding rather than a springboard.

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  22. In previous threads, it was pointed out that evolution has multiple senses, and that if Cornelius Hunter means biological adaptation or common descent, he should be specific.

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  23. Zachriel:

    "Yes, it is certainly evolution."
    ===

    No that is YOUR OPINION. Your opinion is not a fact, it is faith.
    ---

    Zachriel:

    "It is the change in heritable traits in a population."(broken record)
    For instance, we can start with a single bacterium. Over time, we can show that some of its offspring are resistant to antibiotics, and that this resistance is heritable. We can also note that in the presence of antibiotics, there is a tendency for the population to be dominated by the resistant strain.
    ===

    None of these sophisticated mechanics and purposed engineering by the organisms have anything to do with evolution, this is merely your religious faith-based belief. This is the constant broken record being played on an old Hi-Fi that's seen better days. Nothing about the observed behavior of the engineering going on remotely behaves as the dogma insists in the first place and yes you won't like it, but blind undirected forces with no purpose whatsoever guiding life is never observed in any of this. Prove a foundation for blind purposeless forces bringing about guidance driven mechanisms, then we'll talk antibiotic resistance as evolutionary proofs. Until then it's the same old ORTHODOXY as when your holyman Darwin penned it.

    ---

    Zachriel:

    "THAT'S BIOLOGICAL EVOLUTION."
    ===

    No that's a bold faith-based statement and philosophical ASSUMPTION.

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  24. anaxyrus,
    "The gross inefficiencies and the clumsy if adequate constructions seen in some parts of the natural world are improbable only if natural selection is operating with free reign to start from scratch in each species"

    I disagree here. it is the sharing of quirks (actually, neutral traits are best) between different species that provide evidence of common descent.the probability that two species would convergently evolve the same adaptive trait are higher than the probability that they would convergently evolve the same neutral trait. This is why shared neutral traits are such powerful evidence for common descent, with no designer hypothesis needed.

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  25. nanobot74,

    I think we're discussing different things here. I agree with what you have stated. What I said is that in a world without constraints of history, in which natural selection had free reign to "target" some desired result in the morphologic landscape and head toward that result, we wouldn't see these suboptimal quirks in morphology persisting.

    Of course, in reality there are constraints beyond phylogenetic history, such as material availability and the adaptive landscape.

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  26. Eocene

    Your Chihuahua is scary! What could possibly be in that needle?

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

    ReplyDelete
  28. Zachriel: Yes, it is certainly evolution.

    Eocene: No that is YOUR OPINION. Your opinion is not a fact, it is faith.

    It meets the scientific definition.
    http://en.wikipedia.org/wiki/Evolution

    How many legs does a dog have if you call the tail a leg?

    Perhaps you should provide a definition of evolution for discussion.

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  29. anaxyrus,
    "Of course, in reality there are constraints beyond phylogenetic history, such as material availability and the adaptive landscape."

    yes, even quirky arrangements of adaptive traits could be shared through convergence if there was only one way an adaptive trait could "work." usually this is not true, however, as is evidenced by the many different forms of hemoglobin.

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  30. These evolutionary arguments certainly are powerful, but their power comes from their metaphysics. If the evolutionists are correct in their theological and philosophical premises then of course evolution is correct. Its likelihood would be a number divided by zero. And that is infinity. Granted the numerator may be small, but the denominator is zero. So it does not matter how ridiculous evolutionary theory is—it must be a fact.

    The only time we would divide by zero (when comparing evolution to some sort of creator) would be when comparing evolution to ID - i.e. an unidentified designer. The likelihood of ID, as Sober argues, can't even be estimated and would be infinitely small. The same would apply when comparing anything to ID, btw. For example, given no designer, the likelihood that there, at this very moment, would be snow near the loction I now happen to be is ridiculously low (the sun would have to warm Earth enough, weather patterns would have to be permissible etc [heck, there would even have to be an Earth to begin with]). The observation is a heck of a lot likelier than under ID, though. So, I suppose that my hypothesis that the snow actually fell from the sky, having previously been liquid or gaseous H2O, is pure meta-physics...

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  31. Hawks:

    ===
    So, I suppose that my hypothesis that the snow actually fell from the sky, having previously been liquid or gaseous H2O, is pure meta-physics...
    ===

    Well, what is your opinion? If you or someone argued that X must be a fact, even though it is bad science, because Y is so unlikely. Do think that is scientific reasoning? And then, on top of that, Y is said to be unlikely for religious reasons. Do think that is scientific reasoning? And then, on top of that, Y is said to be not allowed in science anyway. Do think that is scientific reasoning?

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  32. anaxyrus:

    ===
    Evolution is a fact; it is observed.
    ===

    It is telling that evolutionists fall back on this equivocation when they are questioned. Evolution, the one that is called a fact, is most definitely *not* observed. Even the evolutionists, when evolutionists explain why it is a fact, acknowledge this. But when called to account, they backpedal, and change the story. Then when you go away, it's back to the first version.


    ===
    Evolutionary theory is an entangled set of hypotheses and observations.
    ===

    Of course. Many patches and explanations are required. But the fact claim is straightforward.

    ===
    The hypothesis of common descent is not beyond the shadow of doubt (since there are plenty of people who doubt it), but it is beyond reasonable doubt given the information that we have from genetics, embryology, morphology, ethology, and paleontology. Scientists consider it absurd that anyone conversant with this data would deny common descent.
    ===

    Yes, it is true evolutionists say this. But not the scientific data. The above statement is simply yet another case of an evolutionist lying about the data. I'm sorry if that sounds harsh, but this is such an extreme misrepresentation of the science it is difficult to understand how it could be a mistake. I could use soft words, such as "inaccurate," but that would be false.


    ===
    It is telling that the major voices speaking out against it have a religious axe to grind.
    ===

    Are you really interesting in detecting axes? Even a slight passing familiarity with the literature and history of evolution would tell you that evolutionists have a "religious axe to grind."

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  33. anaxyrus:

    ===
    Here Mayr is talking about something completely different from Hunter's argument. Common descent became the majority opinion less than two decades after 1859. It is the dominance of natural selection as the agent of evolutionary change that remained a minority opinion until the 1940s (as many scientists favored orthogenesis or some flavor of saltationism). Mayr couldn't replay the tape of life, so he couldn't prove natural selection's prominent role in history.
    ===

    No, Mayr discusses the spectrum of ideas, including divine creation type ideas. This quote illustrates evolution's use of contrastive thinking and reliance on the disprove of a set of alternatives.

    ===
    But to paraphrase A.C. Doyle, when all other possibilities are extinguished, the probability that the sole remaining explanation is correct approaches unity.
    ===

    Who decides what all other possibilities are, and how they are evaluated?

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  34. Hunter:

    Yes, it is true evolutionists say this. But not the scientific data.

    This is incorrect. Data “say” nothing in the absence of a working hypothesis about what they might say.

    The above statement is simply yet another case of an evolutionist lying about the data. I'm sorry if that sounds harsh, but this is such an extreme misrepresentation of the science it is difficult to understand how it could be a mistake.

    The “evolutionist” interprets data in light of the evolutionary hypothesis. That makes her a liar? I don’t think so.

    I could use soft words, such as "inaccurate," but that would be false.

    This from the person who said on the previous thread, giving his views on origins research::

    In fact, I do not hold strongly to any particular idea because the evidence isn't there to justify doing that.

    Hunter may choose extreme skepticism about biological data, but that does not make his position the only conceivably correct position. Persons who choose to interpret evidence in light of an hypothesis may be mistaken, but they can’t be called liars. Honestly, they can’t.

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  35. nanobot74:

    ===
    What a pathetic response. First, you do not even acknowledge that you were mistaken stating that Sober agreed that bad designs were evidence against Creationism/ID (in fact he said the opposite).
    ===

    You are failing to distinguish between an ought and an is. In his book Sober argues evolutionists shouldn't use metaphysical premises. He argues you can't compute the probabilities. Sober's opinion doesn't change the reality of what is, which he documents in his paper, which is what I was referencing. The examples he cites, gill slits and tail bones, are classic metaphysical arguments evolutionists use.


    ===
    Second, you do not acknowledge the significance of this point, i.e. that the bad design argument is completely dispensable as evidence for evolution.
    ===

    Only if evolutionists were to forfeit the fact claim.

    ===
    You seem to think it is the linchpin of evolutionary thought,
    ===

    No, there are several other metaphysical arguments as well, but it is an important one.


    ===
    but in fact it is just a silly piece of rhetoric.
    ===

    Evolutionists continually use it when arguing evolution is a fact. If it were merely silly, dispensable, rhetoric, then it would be easy for you to cite the reference giving the non-silly explanation for why evolution is a fact.

    ReplyDelete
  36. Pedant:

    ===
    The “evolutionist” interprets data in light of the evolutionary hypothesis. That makes her a liar? I don’t think so.
    ===

    Oh I see. so when evolutionists say evolution is beyond any reasonable doubt, a fact, they don't really mean it. We're supposed to just ignore them because it is all just circular reasoning. What they really mean is that if you view the world through evolutionary lenses, then all data perfectly support evolution, even though objectively the data provide no such support.

    ReplyDelete
  37. Cornelius Hunter: Evolution, the one that is called a fact, is most definitely *not* observed.

    What do you mean by "evolution"? Common Descent?

    ReplyDelete
  38. Hunter:

    Oh I see. so when evolutionists say evolution is beyond any reasonable doubt, a fact, they don't really mean it.

    To say something is a fact does not place it beyond any reasonable doubt. How could that possibly be the case, short of divine revelation? I and others have pointed this out repeatedly. And you will no doubt continue to equivocate on this point, as you persist in your (futile) efforts to discredit those pesky evolutionists.

    What they really mean is that if you view the world through evolutionary lenses, then all data perfectly support evolution, even though objectively the data provide no such support.

    When someone tells you what someone else "really means," you can brace yourself for a straw man fallacy. Of course, no one claims that all data perfectly support evolution. Some data support it better than other data. Some data are irrelevant to the evolutionary hypothesis. But to claim that there is no empirical support for the hypothesis is untenable.

    ReplyDelete
  39. Zachriel:

    ===
    What do you mean by "evolution"? Common Descent?
    ===

    What I mean by "evolution" is no different than what evolutionists mean by "evolution" when they claim it is a fact. If you read the literature you'll see they are referring to the claim that natural laws and processes, and only natural laws and processes, created life and its various species.

    Of course natural selection and common descent are important parts of the idea, but they can be forfeited. There could be drift, there could be multiple ancestors, etc. None of this goes agaisnt the over arching idea of evolution.

    ReplyDelete
  40. On further thought, having served on several juries and having been on each occasion instructed by the judge to arrive at a verdict "beyond a reasonable doubt," I would say that evolution really is a scientific fact beyond a reasonable doubt. The key term here is the word "reasonable," and on what is or is not reasonable is open to interpretation, alas.

    I mistakenly took Dr Hunter’s latest formulation, “beyond a reasonable doubt” for his more usual formulation, as in the OP above, “beyond any shadow of a doubt.”

    My interpretation of Dr Hunter's doubts is that they are not reasonable. Alas.

    ReplyDelete
  41. Hunter:

    What I mean by "evolution" is no different than what evolutionists mean by "evolution" when they claim it is a fact. If you read the literature you'll see they are referring to the claim that natural laws and processes, and only natural laws and processes, created life and its various species.

    How dare those evolutionists restrict their notion of fact to natural laws and processes? Perverse liars who dare not admit that they have (metaphysically) ruled out the unobservable and untestable.

    ReplyDelete
  42. Cornelius,

    I said: Common descent became the majority opinion less than two decades after 1859. It is the dominance of natural selection as the agent of evolutionary change that remained a minority opinion until the 1940s

    Cornelius Hunter said: No, Mayr discusses the spectrum of ideas, including divine creation type ideas.


    In Toward a New Philosophy of Biology, the quote you cited is on p.92. Earlier on p. 89 Mayr writes: "Non-Darwinian biologists. Although the biologists accept [sic, should read accepted] evolution and common descent almost unanimously, most of them had reservations about natural selection".

    Earlier in the chapter Mayr indeed discussed creationist ideas, but for most of the 80 year span Mayr discussed these were generally held by non-biologists (as is the case today).

    Yes, evolutionary biology relies on contrastive reasoning. So does science generally. It's not an issue. The opposite of common ancestry of life on Earth is separate creation of the species. If species on Earth did not have separate origins, it logical to infer that they must have had a common origin. They sum to the universal set of possibilities.

    ReplyDelete
  43. Cornelius:
    ====
    By far the most amazing aspect of evolution is not its idea that all things just happened to arise spontaneously
    ====

    Dish, Ham & Hovind pers. comm.?

    Cornelius,
    You were shown that Sober did not argue against ID from the existence of "bad design". Won't you admit you were wrong?

    Here, you are still misrepresenting Sober. In the previous posts you talked about if the existence of maladaptive or suboptimal features ("bad design") was to be considered evidence for evolution.
    Sober said that it is wrong to argue for or against evolution because of the existence of suboptimal design. Darwin's Principle is about how superfluous, suboptimal and neutral similarities support common ancestry.

    Is is not that the mere existence of suboptimal features supports CA or evolution in general, but the fact that (certain, not any) suboptimal and neutral features can be linked by similarity, leading to the discovery of similarity patterns that are highly consistent with common ancestry.

    ReplyDelete
  44. Cornelius Hunter:Who decides what all other possibilities are, and how they are evaluated?

    The relevant scientists, of course. Testable hypotheses are evaluated on the basis of relative likelihood, as you mentioned. If God chose to transform himself into a testable hypothesis, he could mosey up to the starting gate as well.

    ReplyDelete
  45. Hunter:

    Who decides what all other possibilities are, and how they are evaluated?

    anaxyrus, I think that Dr Hunter is referring to his claim that you can't employ contrastive reasoning if you don't know all possible alternative hypotheses. And you can't claim to know all possible hypotheses, because a hypothesis that you haven't thought of may well be possible.

    In short, you don't know what you don't know. But that's the history of science, which plays with the cards in the deck available at any point in time. And that's the history of any human endeavor.

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

    ReplyDelete
  47. Maybe it is time to collect the metphysical arguments in support of the ToE. I could so far identify three:
    1) God would not interfere in nature on a regular basis.
    2) Bad design.
    3) Design of evil.

    Did I miss something? It would be nice if somebody could complete the list.

    ReplyDelete
  48. second opinion,

    I think that any argument about God is not properly classified as metaphysical. Rather, it is classified as theological.

    Until Professor Hunter provides his definition of metaphysics, we can only speculate.

    ReplyDelete
  49. Pedant,

    Concerning contrastive reasoning, there can only be two possibilities in this case: life diverged from common ancestry or it didn't. Unless CH is arguing that Boolean logic is Satan tricking us, then he cannot complain that there are other alternatives, in reality all he could have to complain about is our models and methods for testing between the alternatives.

