Saturday, May 15, 2010

Let the Worship Begin

In 1734 Daniel Bernoulli used cutting edge statistical methods of his day to prove that our solar system must have evolved as a result of a single cause. He who would deny this, concluded the scientist-mathematician, “must reject all the truths, which we know by induction.” Bernoulli’s high confidence was, of course, unwarranted as later years would reveal. But today, almost three centuries later, little has changed.

If you gaze at an illustration of our solar system you will immediately be