    ReplyDelete
  50. Cornelius Hunter: What I mean by "evolution" is no different than what evolutionists mean by "evolution" when they claim it is a fact. If you read the literature you'll see they are referring to the claim that natural laws and processes, and only natural laws and processes, created life and its various species.

    "Natural laws and processes", "created life and its various species" are much too vague to constitute a valid scientific theory. Having read Darwin and more modern literature, biologists propose much more concrete and testable models.

    Cornelius Hunter: By far the most amazing aspect of evolution is not its idea that all things just happened to arise spontaneously but—even more eyebrow raising—its claim that all of this is a scientific fact.

    The most powerful and predictive models in biology have no telic components, and no one has proposed a valid model based on Intelligent Design. The basic claims of the Theory of Evolution, common descent and of adaptative mechanisms are well-established science.

    ReplyDelete
  51. anaxyrus said...

    Concerning contrastive reasoning, there can only be two possibilities in this case: life diverged from common ancestry or it didn't.

    As I understand him, Hunter argues that the evidence is insufficient to conclude that life diverged from common ancestry, or not, thereby declaring your dichotomy false.

    What say you, Professor Hunter?

    ReplyDelete
  52. Pedant:

    As I understand him, Hunter argues that the evidence is insufficient to conclude that life diverged from common ancestry, or not, thereby declaring your dichotomy false.

    What say you, Professor Hunter?


    Whatever he says, the dichotomy is not false. There might be some possible statements where (true/false) would not exhaust all possibilities, but ("life on Earth diverged from universal common ancestry") is not one of them.

    I think you are correct in that he does indeed argue that there is insufficient evidence to evaluate the truth of evolution (here meaning common descent). But that's a different question.

    ReplyDelete
  53. Cornelius Hunter said...

    Zachriel:

    ===
    What do you mean by "evolution"? Common Descent?
    ===

    What I mean by "evolution" is no different than what evolutionists mean by "evolution" when they claim it is a fact. If you read the literature you'll see they are referring to the claim that natural laws and processes, and only natural laws and processes, created life and its various species.


    There's the problem. All this time CH has had his own funny little pet definition of 'evolution' different that the word's usage in the scientific community, and in the rest of the adult world. CH's definition is more kiddy creationist "no one has seen a frog evolve into a horse!" sort of nonsense.

    I'll have to agree with you for once CH. "Evolution" as you define it in your childish ignorant strawman manner certainly isn't a fact.

    ReplyDelete
  54. Cornelius,


    "You are failing to distinguish between an ought and an is."
    All I was doing is pointing out that you consistently misrepresent Sober's views concerning the bad design argument. You have still not admitted that you were mistaken or corrected your posts.

    "In his book Sober argues evolutionists shouldn't use metaphysical premises. He argues you can't compute the probabilities. Sober's opinion doesn't change the reality of what is, which he documents in his paper, which is what I was referencing. The examples he cites, gill slits and tail bones, are classic metaphysical arguments evolutionists use."

    In the paper, Sober uses gill slits and tailbones as examples of traits that are not adaptive, to illustrate their usefulness in determining common ancestry. he is showing that adaptive traits are not useful for demonstrating common ancestry because they could have evolved convergently, while the probability of non-adaptive traits evolving convergently is much lower. How is this metaphysical?

    (concerning the bad design argument, which I said is silly). "Evolutionists continually use it when arguing evolution is a fact. If it were merely silly, dispensable, rhetoric, then it would be easy for you to cite the reference giving the non-silly explanation for why evolution is a fact."

    claiming that the theory of evolution is a fact is by its nature a self-contradictory and silly claim, so I can't help you. the definition you provide for evolution (basically, that no gods or designers ever intervened in life's history) is itself a metaphysical claim, so of course metaphysical arguments are used to back it up. but this is an argument seen in the context of rebutting creationism/ID, as can be seen in your rogue's gallery of quotations in the OP, all of them from anti-creationism texts.

    ReplyDelete
  55. CRDarwin said

    And we can clearly understand these analogies, if species once existed as varieties,
    and thus originated; whereas, these analogies are utterly inexplicable if species are independent creations.

    CRDarwin fancied himself a spin artist. He says he read Malthus for entertainment value. I think the good Parson Malthus taught that the poor should be starved if not killed outright. I don't remember, when Darwin was forced to include a "bibliography" to (the "Historical Sketch" in 3rd edition of) Origin of Species, whether Darwin ever did murmur a word of credit to Malthus. Can you imagine a Creation Science author penning a book called On the Origin of Kinds...and never defining what a Kind is..and never in 6 editions saying what is "the origin of kinds"? That's exactly what CRDarwin got away with (not doing). In all 6 editions of Origin, he never defined species, and (famously) never did say, in Origin, what is the origin of species.

    I like Gertrude Himmelfarb discussion of Darwin and his claims for the eye in her classic. And the review that Richard Owens wrote of Origin is hilarious, with Owen feigning not to understand Darwin's opening (I was much struck with certain facts in the distribution of the inhabitants). Owens fully realized Darwin was feigning astonished discovery there, and Owens did the same. You can always tell which edition of Origin sold at the bookstore each year, by that opening line. As Owens' negative review forced Darwin to retrench and to rework that opening.

    Darwin's evolution was all but discarded by 1900. This used to be openly admitted. But in the last few decades of lionizing him, that is all glossed over and we are told: Darwin and evolution have been a continuous triump since 1859. Instead, after Mendel's genetics became fully known and with the work of others we saw a Second Coming of Darwin in the New Synthesis. By the 1980s, the New Synthesis has become moribund. Whatever the future incarnation of evolutionary theory, we can be sure we will be told, time and again, that we are witnessing the triumph of the genius of Charles Darwin.

    ReplyDelete
  56. anaxyrus:

    ===
    Yes, evolutionary biology relies on contrastive reasoning. So does science generally. It's not an issue.
    ===

    So with a wave of the hand, evolutionists dismiss such arcane conundrums. The fact is, it is not an issue so long as the people using such reasoning stay within its bounds. You cannot make claims beyond your own assumptions. If you contrast X with Y, and find X to be superior, then that is your conclusion (based on the assumptions of your analysis). You cannot then conclude X is a fact without smuggling in unspoken assumptions. This is such obvious, straightforward logic it is remarkable that evolutionists try to obviate it.

    ReplyDelete
  57. Pedant:

    ===
    How dare those evolutionists restrict their notion of fact to natural laws and processes? Perverse liars who dare not admit that they have (metaphysically) ruled out the unobservable and untestable.
    ===

    Such sentiment sounds like scientism or positivism. Yes, there is non scientific pursuits, but true truth really only comes from science. After all, everything else is unobservable and untestable.

    ReplyDelete
  58. geoxus said...

    ===
    You were shown that Sober did not argue against ID from the existence of "bad design". Won't you admit you were wrong?
    ===

    Except I never said that. At least I did not intend to. I did point out that Sober, in the PNAS paper, shows how the argument defeats creationism using the usual metaphysical arguments such as gill slits. I agree with you that Sober does not make these arguments, himself. If I left the impression otherwise, then I take it back.

    ReplyDelete
  59. nanobot74:

    ===
    In the paper, Sober uses gill slits and tailbones as examples of traits that are not adaptive, to illustrate their usefulness in determining common ancestry. he is showing that adaptive traits are not useful for demonstrating common ancestry because they could have evolved convergently, while the probability of non-adaptive traits evolving convergently is much lower. How is this metaphysical?
    ===

    There are two entry points for the metaphysics. One, at the evaluation of the probability of the evidence on separate ancestry. Two, in the assumption that CA and SA represent all possible explanations. Is it obvious now to you?

    ===
    claiming that the theory of evolution is a fact is by its nature a self-contradictory and silly claim, so I can't help you. the definition you provide for evolution (basically, that no gods or designers ever intervened in life's history) is itself a metaphysical claim, so of course metaphysical arguments are used to back it up.
    ===

    No, a hypothesis that god did X, Y or Z is, itself, not metaphysical. It's just a hypothesis. Furthermore, I'm afraid your paraphrase "no gods or designers ever intervened in life's history" isn't quite right. I said evolution = life and the species arose via natural laws and processes. That does not rule out divine action, it just says the divine action is strictly via natural law (what theologians refer to as secondary causes). I don't think evolutionist's hypothesis is particularly metaphysical.

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  60. Pedant:

    ===
    I think that Dr Hunter is referring to his claim that you can't employ contrastive reasoning if you don't know all possible alternative hypotheses. And you can't claim to know all possible hypotheses, because a hypothesis that you haven't thought of may well be possible.
    ===

    Good summary, but it is not that you cannot use contrastive reasoning so much as you need to understand the limitations.

    ===
    In short, you don't know what you don't know. But that's the history of science, which plays with the cards in the deck available at any point in time. And that's the history of any human endeavor.
    ===

    Which is why scientists don't claim that unlikely ideas are actually facts merely because an opposing idea is even worse off.

    ReplyDelete
  61. second opinion:

    ===
    Maybe it is time to collect the metphysical arguments in support of the ToE. I could so far identify three:
    1) God would not interfere in nature on a regular basis.
    2) Bad design.
    3) Design of evil.

    Did I miss something? It would be nice if somebody could complete the list.
    ===

    Take a look at this figure:

    http://www.darwinspredictions.com/Figure15.jpg

    ReplyDelete
  62. anaxyrus:

    ===
    Concerning contrastive reasoning, there can only be two possibilities in this case: life diverged from common ancestry or it didn't.
    ===

    But once again this evolutionary reasoning is meaningless. You are creating proofs out of think air. In this case, you have equivocation on both sides. On the pro side, evolution or CA covers a wide spectrum. So evolutionists claim evolution is a fact because some alleles changes frequency. Great, some moths changed color so life arose in a warm little pond, er somewhere, and then evolved spontaneously into the millions of species and designs we find.

    On the con side, evolutionists make up some metaphysical rebuke of SA, and again conclude evolution is a fact. Great, God wouldn't create parasites so evolution must be true.

    Unbelievably, these are actually are evolutionary arguments for why it is a fact.

    ReplyDelete
  63. Zachriel:

    ===
    "Natural laws and processes", "created life and its various species" are much too vague to constitute a valid scientific theory. Having read Darwin and more modern literature, biologists propose much more concrete and testable models.
    ===

    Sure, evolutionists propose all kinds of explanations and models within evolutionary theory. But they can be forfeited without harming evolution.

    ReplyDelete
  64. Ya know CH, you wouldn't come across as such a disingenuous hypocritical windbag if you'd try discussing actual evolutionary theory for once instead of that childish cartoon version you keep trotting out.

    Just sayin'.

    ReplyDelete
  65. Pedant:

    ===
    As I understand him, Hunter argues that the evidence is insufficient to conclude that life diverged from common ancestry, or not, thereby declaring your dichotomy false.

    What say you, Professor Hunter?
    ===

    There is evidence in favor of evolution and common descent, but the fact is there are substantial scientific problems with evolution and common descent. Yet evolutionists say all the evidence supports evolution. There is a monumental gap between their claims and reality.

    For many people this is hard to believe. But there it is, evolutionists make their claims over and over.

    ReplyDelete
  66. Thorton:

    ===
    Ya know CH, you wouldn't come across as such a disingenuous hypocritical windbag if you'd try discussing actual evolutionary theory for once instead of that childish cartoon version you keep trotting out.
    ===

    Were you much struck? It is amazing how evolutionists respond when you present them with their own claims. They are their own judge.

    ReplyDelete
  67. Cornelius Hunter:

    "Sure, evolutionists propose all kinds of explanations and models within evolutionary theory. But they can be forfeited without harming evolution."
    ===

    This goes back to your term used earlier - the "Scientism" worldview, especially with the selfpromoting intellect your dealing with here. The view here is that scientism is their version of the "Alpha and Omega" beginning and end. Any knowledge outside of scientism's text books isn't worth knowing. This is where ideology and worldview reveal their true ugly nature.

    This is also a parroting of Carl Sagan's "Science is a ever self-correcting process". It's almost identical to the imaginative chemical "self-replicating" magic process they've been insisting here lately that begat all life. This same philosophical mysteriousness is what evolves scientism's thinking to keep Darwinian religion alive as the fittest survivor as mankind's greatest ever Dogmas. But when the evidence leads to the dogmas possible downfall, just throw in a hint of MAYA(All is Illusion) into the discussion and the doctrine is saved once again. Seriously, the cards are stacked in their favour to where they just can't lose.

    ReplyDelete
  68. Zach:

    "It meets the scientific definition.
    http://en.wikipedia.org/wiki/Evolution"
    ===

    Do I hear bias ??? While wiki can have some interesting facts and information found within it's pages, surely you don't expect me to believe in the ideological slant from it's agenda driven members over there on this particular dogma ???

    How much UP can an upchuck chuck if an upchuck could chuck UP ???

    ReplyDelete
  69. Zachriel:

    "How many legs does a dog have if you call a tail a leg?"
    ===

    We've been over and over your love affair with word/term games before. Save these for the Fundies who you and the other gang members use for a perverted sort of entertainment on those other forums. The bait doesn't work here.

    ReplyDelete
  70. Cornelius wrote: There is evidence in favor of evolution and common descent, but the fact is there are substantial scientific problems with evolution and common descent.

    Let's see what those scientific problems are. What are your specific objections to common descent?

    ReplyDelete
  71. Cornelius Hunter: So evolutionists claim evolution is a fact because some alleles changes frequency.

    This event is certainly an example of evolution, has been observed, and is inevitable given the existence of mutations and inequality in reproductive outcomes.

    Great, some moths changed color so life arose in a warm little pond, er somewhere, and then evolved spontaneously into the millions of species and designs we find.

    These are the kinds of mischaracterizations you would expect from Kent Hovind. That evolution happens before our eyes, through processes and at rates that, in conjunction with known historical abiotic environmental change, are sufficient to produce the history of life on Earth, is but one of the lines of evidence that causes us to accept common descent. And again, you are conflating common ancestry and diversification from that ancestry with biogenesis. Our understanding of biogenesis is not at the level of our understanding of evolution post-LUCA.

    It's fair to say that the life we see on Earth arose somewhere at some point in time. Earth has an abiotic history, as best we can tell, of around 700 million years. Somewhere in that interval, life arose on Earth or was introduced from elsewhere. It's an issue of ongoing research, and headway has been made; it might or might not be resolved in our life time.

    We are limited to working with the evidence we have on hand. Sometimes a small sampling of evidence gives us a false impression that is later overturned by a larger sample. We have a huge sample of genetics and morphology supportive of common descent that gets stronger (not weaker) over time as the tree of life becomes better resolved.

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  72. Cornelius,

    In re: the metaphysics in tests of common ancestry, you wrote:

    "There are two entry points for the metaphysics. One, at the evaluation of the probability of the evidence on separate ancestry. Two, in the assumption that CA and SA represent all possible explanations. Is it obvious now to you?"

    Well, yes and no. For point one, given that supernatural hypotheses for SA have been proposed, the scientist evaluating CA vs. SA has two choices: either test those hypotheses or don't (of course, there could be other choices, so I don't want to say it is a fact that there are two choices). As you, and Sober, Paul Nelson and others before you, have pointed out, to test those hypotheses involves all kinds of metaphysical reasoning about how the designer would design, etc. So it seems best to just ignore them altogether. But of course then the scientist falls prey to your and others' claim that he is excluding hypotheses for metaphysical reasons, and is constraining himself from finding the Real Truth. So it's a bit damned-if-you-do, damned-if-you-don't. For many reasons, including that science does not claim to be finding the Real Truth, excluding designer hypotheses seems the best option. For your point two, I agree in principle that there could be more options than common and separate ancestry, although other than some mix of the two I can't imagine what they may be. However, until those options are crystallized from the ether, we can't concern ourselves too much with them as scientists because they are unknown and therefore untestable.

    If these really are your objections to tests of CA, then you should have highly praised Theobald's 2010 paper in Nature (A formal test of the theory of universal common descent). he does not consider designer hypotheses, minimizing those metaphysics, and tests multiple mixtures of CA and SA. Furthermore (and this should have drawn leaps of joy from you), he never says that CA is a fact, only that it is thousands of time more likely than the 2nd best alternative. Finally, the methods he used left the door open to any new hypothesis being inserted and tested with all the others at any time, so unconsidered alternatives can be considered when they become considerable. Instead you posted several largely incoherent criticisms and wound up having to retract one after being corrected by the author himself. Go figure.

    ReplyDelete
  73. Cornelius,

    In ref to the metaphysics in tests of common ancestry, you wrote:

    "There are two entry points for the metaphysics. One, at the evaluation of the probability of the evidence on separate ancestry. Two, in the assumption that CA and SA represent all possible explanations. Is it obvious now to you?"

    Well, yes and no. For point one, given that supernatural hypotheses for SA have been proposed, the scientist evaluating CA vs. SA has two choices: either test those hypotheses or don't (of course, there could be other choices, so I don't want to say it is a fact that there are two choices). As you, and Sober, Paul Nelson and others before you, have pointed out, to test those hypotheses involves all kinds of metaphysical reasoning about how the designer would design, etc. So it seems best to just ignore them altogether. But of course then the scientist falls prey to your and others' claim that he is excluding hypotheses for metaphysical reasons, and is constraining himself from finding the Real Truth. So it's a bit damned-if-you-do, damned-if-you-don't. For many reasons, including that science does not claim to be finding the Real Truth, excluding designer hypotheses seems the best option. For your point two, I agree in principle that there could be more options than common and separate ancestry, although other than some mix of the two I can't imagine what they may be. However, until those options are crystallized from the ether, we can't concern ourselves too much with them as scientists because they are unknown and therefore untestable. (cont.)

    ReplyDelete
  74. (cont.)
    Cornelius,

    If these really are your objections to tests of CA, then you should have highly praised Theobald's 2010 paper in Nature (A formal test of the theory of universal common descent). he does not consider designer hypotheses, minimizing those metaphysics, and tests multiple mixtures of CA and SA. Furthermore (and this should have drawn leaps of joy from you), he never says that CA is a fact, only that it is thousands of time more likely than the 2nd best alternative. Finally, the methods he used left the door open to any new hypothesis being inserted and tested with all the others at any time, so unconsidered alternatives can be considered when they become considerable. Instead you posted several largely incoherent criticisms and wound up having to retract one after being corrected by the author himself. Go figure.

    ReplyDelete
  75. Excuse me Eocene, but do you truly think that evolution should mean whatever you want it to mean, rather than what scientists have used it to mean?

    Seems like you just sprout angry accusations and, unless you are expecting everybody to know some mysterious background that I ignore, heavily charged statements. I note that it would take me forever to try and answer what you say until many things were cleared up. But at the very least it seems like you hold that whatever you define that evolution *is*, we should just accept your definition and shut up.

    That is how you come across. What am I missing? Do you truly want some answer?

    Let me exemplify. Above I was referring to you thinking that your definition of evolution is The Definition. There is another one that just makes my mind twist and twist and not finding what you mean. The bacterial evolution towards antibiotic resistance. It is evolution clear cut. No way around. For once, bacteria without resistance die. Resistant ones grow. I know, my life was saved by antibiotics many many years ago. Thus, those bacteria died. The mechanism is thus one of evolution. Non-resistant bacteria die, resistant ones survive and reproduce, since there are so many, now other non-resistant ones can acquire the resistance by horizontal gene transfer. But you call that "engineered." You say:

    "but blind undirected forces with no purpose whatsoever guiding life is never observed in any of this"

    There seems to be a bit of many levels of misconception there. Do you mean that it will not be evolution unless there is no direction? As in (1) "antibiotics in the environment are a direction"? Or else (2) "the designer is guiding the bacteria towards resistance"? Or do you mean (3) "evolution is just random stuff running randomly from one side to the other"? (If you have something else in mind, let me know.)

    If the first, then that is certainly evolution. An environment select for organisms carrying traits that allow such organisms to grow. Such growth results in such organisms spreading. Then we have more telling evolution in such things. If we re-engineer penicillin, we start finding variants of the penicillinase (the protein providing resistance to penicillin) that now digest the new thing. If we trace the differences in sequence, we find them to be derived from the older penicillinases by mutation. Again, evolution.

    So? What is exactly the problem with this? Please not just angry sentences, tell me the logic why this is not evolution (I don't care if you call it micro).

    ReplyDelete
  76. excuse the double posts.
    Cornelius,
    "No, a hypothesis that god did X, Y or Z is, itself, not metaphysical."

    Ok, then how does one do a non-metaphysical test of such a hypothesis? it seems to me you can either speculate on the nature of the designer (highly metaphysical) or try to eliminate all potential natural causation. the latter seems like a heavy reliance on the very contrastive reasoning that you object to, although i guess as long as someone doing this kind of research never said "it is a fact that god did x" you'd be cool with it.

    ReplyDelete
  77. Cornelius,

    How dishonest you have to be if I try and explain to you your misunderstanding, yet you go and swim in that same B.S. once again? Man, you are a cartoon of a creationist.

    Darwin: "And we can clearly understand these analogies, if species once existed as varieties, and thus originated; whereas, these analogies are utterly inexplicable if species are independent creations."

    Clear cut Cornelius. He does not mean that independent creations can't do that, but that independent creations don't EXPLAIN that. I told you. It is a natural ("natural" as in "it easily follows") outcome of divergence. Not a natural outcome of independent creation. Thus, independent creation does not explain it. Can do it, but does not explain it. Can do it, but does not explain it. Can do it, but does not explain it. Can do it, but does not explain it. Can do it, but does not explain it. Can do it, but does not explain it ...

    Misguided religion drives your pseudoscience, and it matters.

    ReplyDelete
  78. Cornelius:

    Well, what is your opinion? If you or someone argued that X must be a fact, even though it is bad science, because Y is so unlikely. Do think that is scientific reasoning? And then, on top of that, Y is said to be unlikely for religious reasons. Do think that is scientific reasoning? And then, on top of that, Y is said to be not allowed in science anyway. Do think that is scientific reasoning?

    Here is my opinion:

    Observation o has a higher likelihood under hypothesis X than under any other proposed hypotheses.

    Person D, who supports X, says that X has a higher likelihood than Y.

    Y is not a scientific hypothesis and so it is meaningless to compare it to X.

    Person D was wrong to compare X to Y.

    Along comes Person CorneliusHunter and claims that X is religious because Person D was wrong about something.

    Since that something was irrelevant when assessing the evidence for or against X, Person CorneliusHunter is engaging in sophistry.

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

    ReplyDelete
  80. Cornelius wrote:

    Evolution is, they say, beyond any shadow of a doubt, as certain as gravity, nay even more certain. This claim is so obviously false that it begs the question: what are evolutionists thinking?

    You've yet again failed to differentiate between the phenomena attributed to gravity (falling apples and moving planets) and the theory that explains that phenomena (the curvature of space time).

    Given that we having pointed this out to you time and time again, exactly what do you expect us to conclude from your continued ambiguity?

    Should we conclude you're equivocating, as you appear to do when you make the vague claim that evolution is unlikely? Should we conclude you're using your own private definition of "good science", just as you admitted to in regards to empiricism and rationalism? Or should we conclude you're a naive empiricist who can't tell the difference?

    However, we've already brought these issues to your attention as well. And we've done so repeatedly - which leaves us with a disingenuous presentation specifically crafted for the choir that reads your blog.

    So, again, I'll ask, how exactly do you conclude gravitational theory represents "good science," while evolution does not?

    If gravitational theory doesn't represent good science either, then why would comparing it to evolutionary theory a mistake? This would be hand waving.

    And if you're implicitly referring to the empirically observed phenomena we attribute to gravity, then you're equivocating by implicitly comparing it to the theory of evolution rather than the observed phenomena it explains.

    Again, exactly what do you expect us to conclude this sort of continued ambiguity?

    ReplyDelete
  81. Negative Entropy:

    "Excuse me Eocene, but do you truly think that evolution should mean whatever you want it to mean, rather than what scientists have used it to mean?"
    ===

    It should mean what it was originally intended to mean from it's very origin. The average person(poor slob) on the street understands a general definition of evolution to be nothing more than (no God/Intelligence allowed) a theory that all the living forms(species of plants, fish, mammals, birds, etc, etc, etc) on the the Earth have arisen from a single source(one celled common ancestor) which itself came from an inorganic non-living source manipulated by accident for no ryheme or reason by nothing more than physics and chemicals. From that point on the theory is a gradual process by which the present diversity of plant and animal life morphs from the earliest and most primitive organisms by tiny incremental changes of random mutations guided by natural selection for the past countless millions of years.

    The problem is the foundation is never once laid or dealt with and when you press the evolutionist for it you get the bait and switch tactic of definition shell gaming and discussion becomes useless. The examples Cornelius has presented of the sophisticated micro-world and their clearly complex behavior just don't behave the way the unintelligence Gang's demands for it's no purpose no goals allowed dogma. Does that make it simple enough ???

    ReplyDelete
  82. Scott said, "You've yet again failed to differentiate between the phenomena attributed to gravity (falling apples and moving planets) and the theory that explains that phenomena (the curvature of space time). "

    Clear difference...

    1. We directly observe and measure the effects of gravity (from falling apples to galaxies) and then develop theories to explain it.

    2. We can not directly observe and measure molecules evolving into men. Moths changing colors and such is not directly observing the former.

    That's the difference.

    ReplyDelete
  83. Negative Entropy:

    "Seems like you just sprout angry accusations and, unless you are expecting everybody to know some mysterious background that I ignore, heavily charged statements."
    ===

    Well lately this comes from an incident that happened a few days back when my account here was hijacked by some idiot or collective smart*ssed group of disingenuous private-messaging individual idiots(and they know who they are) who hacked and stole my email and google posting account here and replaced the username I chose specifically for this site (Eocene) with the name inside my private details of my account. This email provider help me get it back fortunately. They admitted their system detected the hacker and they are presently investigating the creep/s IP address.

    Now it seems that One would be prepared when coming into a combat setting such as this and appreciate the usual low caliber degraded quality of the majority in such settings. As it turned out I foreknew exactly the type of decadent cowards that I'd be dealing with here and this email account is specifically a junk account I made up to use for no other purpose than Cornelius's blog and the internal account details are bogus as well. I had an experience back in 2007 where my oldest original email was well known and several disturbed cowards loaded my email with viruses, porno, spam and every type of filth/foul content you can imagine. I had to disolve that email I had for well over a decade and never let my personal email out since, though I do have at least 20+ for various purposes. So such experiences tend to sour ones attitude a bit especially when your prophetic intuition/suspicions actually come to life. I don't have time for the moment, but I'll come back and address some of those other points.

    Have a good weekend. *wink*

    ReplyDelete
  84. Neal -

    "We can not directly observe and measure molecules evolving into men. Moths changing colors and such is not directly observing the former."

    You are incorrect.

    The evolution of the White- and Black-bodied Peppered Moth (the example to which I presume you refer) IS an example of an observation of natural selection in action.

    You appear to believe there is a fundamental difference between microevolution and macroevolution. In reality, there simply is not. They are both evolution, but on different scales. The mechanisms of one are the mechanisms of the other. If one works, so to does the other.

    Unles you can propose any good REASON why we should believe otherwise?

    And no, 'we haven't witnessed macroevolution' doesn't cut it, I'm afraid, because it is an unreasonable request. You are demanding the sort of evidence which takes thousands, if not millions of years of direct observation to acquire. How can you possibly consider this a reasonable request?

    All we can observe of macroevolution is it on a small time-scale - which is microevolution. Which has been amply observed and documented many times.

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  85. Ritchie said, "You appear to believe there is a fundamental difference between microevolution and macroevolution. In reality, there simply is not. They are both evolution, but on different scales. ... Unles you can propose any good REASON why we should believe otherwise?"

    Darwin couldn't have said it better.

    The fact is you have to "believe" that there is no difference. You don't have to believe that an apple falls to the ground, you can observe it.

    That's the difference.

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  86. The white pepper moths never actually became extinct. The relative proportions of white and black pepper moths changed. That is all. It could be argued that the pepper moth actually refutes natural selection because white pepper moths survived.

    And I'm not sure you can so easily extrapolate macro from micro evolution until we can determine things like how many mutations it takes to actually change from one species to another. If it only takes one mutation to chnage the color of a pepper moth, and a million mutations to change from one species to another, then it miht be a problem. I know that I'm just making up numbers, but I think the point still stands.

    ReplyDelete
  87. natschuster said:
    ====
    It could be argued that the pepper moth actually refutes natural selection because white pepper moths survived.
    ====

    No, all you can say is that the selective pressure was not strong and sustained enough (+ possible drift effects) to completely eliminate white moths.

    ====
    And I'm not sure you can so easily extrapolate macro from micro evolution until we can determine things like how many mutations it takes to actually change from one species to another
    ====

    That is very naïve. For starters, there is no universally accepted species concept. And if there was one, there would be no such thing as a mutation number threshold. That would make no biological sense. It is not a matter of how many mutations, but which mutations in which genes, and how fixed they become in the populations.

    ReplyDelete
  88. Cornelius in the comments of this post:
    ====
    Except I never said that [Sober argued against ID from the existence of "bad design"]. At least I did not intend to. I did point out that Sober, in the PNAS paper, shows how the argument defeats creationism using the usual metaphysical arguments such as gill slits. I agree with you that Sober does not make these arguments, himself. If I left the impression otherwise, then I take it back.
    ====

    Cornelius in his previous post:
    =====
    As Elliot Sober has observed, Darwin’s Principle (as Sober referred to it) is that biological inefficiencies and bad designs are powerful evidence for the fact of evolution because they show how unlikely are the creation or design alternatives.
    ====

    1. Again, that is no Darwin's Principle. This is what Sober wrote in his paper:
    ====
    Darwin’s Principle. Adaptive similarities provide almost no evidence for common ancestry while similarities that are useless or deleterious provide strong evidence for common ancestry.
    ====
    (my emphasis)
    You presented a straw man.

    2. There you explicitly say that Sober observed that "bad design" favours evolution because they show creationist alternatives unlikely. If you did not intend to say that, well, that was really badly written. Perhaps you are also an evolutionist and we have misunderstood you all along!

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  89. Neal -

    "The fact is you have to "believe" that there is no difference. You don't have to believe that an apple falls to the ground, you can observe it."

    Nonsense. There is no such belief required. Macroevolution is evolution via exactly the same mechanisms as microevolution. This is not a matter of belief, nor of opinion. It is a matter of fact.

    A fact you simply seem to be unaware of.

    ReplyDelete
  90. (cont'd)
    3. If one replaces your false Darwin's Principle with the true Darwin's Principle in your previous post, it becomes a non-sequitur. Your last post was about arguing from the existence of "bad design". Darwin's Principle does not argue for evolution, it rather tell where to find valid evidence for common ancestry (in similarity patterns present in "badly designed" features, not from the existence of the features). Do you get the difference? There was no reason for mentioning Darwin's Principle in that post. It has nothing to do with the arguments from "bad design".

    4. There is no point discussing with you anything any further when you bring up your "metaphysics" folderol.

    ReplyDelete
  91. P.S: In my comment on your previous post, I noted the page numbers of a book, but it seems like I deleted the paragraph where I wrote its name. That was Sober's 2008 Evidence and evolution--The logic behind the science

    ReplyDelete
  92. nat -

    "The white pepper moths never actually became extinct. The relative proportions of white and black pepper moths changed. That is all. It could be argued that the pepper moth actually refutes natural selection because white pepper moths survived."

    No it does not refute natural selction. White Peppered moths have become common again as environmental standards have cleaned up the pollution which darkened the tree bark. While there was plenty of pollution (and thus, dfark tree trunks), white moth numbers plummeted. It is not a point against ToE if just because they never crashed so low as to hit actual extinction.

    "And I'm not sure you can so easily extrapolate macro from micro evolution until we can determine things like how many mutations it takes to actually change from one species to another."

    The evolution of one species into two falls under microevolution. We have recorded one species becoming two many times.

    For an example, go to youtube and search for Salamander's Tale.

    And if this process can make two sub-species from one species (as we have seen it can) and can make two species from one (as we have seen it can), why not two genera from one, or two families from one, or two orders from one...? I'm not actually sure where the threshhold is between microevolution and macroevolution. But the point is that it works on the lowest level. Why not further up?

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  93. oleg:

    ===
    Let's see what those scientific problems are. What are your specific objections to common descent?
    ===

    Well it depends on what you mean by common descent. Even many IDs and creationists accept certain types of common descent, but I suspect you don't mean that. If you mean common descent via evolution, then you could look at the many failed predictions. For that you can look here:

    http://www.darwinspredictions.com/

    Another way is by the many failed explanations and lack of scientific evidence for the proposed evolutionary creations. This would be a long list. One item we discussed recently is the creation of a typical protein.

    The typical evolutionary response to the tremendous scientific problems with their idea is to argue that the problems do not falsify evolution. Their metaphysics leads them to the position that evolution is a fact. This presents a very high burden of proof for science. No matter that there are monumental problems, a long trail of false predictions, etc. The only way for science to over turn evolution would be some sort of absolute proof that evolution is impossible. It would be hard to imagine better evidence against the theory, but given its flexibility, it is true that the evidence does not absolutely falsify it. So evolutionists seem to take this as sanctioning the fact claim.

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  94. anaxyrus:

    ===
    "Great, some moths changed color so life arose in a warm little pond, er somewhere, and then evolved spontaneously into the millions of species and designs we find."

    These are the kinds of mischaracterizations you would expect from Kent Hovind.
    ===

    No, I'm afraid that is not a mischaracterization. Evolutionists sometimes suggest such minor change as sufficient evidence for all of evolution.

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  95. anaxyrus:

    ===
    That evolution happens before our eyes, through processes and at rates that, in conjunction with known historical abiotic environmental change, are sufficient to produce the history of life on Earth, is but one of the lines of evidence that causes us to accept common descent.
    ===

    Sufficient to produce the history of life on Earth? Evolutionists in their honest moments admit this is false. This neo Darwinist view does not enjoy the evidential support evolutionists once claimed. It is not clear that alleles changing frequencies + time = millions of species with all kinds of new designs. Evolutionists cannot even explain how a single new protein could arise.

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  96. Negative Entropy:

    ===
    Misguided religion drives your pseudoscience, and it matters.
    ===

    I've asked you to explain what misguided religion and what pseudoscience you are referring to, and how the former drives the latter. But you seem to be ignoring the question.

    ReplyDelete
  97. Geoxus:

    ===
    You presented a straw man.
    ===

    How so?

    ReplyDelete
  98. Cornelius,
    Conflating ideas seems to be a big hobby of yours. you wrote in response to Oleg "If you mean common descent via evolution.." and then a long bit about perceived problems with the mechanisms of evolution. common descent is a pattern, independent of mechanism, as has been pointed out to you many times before. in fact, in one of your more lucid moments, you agreed that common descent of diatoms was a compelling hypothesis. why is it compelling and why is common descent of vertebrates, which is demonstrated using the same types of data, not? this is around the 10th or so time this question has been asked.

    ReplyDelete
  99. Cornelius wrote: Well it depends on what you mean by common descent. Even many IDs and creationists accept certain types of common descent, but I suspect you don't mean that. If you mean common descent via evolution, then you could look at the many failed predictions.

    Umm, common descent is common descent. You know, the tree of life. DO you accept it or not? That isn't a trick question, unless you want to make it so.

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  100. Cornelius -

    Seriously, doesn't it ever trouble you that you think you know more about science than actual scientists do?

    You're like the little boy who insisted all clocks in town but his were wrong - and it turns out he doesn't really understand much about clocks anyway.

    I mean I will grant it's not conclusive. But when you're telling scientists (pretty much all of them) that you think you know better about their own field of expertise, that's usually a pretty big hint that you're the one who's got it wrong.

    ReplyDelete
  101. Hunter:

    Evolutionists cannot even explain how a single new protein could arise.

    Arise? Spontaneously? Out of the Primordial Soup?

    What are you asking for, a movie? (Nobody was there to film it, as far as we know.)

    Why is it necessary for science to recreate the origin of life in order to be credible amount the subsequent history of life? What does that have to do with the Theory of Evolution?

    Happy New Year!

    ReplyDelete
  102. Correction:

    Why is it necessary for science to recreate the origin of life in order to be credible about the subsequent history of life?

    And what, indeed, does that have to do with the Theory of Evolution? (Praised be its name!)

    ReplyDelete
  103. Ritchie:

    I mean I will grant it's not conclusive. But when you're telling scientists (pretty much all of them) that you think you know better about their own field of expertise, that's usually a pretty big hint that you're the one who's got it wrong.

    You don't seem to understand that Professor Cornelius Hunter is a pioneer in anti-evolution research. It doesn't matter that he's wrong - he's original. Unlike Intelligent Design Creationists he doesn't argue that Design is correct because evolution is incorrect. He argues only that evolution is incorrect, and coyly offers no alternative . That kind of intellectual asceticism is exemplary. Hunter stands alone on his Peak in Darien.

    And let's not forget the careful documentation of religious and metaphysical presuppositions that Hunter has uncovered in evolutionary thought. Going back well before Hume and Paley. Indeed, before Kant and Spinoza and even William of Ockham. He may soon uncover such presuppositions in the writings of the Milesian school. In the meantime, read Science's Blind Spot.

    So, back off Buster... and have a Happy New Year!

    ReplyDelete
  104. Hi, just wanted to wish you all a very happy new year!!
    I hope it is good for all of you :)

    ReplyDelete
  105. oleg:

    ===
    Umm, common descent is common descent. You know, the tree of life. DO you accept it or not? That isn't a trick question, unless you want to make it so.
    ===

    OK, the tree of life. That has been falsified many times over. There are mismatches at all levels. Only a precommittment to CD could overlook these many contradictions.

    ReplyDelete
  106. Geoxus wrote:

    Cornelius in the comments of this post:
    ====
    Except I never said that [Sober argued against ID from the existence of "bad design"]. At least I did not intend to. I did point out that Sober, in the PNAS paper, shows how the argument defeats creationism using the usual metaphysical arguments such as gill slits. I agree with you that Sober does not make these arguments, himself. If I left the impression otherwise, then I take it back.
    ====

    Cornelius in his previous post:
    =====
    As Elliot Sober has observed, Darwin’s Principle (as Sober referred to it) is that biological inefficiencies and bad designs are powerful evidence for the fact of evolution because they show how unlikely are the creation or design alternatives.



    It's not the first time Cornelius says that Sober has made this claim. From June 26th, 2009:

    But Sober mysteriously fails to explain the obvious. The elephant in the room is ignored as Sober moves on to an analogy about term papers. The reason the denominator is so small is that a religious premise about divine intent was smuggled in. The reason those creationist concerns about insuperable boundaries do not hold is because common ancestry is likely. And common ancestry is likely because nature's designs given separate ancestry is unlikely. And those designs given separate ancestry are unlikely because god would not have given us our "useless" tailbones.

    Is Cornelius being disingenious?

    ReplyDelete
  107. It could be argued that the pepper moth actually refutes natural selection because white pepper moths survived.

    I think we have a genuine "then why are there still monkeys" type argument here. If the black moths evolved from the white ones, then why are there still white moths?

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  108. Cornelius wrote: OK, the tree of life. That has been falsified many times over. There are mismatches at all levels.

    Can you be a little more specific, Cornelius?

    ReplyDelete
  109. Hawks:

    ===
    Is Cornelius being disingenious?
    ===

    Yes, I said "inefficient and bad designs" rather than "deleterious designs." Terribly disingenuous.

    ReplyDelete
  110. oleg:

    ===
    Can you be a little more specific, Cornelius?
    ===

    Sure, here are some examples. The genomes of eukaryotes, prokaryotes and archaea don't fit well into a common descent model. So for early life there are several different topologies to consider, none of which work very well. Perhaps the archaea split off from the eukaryote lineage, or perhaps the bacteria split off from the archaea lineage. Perhaps the bacteria split off from the eukaryote lineage. Evolutionists have even considered a fusion of the archaea and bacteria lineages to produce the eukaryotes.

    The problem is that none of the solutions are strongly supported. Very different evolutionary relationships are indicated by different molecular sequences. So an emerging hypothesis is that there wasn't the traditional type of vertical evolution between generations after all, but an amazing horizontal evolution (far beyond anything known) where evolution occurs within a population.

    Another example are the many significant differences between nearby branches in the tree of life. Everything from the genomes (completely different proteins for as much as a fifth of the proteome) to development (different embryonic development pathways). Needless to say these falsified predictions, and do not fit the common descent model.

    Another example are the many significant similarities between distant branches in the tree of life. Both morphological as well as molecular comparisons show extremely high similarities that don't make sense on the common descent model.

    Not surprisingly there have been papers in recent years suggesting the tree model is not that fruitful.

    ReplyDelete
  111. Hunter, creating refreshing breeze with rapid hand movements:

    Sure, here are some examples.

    Followed by more than 200 words of unsupported assertions.

    Not a single reference to the scientific literature.

    ReplyDelete
  112. Pedant:

    "Followed by more than 200 words of unsupported assertions.

    Not a single reference to the scientific literature."
    ===

    All he did was expose the religiosity of your beliefs for what they truly are = "FAITH"

    ReplyDelete
  113. Cornelius Hunter said...

    Sure, here are some examples. The genomes of eukaryotes, prokaryotes and archaea don't fit well into a common descent model. So for early life there are several different topologies to consider, none of which work very well. Perhaps the archaea split off from the eukaryote lineage, or perhaps the bacteria split off from the archaea lineage. Perhaps the bacteria split off from the eukaryote lineage. Evolutionists have even considered a fusion of the archaea and bacteria lineages to produce the eukaryotes.

    The problem is that none of the solutions are strongly supported. Very different evolutionary relationships are indicated by different molecular sequences. So an emerging hypothesis is that there wasn't the traditional type of vertical evolution between generations after all, but an amazing horizontal evolution (far beyond anything known) where evolution occurs within a population.

    Another example are the many significant differences between nearby branches in the tree of life. Everything from the genomes (completely different proteins for as much as a fifth of the proteome) to development (different embryonic development pathways). Needless to say these falsified predictions, and do not fit the common descent model.

    Another example are the many significant similarities between distant branches in the tree of life. Both morphological as well as molecular comparisons show extremely high similarities that don't make sense on the common descent model.

    Not surprisingly there have been papers in recent years suggesting the tree model is not that fruitful.

    =========================
    How similar is the Chimp-Human genome?

    ReplyDelete
  114. Cornelius Hunter: Sure, here are some examples. The genomes of eukaryotes, prokaryotes and archaea don't fit well into a common descent model. So for early life there are several different topologies to consider, none of which work very well. Perhaps the archaea split off from the eukaryote lineage, or perhaps the bacteria split off from the archaea lineage. Perhaps the bacteria split off from the eukaryote lineage. Evolutionists have even considered a fusion of the archaea and bacteria lineages to produce the eukaryotes.

    The situation is not as confused as you would make it appear. Yes, different researchers have proposed many different ideas over the years, but some aspects of eukaryote origins have been constrained for sometime now and not all of the models are equally well supported.

    The following ideas are standing up well :

    Archaea and Eukaryota are sister groups.
    Eukaryotes, after splitting from stem-archeans, acquired mitochondria through the engulfment of alpha proteobacteria.
    Genetic material from captured proteobacteria was transferred to the eukaryote nucleus.
    Horizontal gene transfer (well known in "prokaryotes" and also seen in eukaryotes today) was widespread early in life's history.

    The tree of life is a model developed to explain the diversification of eukaryote (largely animal) life. Even here there is enough anastomosis from hybridization and HGT to ensure that the tree is not a perfect model of evolution. But there is enough branching structure within eukaryotes and even to a lesser extent within bacteria and archaea to make the tree a useful model.

    C. DeDuve. 2007. The orgin of eukaryotes: a reappraisal. Nature Reviews Genetics 8:395-403.
    Poole and Penny. 2006. Evaluating hypotheses for the origin of eukaryotes. Bioessays 29:74-84.
    Koonin. 2009. Darwinian Evolution in the light of genomics. Nucleic Acids Research 37:1011-1034.

    ReplyDelete
  115. Cornellus,

    Happy New Year. Thanks for another year of great science. Your posts are very much appreciated.

    .

    ReplyDelete
  116. Cornelius:

    Yes, I said "inefficient and bad designs" rather than "deleterious designs." Terribly disingenuous.

    This is what you actually said (emphasis added):

    But Sober mysteriously fails to explain the obvious. The elephant in the room is ignored as Sober moves on to an analogy about term papers. The reason the denominator is so small is that a religious premise about divine intent was smuggled in. The reason those creationist concerns about insuperable boundaries do not hold is because common ancestry is likely. And common ancestry is likely because nature's designs given separate ancestry is unlikely. And those designs given separate ancestry are unlikely because god would not have given us our "useless" tailbones.

    You were saying...?

    ReplyDelete
  117. My posts keep disappearing. I find that very annoying.

    ReplyDelete
  118. Your other objections are too vague to address them. Wolves and thylacines may have some similarities, but they are not exactly mirror images of each other.

    From a broader perspective, you seem to hold a rather naive viewpoint on how scientific theories live and die. No scientific theory is perfect. Every theory has a limited domain where it is valid and it makes no sense to apply it outside of that domain.

    To give you an example, Newton's theory of gravity works in the limit of slow speeds and weak gravitational fields. Mercury, the planet closest to the sun, experiences the strongest gravitational pull and moves fastest in its orbit. There are well characterized deviations of Mercury's orbit from the predictions of Newtonian mechanics. These discrepancies are accounted for by Einstein's general relativity. Does this mean Newton's theory is invalid? No, it doesn't. We still use it with great success in spacecraft navigation. We just know not to rely on it situations where the theory is inapplicable.

    The same goes for the tree of life. The concept works well for multicellular organisms whose genes are transferred vertically. It does not work well at early stages of evolution where horizontal transfer dominates. Does this invalidate the concept altogether? No, it simply shows that the idea has a limited domain of validity. The important point is that said domain exists and is vast, so the theory is useful. You can't point to HGT and argue that humans and chimps therefore fo not share a common ancestor.

    ReplyDelete
  119. Here is a third attempt to post a comment. I suspect that the problem may be caused by a link to Telic Thoughts, so I will remove it and post it separately if I can.

    Cornelius wrote: Sure, here are some examples. The genomes of eukaryotes, prokaryotes and archaea don't fit well into a common descent model. So for early life there are several different topologies to consider, none of which work very well. Perhaps the archaea split off from the eukaryote lineage, or perhaps the bacteria split off from the archaea lineage. Perhaps the bacteria split off from the eukaryote lineage. Evolutionists have even considered a fusion of the archaea and bacteria lineages to produce the eukaryotes.

    I remember having a discussion on this very subject with Paul Nelson at Telic Thoughts. Sure, horizontal gene transfer messes up phylogenies at the level of early single-cell organisms. However, HGT is insignificant in metazoa, vertical gene flow is clearly dominant and ancestral relations are traceable. Follow this link (see below) to the beginning of our discussion if you are interested in details. There are relevant quotes from Doolittle and Woese showing what they think of the tree of life at the metazoan level. In a nutshell, they think it stands.

    The discussion went back and forth several times, but Nelson never explained how prevalence of HGT at the early stages of life invalidates the tree structure of ancestral relations for multicellular organisms. It doesn't in my view and in the view of biologists who worked on this. Maybe you should explain why you think it does.

    ReplyDelete
  120. It seems that the comment, sans the link, went through. Here is the link to my discussion with Nelson: http://telicthoughts.com/a-disclaimer-for-behe-2/#comment-245824

    ReplyDelete
  121. More of what Cornelius wrote (and I haven't done an exhaustive search)

    Sept 17, 2009:

    In what Sober has labeled Darwin's Principle, the evolutionary argument is not that the evidence makes common ancestry probable but that it makes the creation concept of separate ancestry improbable.

    Sober will not mention that this means the argument entails religious premises.


    July 27th, 2009:

    As Elliott Sober has pointed out, evolution's truth status comes from the assumed unlikeliness of design, and all the theology entailed therein. It is, as Sober put it, Darwin's Principle.

    June 3rd, 2010:

    As Elliott Sober explained recently (though it has been obvious for centuries), the strength of the evolutionary argument is not in its driving up the probability of evolution, but in its driving down the probability of creation or design.

    Shall we let other readers decide if Cornelius is being disingenuous or not?

    ReplyDelete
  122. Cornelius Hunter: Evolutionists cannot even explain how a single new protein could arise.

    Gene duplication, mutation, voila new protein. That seems to be the most common route.

    ReplyDelete
  123. Neal wrote:

    Clear difference...

    1. We directly observe and measure the effects of gravity (from falling apples to galaxies) and then develop theories to explain it.


    Neal,

    We directly observe and measure biology adapting to it's environment. We observe change in heritable traits in a population. We observe specific patterns in the fossil record, etc. This is separate from any specific underlying theory that explains these observations, such as common decent. This is the equivocation we're referring to.

    Perhaps the following questions will clarify this further.

    How do you know that observations of apples falling and planetary motion are both caused by a single natural force in reality? How do you know this is a single uniform force, rather than a constantly varying force that requires constant intersession by an intelligent agent to compensate?

    You don't. We assume they are both caused by the same uniform natural force because we've developed a theory that allows us to predict how they will both move. And that prediction is overwhelmingly observed for both objects local to the earth and objects in space.

    However, in situations where both quantum effects and strong-field gravity are important, the consistency of these predictions are violated. This is not to say that we do not observe some kind of phenomena at this scale, but the interactions between both forces is so complex at this level that we're having difficulty creating a working theory of quantum gravity to unify them.

    ReplyDelete
  124. Cornelius Hunter: It is not clear that alleles changing frequencies + time = millions of species with all kinds of new designs.

    The last few decades have shown that new morphologies (if that's what you mean by designs) are indeed not simply due to new alleles and frequencies, but more importantly depend upon heterochrony and other changes in gene regulation.

    Modern evolutionary theory is not the neoDarwinism of the 1950s.

    ReplyDelete
  125. Furthermore, rather than a natural force, It's possible that an army of slide rule toting demons have chosen to constantly push and pull on objects in a way that only appears to be a natural process. These demons might have some mysterious reason for consistently moving objects in the specific way we observe; and God might have some mysterious reason for allowing them to do so.

    But this also means these demons might have some mysterious reason to moving objects differently five billion yeas from now, five years from now or five minutes from now, as they would be agents that make choices. We simply have no way of knowing gravity will remain uniform due to the problem of induction. Instead, we assume the prediction will continue to hold because we assume the underlying explanation for that phenomena is a uniform natural force, rather than an agent that makes choices.

    Clearly, if supernatural agents exist, it's a logical possibility that phenomena we attribute to gravity could actually be caused by the actions of mysterious intelligent agents. However, science discards this theory because it fails to provide an underlying explanation as to why why demons would consistently push and pull on objects according to their mass.

    Since he has yet to claim gravitational theory is "bad science", apparently Cornelius doesn't think the uniform movement of of objects without the constant invention of a supernatural intelligent agent is absurd. Of course, this comes as no surprise as God using a natural force as a secondary cause to move objects in a consistent manner likely agrees with Cornelius' personal theological views about the specific roles, or the lack there of, that supernatural agents play in our universe.

    Nor has Cornelius suggested gravitational theory is "bad science" because it does not explicitly credit an intelligent designer for the origin of that force.

    Cornelius, are these merely a coincidences?

    ReplyDelete
  126. Geoxus:

    ===
    You presented a straw man.
    ===

    Cornelius:
    ===
    How so?
    ===

    OK. Baby steps. Can you see the difference between what you said Darwin's Principle was (the specific fragments I quoted before) and what Sober actually wrote (I quoted two coincident definitions of Darwin's Principle directly from Sober 2008 and Sober 2009)?
    I explained it twice.

    ReplyDelete
  127. oleg:

    ===
    Your other objections are too vague to address them.
    ===

    What's vague about different proteins in nearby twigs of the tree? Is falsification of the tree of life in the set of possible answers for you?

    ===
    From a broader perspective, you seem to hold a rather naive viewpoint on how scientific theories live and die. No scientific theory is perfect. Every theory has a limited domain where it is valid and it makes no sense to apply it outside of that domain.

    To give you an example, Newton's theory of gravity works in the limit of slow speeds and weak gravitational fields. Mercury, the planet closest to the sun, experiences the strongest gravitational pull and moves fastest in its orbit. There are well characterized deviations of Mercury's orbit from the predictions of Newtonian mechanics. These discrepancies are accounted for by Einstein's general relativity. Does this mean Newton's theory is invalid? No, it doesn't. We still use it with great success in spacecraft navigation. We just know not to rely on it situations where the theory is inapplicable.

    The same goes for the tree of life. The concept works well for multicellular organisms whose genes are transferred vertically. It does not work well at early stages of evolution where horizontal transfer dominates. Does this invalidate the concept altogether? No, it simply shows that the idea has a limited domain of validity. The important point is that said domain exists and is vast, so the theory is useful. You can't point to HGT and argue that humans and chimps therefore fo not share a common ancestor.
    ===

    And of course I didn't do that. You asked for evidence against the tree of life, and I provided it. I'm happy to discuss the philosophical issues you raise here, but first please read the very brief discussion here (Sections 1.1 to 1.3):

    http://www.darwinspredictions.com/#_1.1_How_to



    ===
    I remember having a discussion on this very subject with Paul Nelson at Telic Thoughts. Sure, horizontal gene transfer messes up phylogenies at the level of early single-cell organisms.
    ===

    No, much more than HGT is used in the horizontal evolution model of early life.


    ===
    However, HGT is insignificant in metazoa, vertical gene flow is clearly dominant and ancestral relations are traceable.
    ===

    So why then do you dismiss the problems with the tree of life at those levels?

    ReplyDelete
  128. Geoxus:

    ===
    Can you see the difference between what you said Darwin's Principle was (the specific fragments I quoted before) and what Sober actually wrote (I quoted two coincident definitions of Darwin's Principle directly from Sober 2008 and Sober 2009)?
    ===

    "Inefficient and bad design" is not a strawman version of "deleterious traits." If you have a real strawman rather than mere empty accusations, then all you need to do is spell it out. So far all I've seen are snippets with vague accusations. So I asked you to clarify, and yet again, all we see are the usual vague accusations.

    ===
    I explained it twice.
    ===

    No, what you've provided is much indignation with no substance to back it up.

    ReplyDelete
  129. anaxyrus:

    ===
    Cornelius Hunter: Evolutionists cannot even explain how a single new protein could arise.

    Gene duplication, mutation, voila new protein. That seems to be the most common route.
    ===

    Evolutionists engage in theory protectionism because their theory must not be falsified. Here you have a clear cut evidential problem for the theory, and in typical fashion evolutionists sweep it under the rug.

    We're told that new proteins usually arise via mechanisms such as gene duplication. But that avoids the problem (ie, new proteins that cannot be so explained, and the origin of the gene that was duplicated).

    ReplyDelete
  130. OK, here it goes again. That last comment was not an accusation. It was just a question. I am trying to clarify, but I need to know what need to be clarified.

    ===
    "Inefficient and bad design" is not a strawman version of "deleterious traits."
    ===

    Yes, there is no straw man there, that is not the problem ("Inefficient and bad design" is not necessarily deleterious, but that is just a detail and I have no problem with it).

    Let's compare false and true Darwin's Principles (DP) again.

    Cornelius in his previous post:
    =====
    As Elliot Sober has observed, Darwin’s Principle (as Sober referred to it) is that biological inefficiencies and bad designs are powerful evidence for the fact of evolution because they show how unlikely are the creation or design alternatives.
    ====

    Sober 2009:
    ====
    Darwin’s Principle. Adaptive similarities provide almost no evidence for common ancestry while similarities that are useless or deleterious provide strong evidence for common ancestry.
    ====

    ReplyDelete
  131. (cont'd)
    So, your DP (fDP):
    There are biological inefficiencies and "bad design" -> Design is very unlikely -> Evolution is a better hypothesis

    Sober's DP (tDP):
    Adaptive similarities -> Almost no evidence for common ancestry (CA)
    Useless or deleterious similarities -> Strong evidence for common ancestry

    -fDP is an argument that can follow from the separate examination of the features of different organisms, no comparison needed.

    -tDP can only follow from the comparison between features of different organisms. The mere observation of non-adaptive traits in different organisms provides no evidence under tDP.

    -fDP is an argument for evolution.

    -tDP is a rule for discriminating between good and bad evidence for CA (not an argument for CA by itself).

    -fDP is about the existence of "bad desgin"

    -tDP is about adaptive and non-adaptive (useless or deleterious) similarities.

    Can you see it now?

    ReplyDelete
  132. Geoxus said...

    Cornelius in his previous post:
    =====
    As Elliot Sober has observed, Darwin’s Principle (as Sober referred to it) is that biological inefficiencies and bad designs are powerful evidence for the fact of evolution because they show how unlikely are the creation or design alternatives.
    ====

    Sober 2009:
    ====
    Darwin’s Principle. Adaptive similarities provide almost no evidence for common ancestry while similarities that are useless or deleterious provide strong evidence for common ancestry.


    Wow CH. Either you have the worst reading comprehension skills on the planet or you were being deliberately dishonest in misrepresenting Sober.

    Which is it?

    ReplyDelete
  133. Cornelius,

    I did not "dismiss the problems with the tree of life" at the base level. I pointed out that the theory predicting a monophyletic tree is not applicable in the domain where HGT plays a significant role. If genes are not primarily passed vertically then we have no reason to expect that ancestral relations can be determined by genetic analysis.

    This in no way invalidates the applicability of the tree at higher levels, where genes are passed primarily from ancestors to descendants. Paul Nelson seemed unwilling to acknowledge that and kept making vague references to a "corrosive effect" on the structure of the entire tree. As hard as I pressed him on that, he could not specify what exactly the effect was. Maybe you can explain that to me. Or perhaps you can agree with me that the tree model may be applicable to metazoans.

    As to your objection about different proteins at nearby twigs of the tree, this is, as I said, vague. You will have to unpack that for me.

    ReplyDelete
  134. Hunter:

    What's vague about different proteins in nearby twigs of the tree? Is falsification of the tree of life in the set of possible answers for you?

    How about those different proteins between chimpanzee and human that Hunter has repeatedly claimed to exist? Do they exist? He has yet to cite a reference. If they don't exist, there is no falsification of the tree of life.

    Time to put up or shut up?

    ReplyDelete
  135. oleg:

    ===
    I did not "dismiss the problems with the tree of life" at the base level. I pointed out that the theory predicting a monophyletic tree is not applicable in the domain where HGT plays a significant role. If genes are not primarily passed vertically then we have no reason to expect that ancestral relations can be determined by genetic analysis.
    ===

    But again, you are invoking an unknown epicycle. The type of massive horizontal evolution and its mechanisms, that are needed, have never been observed (you seem to be confusing this with today's HGT -- two very different things). There is no scientific evidence for this, aside from the presuppposition of evolution.

    ===
    This in no way invalidates the applicability of the tree at higher levels, where genes are passed primarily from ancestors to descendants.
    ===

    I didn't say it did. Again, there are problems at all levels.

    ===
    As to your objection about different proteins at nearby twigs of the tree, this is, as I said, vague. You will have to unpack that for me.
    ===

    Two species in the same genera, or even two variants within the same species, can have different proteins. IOW, there are species that have unique proteins, not found elsewhere in any other species. The fruit fly is a good example that has been studied quite a bit. This is much greater change than common descent predicted.

    Findings in recent years that the set of amino acid sequences that can produce a given protein is a relatively small subset in the set of of all possible such sequences don't help. Also, there is scant evidence for a pathway of intermediates, leading proteins. This is why the origin of proteins is a problem for evolution.

    ReplyDelete
  136. Ritchie and Geo:

    But selective pressure was not enough to drive the white pepper moths to extinction. So how can it be a force in creating a new species?

    And I understand that the California Newts can and do interbreed, so it is very questionable whether they are different species. Saying that they are possible incipient species, is speculative, at best.

    ReplyDelete
  137. Cornelius Hunter said...

    Findings in recent years that the set of amino acid sequences that can produce a given protein is a relatively small subset in the set of of all possible such sequences don't help.


    It doesn't hurt one bit either. Unless you're going to continue to make your incredibly stupid claim that evolution had to have all the parts of the protein spontaneously appear and assemble all at once. You really want to ride that train again?

    Also, there is scant evidence for a pathway of intermediates, leading proteins.

    Scant evidence doesn't equal no evidence.

    This is why the origin of proteins is a problem for evolution.

    Yeah yeah CH, we know. Every disingenuous strawman you make up from whole cloth is a 'problem' for evolution. That's why the scientific community is trembling at the knees over your, ahem, devastating critiques.

    ReplyDelete
  138. natschuster said...

    Ritchie and Geo:

    But selective pressure was not enough to drive the white pepper moths to extinction. So how can it be a force in creating a new species?


    The rain last night didn't cause any flooding in my backyard. So how can rain be a force to cause flooding?

    Seriously nat, you need to be embarrassed in asking such a dumb question without bothering to think it through.

    ReplyDelete
  139. Cornelius,

    I see that now you are starting to learn better rhetorics. Yes, ignore the point, and go fishing for my verbosity by asking the wrong question. The question is not "what" misguided religion. Once you identify the proper question, how your pseudoscience follows is natural (as in explained). But you already know this. After all, it is you who decided to dedicate your life to "this."

    Misguided religion drives your pseudoscience, and it matters.

    ReplyDelete
  140. Hey Eocene,

    I don't think that what you describe as what "The average person(poor slob) on the street" understands as evolution is really what the average person understands (if at all). It sounds much more like an emotionally charged pseudo-definition proper for creationist propaganda. In any event, I see no reason why scientists should use such a convoluted definition to follow your fancy, when it is only proper to "lie the foundations" where they belong.

    Let me try and be very explicit. You seem to want evolution to include origin of life. I don't see why at all (it would help if you told me exactly how it follows that we have to know how life started before we can know that evolution does indeed happen, has indeed happened), unless you were desperately seeking for a reason to reject the theory. For all I know, evolution is a solid theory at par with gravitation (only you need more knowledge to understand this). Not knowing how life started does not change this reality.

    This is kind of how I see it (bad metaphor warning). Suppose you know how to make a pie. You detail the instructions for pie making, and all the varieties of pie you can make, then I come to you and I tell you that your pie recipes are all lies because you do not know who was the first person to mix flour and other ingredients to bake something. Not only that, I further accuse you of not knowing how the atoms behave while mixing and cooking the dough, and, if you do know, I insist that you misrepresent the facts to continue with your religion of false pie making, and that you have a ridiculous notion that heat can bake pies randomly. If you bake a pie I contend that you cannot define pie making to exclude who first mixed ingredients, how the atoms behave, and heat randomly baking pies. Well, asking for the origin of life, and asking for explanations about misrepresented molecular details, while asking knowledgeable people to stick to misrepresented, charged, misguided, straw-man, definitions of evolution is just like that.

    ReplyDelete
  141. Cornelius wrote: Two species in the same genera, or even two variants within the same species, can have different proteins.

    Wouldn't you expect descent with modification to result in differences? Again, you might argue how strongly two closely related species should be expected to diverge. That would have to be a quantitative argument. So far you're just stressing the presence of differences, which is what I find vague.

    But again, you are invoking an unknown epicycle. The type of massive horizontal evolution and its mechanisms, that are needed, have never been observed (you seem to be confusing this with today's HGT -- two very different things). There is no scientific evidence for this, aside from the presuppposition of evolution.

    Of course, we are talking about early evolution, which cannot be observed at the moment. But it was not me who dragged it in. I have stressed many times that I would like to see how this creates a problem for the tree of life at the level of metazoans. It doesn't, so drop the subject or show its relevance.

    Findings in recent years that the set of amino acid sequences that can produce a given protein is a relatively small subset in the set of of all possible such sequences don't help. Also, there is scant evidence for a pathway of intermediates, leading proteins. This is why the origin of proteins is a problem for evolution.

    You're talking again in circumspect terms. Which studies? What did the authors conclude?

    ReplyDelete
  142. nat -

    "But selective pressure was not enough to drive the white pepper moths to extinction."

    I think the term you want is 'natural selection' rather than 'selection pressure'. And it only failed to drive the white moths to extinction within a particular time frame. But it did send the numbers of white moths into freefall. Given the declining numbers it is reasonable to conclude that the white moths may well have eventually died out if the pollution levels had persisted for longer.

    "So how can it be a force in creating a new species?"

    What this particular study shows is not new species arising, it shows various physical traits being selected for and against - and that the concept of 'desireable traits', ie fitness, is relative to the surrounding environment.

    "And I understand that the California Newts can and do interbreed,"

    If you are referring to the Californian salamanders, then you will have to elaborate. The ones referred to in the Salamander's Tale are Ensatina eschscholtzii and Ensatina klauberi, and they do not directly interbreed (thus justifying referring to them as different species) - even though they are linked by a continuous chain of living intermediaries with whom they can breed. That is why they are a ring species.

    ReplyDelete
  143. Thorton:

    The point is that the pepper moth experiment does not prove natural selection. The rain in my backyard doesn't prove that rain can cause flooding either. I need to see it happen before I can say that rain can cause flooding.

    Now, if Darwinism is true, then I would expect the white pepper moths t become extinct. The fact that they didn't become extinct cna mean one of three things. One possibilty is that natural selection does not give organisms enough of a selective advantage to drive others without the adavantage to extinction, which means that it cannot create new species. Another possibilty is that black coloration does nto give a moth enough of an advantage to drive the white moths to extinction. I have a problem with this approach because I can't think of a biiger advantage for a moth than bring able to hide from predators. Another possibilty is that there ust wasn't enough for the white moth to become extinct. The problem I have with this approach is that species have been observed going extinct in a very short time. Anyway, the pepper moth does not porvide proof that natural selection can do anything more than change the proportions within a species. Was that enough thought for you?

    ReplyDelete
  144. natschuster,

    The pepper moth example is just a particular case of NS. It wasn't strong enough in that case. And speciation is a complex and multifactorial process, in which NS may play an important role, but rarely (if ever) explains it all. Two papers on this: Grant & Grant 2006 (Nature); Nosil & Sandoval 2008 (PLoS One). You may want to look for more of the work by Peter & Rosemary Grant if you are interested in NS and speciation in the wild, they have two books IIRC.

    ReplyDelete
  145. (cont'd)
    ====
    And I understand that the California Newts can and do interbreed, so it is very questionable whether they are different species.
    ====

    They form a ring species, and not everybody accepts the biological species concept. I don't, lots of systematists don't. One of its shortcomings is that if you accept it, you must reject the existence of species in organisms with asexual reproduction. The species problem is still unresolved. I recommend you De Queiroz 2007(doi: 10.1080 / 10635150701701083).

    ====
    Saying that they are possible incipient species, is speculative, at best.
    ====

    I don't know if you are referring a particular study, but you are probably exaggerating. Are you sure you understand the methodology?

    ReplyDelete
  146. natschuster: Now, if Darwinism is true, then I would expect the white pepper moths t become extinct.

    Um, no it's not. Nor is extinction a necessary result of natural selection or speciation. Where did you get that idea?

    ReplyDelete
  147. natschuster said...

    The point is that the pepper moth experiment does not prove natural selection.


    The observed results were an empirical example of natural selection in action. That is not in dispute.

    Now, if Darwinism is true, then I would expect the white pepper moths to become extinct.

    Why would you expect that? The changing environment gave the dark variation a statistical survival advantage over the light ones. That advantage was reflected in the population ratio change. That's the definition of natural selection - the process of differential reproductive success. It doesn't mean that every light moth will die and every dark moth will survive.

    Every year there is one baseball team that is statistically better than the others. Do you think that means the team should go 162-0?

    Natural selection is one of many factors that go into speciation events. You'd know that if you had bothered to read the Berkeley - Understanding Evolution links you were given. But apparently you enjoy staying as ignorant as you can.

    ReplyDelete
  148. Zachriel:

    Doesn't natural selection mean that the organisms that have some survival advantage survive, and those that don't have it, don't survive. And this process, repeated enough times, will result in a new species?


    According to this:

    http://www.santarosa.edu/lifesciences2/ensatina2.htm

    the California salamander sub-species at the ends of the ring do interbreed. Thye just don't do it a lot.

    ReplyDelete
  149. I think I got it, natural selection works to create new species, except where it doesn't. For a theory with so much power and evidence, evolution sure requires a lot of apologetics, special pleading, etc.

    ReplyDelete
  150. natschuster said...

    Doesn't natural selection mean that the organisms that have some survival advantage survive, and those that don't have it, don't survive. And this process, repeated enough times, will result in a new species?


    No. You are confusion extinction events with speciation events. Those are two completely different things.

    Natural selection can and does play a part in both, but the overall processes are not the same.

    Please quit being such a lazy lump and the explanation of speciation you've been shown multiple times now.

    ReplyDelete
  151. Geoxus:

    ===
    -fDP is an argument that can follow from the separate examination of the features of different organisms, no comparison needed.

    -tDP can only follow from the comparison between features of different organisms. The mere observation of non-adaptive traits in different organisms provides no evidence under tDP.

    -fDP is an argument for evolution.

    -tDP is a rule for discriminating between good and bad evidence for CA (not an argument for CA by itself).

    -fDP is about the existence of "bad desgin"

    -tDP is about adaptive and non-adaptive (useless or deleterious) similarities.

    Can you see it now?
    ===

    Unbelievable. You've got to be kidding. This is what all the huffing and puffing was about? You are reading all kinds of details into my description that aren't there. You say:

    ===
    -fDP is an argument that can follow from the separate examination of the features of different organisms, no comparison needed. ...

    -fDP is about the existence of "bad desgin"
    ===

    Ridiculous--I said no such thing. In fact I have repeatedly explained the exact opposite, that Sober's "Darwin's Principle" is based on the ratio of the probability of the evidence on CA divided by the probability of the evidence on SA. For example:


    #########
    http://darwins-god.blogspot.com/2009/06/sober-rebukes-evolutions-religion.html

    He [Sober] explains that for "useless" designs, the likelihood ratio (the ratio of the probability of the design on common ancestry to the probability of the design on separate ancestry) is large because the denominator (the probability of the design on separate ancestry) is so small.
    #########


    #########
    http://darwins-god.blogspot.com/2010/10/judge-jones-i-was-taken-to-school.html

    Elliot Sober, a philosopher who analyzes evolutionary arguments in great detail has explained how the argument works in terms of likelihood ratios. Sober refers to the argument as Darwin's Principle.
    #########


    #########
    http://darwins-god.blogspot.com/2010/12/it-didnt-begin-or-end-with-darwin.html

    In the paper Sober clearly explains that Darwin’s Principle, which demonstrates species are not separated by insuperable boundaries, is based on the ratio of (i) the probability of evidence on common ancestry divided by (ii) the probability of evidence on separate ancestry. The key is that the argument is compelling not because of the former being high, but because of the latter being low.
    #########


    #########
    http://darwins-god.blogspot.com/2009/06/evolutions-religion-revealed.html

    And what is this powerful evidence for common ancestry? Sober points out that the strong arguments used by Darwin are not from adaptive designs (i.e., designs that increase fitness), but rather useless or even deleterious designs (Sober cites our tailbone and gill slits in the human fetus as examples). He summarizes this in what he calls Darwin's Principle:

    "Adaptive similarities provide almost no evidence for common ancestry while similarities that are useless or deleterious provide strong evidence for common ancestry." --Sober

    And why are useless or deleterious similarities so helpful? It is not because they raise the probability of common ancestry, but rather because they lower the probability of separate ancestry. In other words, the reason common descent is a no-brainer is that the alternative, separate ancestry, is extremely unlikely.
    #########

    ReplyDelete
  152. Psst...hey Cornelius, here's another hint.

    When you make a ridiculous claim and someone asked you to back it up with a reference, merely citing examples of where you yourself have previously made the same ridiculous claim doesn't do much for your credibility.

    ReplyDelete
  153. oleg:

    ===
    Cornelius wrote: Two species in the same genera, or even two variants within the same species, can have different proteins.

    Wouldn't you expect descent with modification to result in differences? Again, you might argue how strongly two closely related species should be expected to diverge. That would have to be a quantitative argument. So far you're just stressing the presence of differences, which is what I find vague.
    ===

    No, this was a surprise for evolutionists. There's nothing vague about genes and proteins. We're talking about a thousand or so nucleotides, coding for several hundred amino acids that comprise the protein primary structure. It is true we don't have hard and fast numbers, but we're nowhere close to what evolution needs. It would be like saying "Since we can't calculate the *exact* probability of finding a needle in a haystack, therefore we cannot say it is a problem." Even bounding cases are ridiculuous for evolution.

    Here's an example. For a 300 amino acid protein, let's assume that half the protein's amino acid sequence is completely arbitrary. That is, the protein's function is completely insensitive to the amino acid identity at half the residues. Then for the other half, let's say that instead of having to get the right amino acid out of 20, let's say the problem is equivalent to merely getting the right one out of 5.

    These are ridiculously unrealistic, conservative assumptions, but even here evolution would have to search through a space of 5^150 different sequences. That's worse than a 1 in 10^100 longshot. It means evolution isn't likely to find protein sequences via drift. What would be needed is a set of intermediates, ending at the extant proteins we observe. But there is no scientific evidence that the universe of protein sequence space has all kinds of bridges, of functional sequences, between the different protein sequence subspaces. And even if there were such evidence, while it would help with the "gene duplication + mutation" method to get to a different protein, it still doesn't help with evolution finding functional protein sequences for the first time (from some random sequence that just happened to arise).


    ===
    Of course, we are talking about early evolution, which cannot be observed at the moment. But it was not me who dragged it in.
    ===

    Evolutionists claim evolution is a fact. That includes early evolution.


    ===
    You're talking again in circumspect terms. Which studies? What did the authors conclude?
    ===

    I discuss a couple of recent papers here:

    http://darwins-god.blogspot.com/2010/12/how-proteins-evolved.html

    ReplyDelete
  154. Cornelius Hunter said...

    Here's an example. For a 300 amino acid protein, let's assume that half the protein's amino acid sequence is completely arbitrary. That is, the protein's function is completely insensitive to the amino acid identity at half the residues. Then for the other half, let's say that instead of having to get the right amino acid out of 20, let's say the problem is equivalent to merely getting the right one out of 5.

    (snip the rest of the strawman)


    Amazing. You did go back to your incredibly stupid argument that evolution had to have all the parts of the protein spontaneously appear and assemble all at once.

    No matter how low the intellectual honesty bar is set, you always manage to slither below it. No wonder the DI likes you.

    ReplyDelete
  155. So, it's the old creationist argument along the lines OMG, finding 1 protein sequence out of 10^150 is so hard! It's time you learned a new trick, Cornelius.

    I've addressed that ridiculous argument here. In short, if even a stupid Ising magnet can find its ground state out of 10^500 microstates in a few thousand steps, your "problem" does not look insurmountable. Evolution is not equivalent to a random walk, there is feedback.

    ReplyDelete
  156. Ritchie:

    ===
    Seriously, doesn't it ever trouble you that you think you know more about science than actual scientists do?

    You're like the little boy who insisted all clocks in town but his were wrong - and it turns out he doesn't really understand much about clocks anyway.

    I mean I will grant it's not conclusive. But when you're telling scientists (pretty much all of them) that you think you know better about their own field of expertise, that's usually a pretty big hint that you're the one who's got it wrong.
    ===

    Yeah, good point. How could all those people be wrong ... that certainly has never happened before. I guess the whole universe did just happen to pop out of nowhere.

    ReplyDelete
  157. oleg:

    ===
    So, it's the old creationist argument along the lines OMG, finding 1 protein sequence out of 10^150 is so hard! It's time you learned a new trick, Cornelius.
    ===

    Yeah, how silly of me. We all know proteins spontaneously arise.


    ===
    I've addressed that ridiculous argument here. In short, if even a stupid Ising magnet can find its ground state out of 10^500 microstates in a few thousand steps, your "problem" does not look insurmountable. Evolution is not equivalent to a random walk, there is feedback.
    ===

    Look what evolution is doing to you. The evolutionist's analogy between evolution and a magnet is not even wrong. You rub your eyes in disbelief. Is a smart guy really saying this? Yes, he is. It is another example of how evolution corrupts science. If evolution were not at stake evolutionists would never make these absurd arguments. Here, the professor proposes a "simple magnet" as a useful analogy to evolution finding good genes. The analogy is not even wrong, it is completely out to lunch. Yes, a simple magnet easily defeats big entropy barriers. And that is completely irrelevant to the problem of evolution finding good genes.

    ReplyDelete
  158. Sorry, Cornelius, but it's your analogy that's out to lunch. You are assuming that protein space (or a substantial chunk thereof) must be randomly sampled to find a functioning sequence. That's plain wrong. There is feedback and that's precisely what makes it much easier to get there. Dembski and Marks are groping in the dark with all their fancy footwork, but their main problem is that they start with random sampling as the baseline.

    ReplyDelete
  159. I'll point out to CH yet again:

    You can't calculate the probability of a long term iterative process like evolution by taking a one-time snapshot of the results. You have to take into account the history and the mechanisms of the process.

    CH, do you have a pathological condition that prevents you from understanding this simple concept? Do the words have too many syllables?

    ReplyDelete
  160. oleg:

    ===
    Sorry, Cornelius, but it's your analogy that's out to lunch. You are assuming that protein space (or a substantial chunk thereof) must be randomly sampled to find a functioning sequence. That's plain wrong.
    ===

    No, I didn't say that. Here's what I said:

    ####
    These are ridiculously unrealistic, conservative assumptions, but even here evolution would have to search through a space of 5^150 different sequences. That's worse than a 1 in 10^100 longshot. It means evolution isn't likely to find protein sequences via drift. What would be needed is a set of intermediates, ending at the extant proteins we observe. But there is no scientific evidence that the universe of protein sequence space has all kinds of bridges, of functional sequences, between the different protein sequence subspaces. And even if there were such evidence, while it would help with the "gene duplication + mutation" method to get to a different protein, it still doesn't help with evolution finding functional protein sequences for the first time (from some random sequence that just happened to arise).
    ####



    ===
    There is feedback and that's precisely what makes it much easier to get there.
    ===

    Yes, that is what is needed. But there is no scientific evidence for the "feedback" that would be needed to get to the new protein.

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  161. cornelius Hunter said...

    ===
    There is feedback and that's precisely what makes it much easier to get there.
    ===

    Yes, that is what is needed. But there is no scientific evidence for the "feedback" that would be needed to get to the new protein.


    Every generation that experiences differential reproductive success and lives to produce another generation is feedback. Some guy named Darwin first wrote about it over 150 years ago.

    It must consciously pain you to pretend to be so clueless about the most basic concepts of evolutionary science. Or at least it should.

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  162. I understand perfectly well what you said, Cornelius, no need to repeat that.

    You are looking at a system consisting of N subunits, each of which can be in one of m states. The old creationist claim is that there is just one functional state, so it would take about m^N trials to find one by randomly searching through the space of states. You "generously" reduce the space of states to n^N, where n is a fraction of m. A random search will still take an exponentially long time of order n^N.

    Thanks for being this generous, but nature does not look for functional proteins by randomly picking this protein, then discarding it and starting from scratch. This is not the right model of nature. It lacks feedback known as (wait for it!) natural selection.

    Take a model with feedback and crunch some numbers. That's how a magnet finds its ground state in a time linear, rather than exponential, in N when we cool it down. Thanks to feedback from the environment (temperature difference).

    You are right that we do not have a quantitatively correct model of this process, but that is no excuse to use the mind-bogglingly stupid idea of a random search.

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  163. Cornelius,
    "And why are useless or deleterious similarities so helpful? It is not because they raise the probability of common ancestry, but rather because they lower the probability of separate ancestry. In other words, the reason common descent is a no-brainer is that the alternative, separate ancestry, is extremely unlikely."

    Just like any hypothesis is supported because the null hypothesis is shown to be unlikely (p<0.05). In the case of common ancestry, the separate ancestry null hypothesis is based on what we would expect from convergence and/or lateral gene transfer. God/designer is not considered because we don't know how god/designer would design (as Sober suggested). See Theobald (2010) in Nature for an example. CA is much more strongly supported than SA without any consideration of god/designer. Sorry, Cornelius, you have no point.

    ReplyDelete
  164. oleg:

    ===
    Thanks for being this generous, but nature does not look for functional proteins by randomly picking this protein, then discarding it and starting from scratch.
    ===

    I agree it sounds rather silly, but that's evolution for you. No teleology, remember? No design. I'm not the one who made it up.


    ===
    This is not the right model of nature. It lacks feedback known as (wait for it!) natural selection.
    ===

    Again, as I have explained, you don't have functional intermediates:

    ####
    What would be needed is a set of intermediates, ending at the extant proteins we observe. But there is no scientific evidence that the universe of protein sequence space has all kinds of bridges, of functional sequences, between the different protein sequence subspaces.
    ####

    What you are envisioning oleg is a fitness landscape in sequence space, leading to the different protein designs. So if you're halfway to protein, then such a gene does you some good. And locally, mutations that take you toward a protein will be a bit more advantageous, whereas mutations that take you away from it will reduce fitness. There is no scientific evidence for this.


    ===
    Take a model with feedback and crunch some numbers.
    ===

    Sure, it would work great. But we have to stick to reality, not evolutionary requirements that otherwise are unsupported.

    ReplyDelete
  165. Cornelius Hunter said...

    What you are envisioning oleg is a fitness landscape in sequence space, leading to the different protein designs. So if you're halfway to protein, then such a gene does you some good. And locally, mutations that take you toward a protein will be a bit more advantageous, whereas mutations that take you away from it will reduce fitness. There is no scientific evidence for this.


    Oh goody! CH starts with the incredibly stupid assertion that proteins must spontaneously self assemble. Then he goes for the daily double of stupidity by throwing in the old "what good is half an eye" equally ridiculous creationist strawman.

    A simple Google Scholar search for protein evolution turned up over 2.6 million hits, such as

    "Functional genomic analysis of the rates of protein evolution
    Wall et al.
    PNAS April 12, 2005 vol. 102 no. 15 5483-54

    Abstract: The evolutionary rates of proteins vary over several orders of magnitude. Recent work suggests that analysis of large data sets of evolutionary rates in conjunction with the results from high-throughput functional genomic experiments can identify the factors that cause proteins to evolve at such dramatically different rates. To this end, we estimated the evolutionary rates of >3,000 proteins in four species of the yeast genus Saccharomyces and investigated their relationship with levels of expression and protein dispensability. Each protein's dispensability was estimated by the growth rate of mutants deficient for the protein. Our analyses of these improved evolutionary and functional genomic data sets yield three main results. First, dispensability and expression have independent, significant effects on the rate of protein evolution. Second, measurements of expression levels in the laboratory can be used to filter data sets of dispensability estimates, removing variates that are unlikely to reflect real biological effects. Third, structural equation models show that although we may reasonably infer that dispensability and expression have significant effects on protein evolutionary rate, we cannot yet accurately estimate the relative strengths of these effects. "

    I wonder what all those scientists in all those research papers were writing about since Cornelius has declared protein evolution has no evidence and is impossible?

    Good job there CH.

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  166. This comment has been removed by the author.

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  167. Cornelius Hunter said...

    What would be needed is a set of intermediates, ending at the extant proteins we observe. But there is no scientific evidence that the universe of protein sequence space has all kinds of bridges, of functional sequences, between the different protein sequence subspaces.


    CH, you may want to read this paper before you embarrass yourself even further:

    The continuity of protein structure space is an intrinsic property of proteins
    Skolnick et al
    PNAS September 15, 2009 vol. 106 no. 37 15690-15695

    Abstract: The classical view of the space of protein structures is that it is populated by a discrete set of protein folds. For proteins up to 200 residues long, by using structural alignments and building upon ideas of the completeness and continuity of structure space, we show that nearly any structure is significantly related to any other using a transitive set of no more than 7 intermediate structurally related proteins. This result holds for all structures in the Protein Data Bank, even when structural relationships between evolutionary related proteins (as detected by threading or functional analyses) are excluded. A similar picture holds for an artificial library of compact, hydrogen-bonded, homopolypeptide structures. The 3 sets share the global connectivity features of random graphs, in which the local connectivity of each node (i.e., the number of neighboring structures per protein) is preserved. This high connectivity supports the continuous view of single-domain protein structure space. More importantly, these results do not depend on evolution, rather just on the physics of protein structures. The fact that evolutionary divergence need not be invoked to explain the continuous nature of protein structure space has implications for how the universe of protein structures might have originated, and how function should be transferred between proteins of similar structure.

    So the evidence shows all biologically relevant proteins are closely related, and almost all can be derived from any of the others by no more than seven structural changes.

    Kinda kicks a hole in your creationist strawman "sequence space is too large", doesn't it?

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  168. Thorton:

    When you make a ridiculous claim and someone asked you to back it up with a reference, merely citing examples of where you yourself have previously made the same ridiculous claim doesn't do much for your credibility.

    When Hunter quote-mines a scientific paper and his critics point out the he’s misrepresented the point of the paper, he finds it safer to keep repeating his interpretation of the quote. He seems to think his supporters are too lazy or dumb to notice. But his critics notice.

    Maybe his reluctance to provide references in support of so many of his sweeping assertions, as in this thread, reflects a concern that the actual references don’t say what he thought they said.

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  169. nat -

    "Doesn't natural selection mean that the organisms that have some survival advantage survive, and those that don't have it, don't survive."

    Not immediately. An entire species does not drop stone dead the very moment one of their number develops some survival advantage. They have to be outcompeted - which takes time.

    "According to this:

    http://www.santarosa.edu/lifesciences2/ensatina2.htm

    the California salamander sub-species at the ends of the ring do interbreed. Thye just don't do it a lot."

    You are becoming confused. In the north they may (though it is rare) but in the south they do not. That is kinda how a ring species works. The very page you cited says so: "To the south near Cuyamaca State Park, klauberi and eschscholtzi meet and apparently fail to interbreed under natural conditions even though they are narrowly sympatric"

    "I think I got it, natural selection works to create new species, except where it doesn't. For a theory with so much power and evidence, evolution sure requires a lot of apologetics, special pleading, etc."

    Nat, you are like a kid with a helium balloon holding it up as an irrefutable flaw in the theory of gravity: "Oh right, I got it - gravity works to pull things down, except where it doesn't! Pah, this 'theory of gravity' sure requires a lot of special pleading!"

    I think it's time you admitted a simple truth to yourself - you are actively TRYING to not understand the theory of evolution. You just don't want it to make sense, and you are desperately clutching at straws trying to make it sound illogical or flawed. But all you are really doing is showing that you don't understand it, and more so, that you are actively TRYING not to, presumably so you can then justify saying 'Well I've been looking into this whole 'evolution' thing and it just doesn't make sense.'

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  170. Cornelius -

    "Yeah, good point. How could all those people be wrong ... that certainly has never happened before."

    When one disagrees with the many, it is far more common for the one to be in the wrong. Not that I imagine this will give you even a fraction of a moment's pause, so great is your self-belief, and so small is your willingness to put your assertions to the test.

    "I guess the whole universe did just happen to pop out of nowhere."

    What has the origin of the universe got to do with evolution?

    Oh yeah - the scientific explanations of both contradict your religious beliefs. Therefore both must be wrong. Silly me.

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  171. Cornelius wrote:

    What you are envisioning oleg is a fitness landscape in sequence space, leading to the different protein designs. So if you're halfway to protein, then such a gene does you some good. And locally, mutations that take you toward a protein will be a bit more advantageous, whereas mutations that take you away from it will reduce fitness. There is no scientific evidence for this.

    There is no evidence for this? That's a pretty strong assertion. I just need to provide one counter example to disprove it, right?

    Here is an excerpt from M. Soskine and D. S. Tawfik, Nature Reviews Genetics 11, 572 (2010). doi:10.1038/nrg2808.

    "Protein fitness

    Fitness is an organismal feature that relates to population growth rates. What then does the term 'protein fitness' mean? Proteins are a key component of organismal fitness. Under some conditions, variation in only one protein contributes to fitness, and the effects of mutations in this protein can be directly connected to organismal fitness. In the presence of antibiotics, for example, the survival of a microorganism depends on the function of a single protein that mediates resistance, such as an enzyme that degrades the antibiotic. In such cases, the level of physiological function exerted by this protein can be easily measured and is denoted as protein fitness (Wp). Wp would be proportional to the concentration of folded, active enzyme in a living cell (protein level or dosage) and to the activity per protein molecule (for example, the catalytic efficiency of the degrading enzyme, kcat/KM). Such simple scenarios enable the description of the distribution of fitness effects for an individual protein and allow it to be compared to the distribution of fitness effects of mutations in an intact organism."

    Discuss.

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  172. This is a test. Blogger commenting system sucks.

    ReplyDelete
  173. Cornelius,

    I drew logical conclusions from your previous post. Sure, I might have been wrong, but please show me wrong. I fail to see the relevance of the likelihood ratio representation. How is that the exact opposite of what I said? You can make likelihood ratio representations for both fDP and tDP.

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  174. cont'd

    I checked the previous articles you cited. You have represented Darwin's Principle correctly in the past. That makes me think that perhaps the cause of all of this discussion was just some terribly bad writing on your part. But then, tDP is irrelevant in the context of your previous post. Why would you bring it up? I don't know what to think. Either you were honest but you inserted a really poorly written reference to a random concept, or you tried to mislead your readers about what Sober said (just in the previous post but not in posts before that one, which is odd). I'd like to think the best of you, so I'm leaning toward the former.

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  175. cont'd

    I anticipate that your next answer won't clarify much. Here's a better way to settle it. Do you know any linguistics expert? Send him or her your previous post and Sober 2009 (or the relevant passage) and ask him or her if your representation of DP is misleading. Perhaps the other readers can help too. Anybody else thinks fDP is not a misleading representation of tDP? Anybody else knows a linguistics expert?

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  176. Ritchie:

    The textbooks all site the pepper moth as proof of natural selection, and therefore as proof of evolution, which is species to species change. No one questions that some organisms do better than others. Survivors survive. The question is whether this can change one species into another. The pepper moth doesn't prove this.

    Some of the papers linked to the site I sited, say that the salamanders should all be considered morphs of one species. If they can and do interbreed, even though they don't over part of their range, then they may still be one species. Many species do show intraspecies, preferential and selective mating.

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  177. natschuster said...

    Ritchie:

    The textbooks all site the pepper moth as proof of natural selection, and therefore as proof of evolution, which is species to species change. No one questions that some organisms do better than others. Survivors survive. The question is whether this can change one species into another. The pepper moth doesn't prove this


    You were still too lazy to read the U. Berkeley overview of speciation I see. You must truly love wallowing in ignorance.

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  178. Every time I look closer at what the textbooks present as evidence for evolution, like the pepper moth, Haeckel's embryo drawings, etc. I discover problems. I can't help but be skeptical.

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  179. Thorton:

    I looked at it. It was all about repordcutive isolation. Does this means that natural selection has nothing to do with it? Then why do textbooks mention the pepper moths and natural selection? I'm confused.

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  180. natschuster said...

    Every time I look closer at what the textbooks present as evidence for evolution, like the pepper moth, Haeckel's embryo drawings, etc. I discover problems. I can't help but be skeptical.


    You don't look at textbooks, or scientific papers, or college/university science websites like U. Berkeley. You look at Creationist anti-science propaganda sites like AIG or UncommonlyDense, then parrot back their nonsense without the slightest bit of understanding.

    That's why you stay such an ignorant git.

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  181. Thorton:

    I learned about the pepper moth form textbooks. I learned about Haeckel's fraud from an article in Natural History magazine by S.J. Gould. I sited the Salamander website above. I looked at the website you linked. That's how I konw that it focuses on reproductive isolation, and not natural selection.

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  182. natschuster said...

    Thorton:

    I learned about the pepper moth form textbooks.


    Bull. You've never read a college level biology text in your life. Probably not even a high school level one.

    I learned about Haeckel's fraud from an article in Natural History magazine by S.J. Gould.

    But you didn't understand it, or the context in which the drawings are shown now. You are just mindlessly repeating bogus claims about them you get from those creationist sites.

    I sited the Salamander website above.

    You mean you skimmed it looking for snippets to quote-mine.

    I looked at the website you linked. That's how I konw that it focuses on reproductive isolation, and not natural selection.

    But you didn't read it with the intention of gaining comprehension. Like always, you skimmed it looking for buzzwords to misinterpret just to reinforce the crap you got from your creationist sources.

    You love ignorance so much, then stay ignorant.

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  183. Thorton:

    I use to teach High School biology. I'm familiar with the textbooks.

    What does context have to do with Haeckel's fraud? What possible difference could the context make? The man admitted to faking the drawings.

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  184. oleg:

    ===
    There is no evidence for this? That's a pretty strong assertion. I just need to provide one counter example to disprove it, right?
    ===

    There is no evidence that it is a general property of proteins. Sure, I have no doubt that out of the many proteins in nature there are some unusual ones that have a larger sequence subspace, such that they can tolerate a wider variation in their sequence. And there are cases of proteins that can morph into another protein. A well known example is through a frameshift, meaning that for a significant segment of the sequence, all the DNA codings for the amino acids are changed. It is a single mutation that changes many amino acids and raises another question. More below on that, but there is no evidence that it is a general property of proteins that there exist bridges in sequence space forming a series of functional intermediates. Also, what we do know suggests the opposite. It doesn't prove it, but what we do know is proteins are pretty sensitive to change. Their function degrades pretty rapidly with sequence changes.

    What I wanted to mention is the thought experiment that we find such functional bridges in sequence space. Connecting all or many of the thousands of different proteins are bridges in sequence space forming a series of functional intermediates. And the functions of the intermediates are likely to be useful in particular to an organism undergoing mutations going between to two proteins. IOW, you not only need the bridge, but you also need for those particular proteins that are the intermediates to be useful.

    So consider that we discover all these conditions are met, such that proteins pretty easily can slide around in sequence space. Or, another possibility, that the fitness landscape funnels down to each of the thousands of different proteins, such that if you chose pretty much *any* random sequence, random mutations could fairly easily lead it to a native protein we observe today via natural selection.

    These are the sorts of conditions evolution needs. It is not what science is telling us, but consider the thought experiment where we discover that this is indeed the case. It would be an incredible example of someone monkeying with the fundamentals of matter and biochemistry. Now as for your example paper:

    ====
    Here is an excerpt from M. Soskine and D. S. Tawfik, Nature Reviews Genetics 11, 572 (2010). doi:10.1038/nrg2808.

    "Protein fitness

    Fitness is an organismal feature that relates to population growth rates. What then does the term 'protein fitness' mean? Proteins are a key component of organismal fitness. Under some conditions, variation in only one protein contributes to fitness, and the effects of mutations in this protein can be directly connected to organismal fitness. In the presence of antibiotics, for example, the survival of a microorganism depends on the function of a single protein that mediates resistance, such as an enzyme that degrades the antibiotic. In such cases, the level of physiological function exerted by this protein can be easily measured and is denoted as protein fitness (Wp). Wp would be proportional to the concentration of folded, active enzyme in a living cell (protein level or dosage) and to the activity per protein molecule (for example, the catalytic efficiency of the degrading enzyme, kcat/KM). Such simple scenarios enable the description of the distribution of fitness effects for an individual protein and allow it to be compared to the distribution of fitness effects of mutations in an intact organism."

    Discuss.
    ====

    (cont).

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  185. oleg:

    (cont.)

    So what this paper is talking about is the fact that you can map the protein sequence space to organismal fitness. No surprise there. In sequence space, the subspace that codes for a particular protein is quite small--a sliver. Much work has been done in measuring the function of the protein itself (catalytic efficiency for example) as a function of small variations about the sliver (eg, single mutations). As I said, the function falls off fairly rapidly. And you can imagine going further, and not merely mapping to the protein function itself, but mapping to the organism's fitness. But that is a more difficult experiment. If you inject a few mutations such that the protein function falls off, then likely you'll see some degradation in the organism's fitness. Btw, while removing a working protein from the organism's repetoire obviously can do some harm to its fitness, a more difficult problem is finding useful functional proteins to add. If you just add some functional protein, it may not be of particular help to the overall fitness. It depends on what is already there, etc.

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  186. natschuster said...

    Thorton:

    I use to teach High School biology. I'm familiar with the textbooks.


    If you did I feel sorry for your students, because you're vastly unqualified and incompetent in the subject.

    What does context have to do with Haeckel's fraud? What possible difference could the context make? The man admitted to faking the drawings.

    That was well over 100 years ago. The only time the drawings are shown in textbooks now is in discussions of the history of embryology, with the caveat that the drawings are not considered valid. No textbook anywhere still uses them as support of evolutionary theory.

    The whole 'Haeckel's drawings still used' issue raised by creationists now is a bigger dishonest fraud that Haeckel ever was.

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  187. This comment has been removed by the author.

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  188. nat wrote:
    "I use to teach High School biology."

    Scary. Did you get fired for incompetence?

    "I'm familiar with the textbooks."

    But have you READ them? Your comments reflect a profound unfamilarity with the basics of evolutionary theory.

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  189. Before we go any further, Cornelius, would you like to retract your sweeping assertion about a complete lack of scientific evidence for a fitness landscape that proteins can climb?

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  190. oleg said...

    Before we go any further, Cornelius, would you like to retract your sweeping assertion about a complete lack of scientific evidence for a fitness landscape that proteins can climb?


    I'm still wating for him to retract this boner...

    Cornelius: "Yes, that is what is needed. But there is no scientific evidence for the "feedback" that would be needed to get to the new protein."

    ..but I'm not holding my breath. I wonder why he thinks the fact that each generation's heritable genetic variations are filtered by selection and used for the next generation doesn't qualify as feedback.

    I get the feeling that too often CH's knee-jerk creationist reflex makes his fingers type before his brain cuts in.

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  191. OK, after 2 tries, I'll skip the formatting:

    On the subject of protein fitness landscapes, this is an interesting paper.

    www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0000096

    Abstract:

    The fitness landscape in sequence space determines the process of biomolecular evolution. To plot the fitness landscape of protein function, we carried out in vitro molecular evolution beginning with a defective fd phage carrying a random polypeptide of 139 amino acids in place of the g3p minor coat protein D2 domain, which is essential for phage infection. After 20 cycles of random substitution at sites 12–130 of the initial random polypeptide and selection for infectivity, the selected phage showed a 1.7×104-fold increase in infectivity, defined as the number of infected cells per ml of phage suspension. Fitness was defined as the logarithm of infectivity, and we analyzed (1) the dependence of stationary fitness on library size, which increased gradually, and (2) the time course of changes in fitness in transitional phases, based on an original theory regarding the evolutionary dynamics in Kauffman's n-k fitness landscape model. In the landscape model, single mutations at single sites among n sites affect the contribution of k other sites to fitness. Based on the results of these analyses, k was estimated to be 18–24. According to the estimated parameters, the landscape was plotted as a smooth surface up to a relative fitness of 0.4 of the global peak, whereas the landscape had a highly rugged surface with many local peaks above this relative fitness value. Based on the landscapes of these two different surfaces, it appears possible for adaptive walks with only random substitutions to climb with relative ease up to the middle region of the fitness landscape from any primordial or random sequence, whereas an enormous range of sequence diversity is required to climb further up the rugged surface above the middle region.

    Especially noteworthy: they start with a random protein.

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  192. What is it about the above url that made blogger eat the post containing it?

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  193. natschuster: The textbooks all site the pepper moth as proof of natural selection, and therefore as proof of evolution, which is species to species change.

    It's not "proof of evolution," but an observed instance of selection in nature, as predicted by Darwin.

    natschuster: Some of the papers linked to the site I sited, say that the salamanders should all be considered morphs of one species. If they can and do interbreed, even though they don't over part of their range, then they may still be one species. Many species do show intraspecies, preferential and selective mating.

    That's a matter of definition and convenience. That species do not have distinct boundaries is crucial evidence that Darwin discussed in Origin of Species.

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  194. nat -

    "The textbooks all site the pepper moth as proof of natural selection, and therefore as proof of evolution, which is species to species change."

    It is an easy-to-understand example of how environmental circumstances determine natural selection. A change in environment can cause a deleterious variation to become an advantageous one. I cannot understand why you consider it a fatal flaw in the argument that number of white moths never quite hit extinction. They DID plummet - THAT is the relevant result.

    "Some of the papers linked to the site I sited, say that the salamanders should all be considered morphs of one species. If they can and do interbreed, even though they don't over part of their range, then they may still be one species. Many species do show intraspecies, preferential and selective mating."

    And that is exactly how it should be if evolution did occur via natural selction - there would be a complex web of relatives linking all species. In this particular case, the intermediaries all happen to be alive, whereas the ones between, say, a human and a chimpanzee happen to be dead. This example of the salamanders just shows us in the geographical dimension what must occur in the time dimension.

    "What does context have to do with Haeckel's fraud?"

    Haeckel's theory is not part of modern evolutionary biology. Please dismiss it - scientists did decades ago!

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  195. Again my post got eaten.

    Geoxus:

    "Perhaps the other readers can help too. Anybody else thinks fDP is not a misleading representation of tDP?"

    Very misleading indeed. Cornelius says:

    "In other words, it doesn’t matter that common descent is not a good theory. It must be true because the alternative is even worse."

    Let's deconstruct this. It's based on the criterion that if there are two hypotheses H1 and H2, then we prefer H1 if the likelihood ratio L1/L2 = Prob(data given H1)/Prob(data given H2) is sufficiently large. That seems like a reasonable procedure.

    You have to realize that even if an hypothesis is true, the likelihood of a given data set can be very small. However, this does not mean that the hypothesis is no good, as Cornelius tries to imply with his "it doesn’t matter that common descent is not a good theory". Here is an example loosely based on Sober's paper: suppose we have an urn with 10000 balls, 8000 of which are green and the rest white. H1 says (correctly) 80% of the balls in the urn are green, H2 says (incorrectly) 20% of the balls in the urn are green. Then we randomly draw 1000 balls, and we find that 800 are green. The likelihood of this outcome is only 3% if H1 is true. Does this mean that H1 is not a good hypothesis? Of course not, because we know it is true. The likelihood of H2 is about 10^-423, and the likelihood ratio therefore ~10^421, so we should strongly prefer H1 over H2, even if the likelihood of the data given H1 is not very large.

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  196. Guys,

    Comment disappearance seems to relate more to a combination of both, length and formatting (use of italics, bold, and other html), than just to including URLs. Sometimes my comments don't want to stick. If I reduce them in length then they do, or else if I eliminate part of the formatting, and so on.

    Maybe it is good if we then have to be succinct and get to the point.

    :)

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  197. Cornelius Hunter

    It is curious that you are now arguing so vehemently about common descent since you have earlier stated: "Of course natural selection and common descent are important parts of the idea, but they can be forfeited."

    Common descent or descent from a handful of ancestors is something you would expect from the laws of thermodynamics and the way biological systems propagate. So that we actually find common descent is not that surprising.

    But while common descent is a central idea of the ToE it is not the discriminating one. Even if every species living today originated on its own we would still not expect that these complex biological system “just happened to arise spontaneously“ but that they developed slowly in a stepwise process.
    In contrast to your OP it is exactly the other way around. Creationist claim that highly complex systems just happened to arise spontaneously (by being created) which is according to the laws of thermodynamics infinitely unlikely. Thus there should be a process that increases the complexity in tiny steps that are small enough to have a reasonable probability to actually happen. And this is exactly the process that we find – common descent with modification.

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  198. This comment has been removed by the author.

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  199. anaxyrus said:

    Modern evolutionary theory is not the neoDarwinism of the 1950s.

    Yup. Has anybody read:
    Evolution—the Extended Synthesis?

    Also good news, "the modern synthesis" was reprinted by the same editorial house. Maybe a good idea to get these books and see where the basic thinking was and is now going.

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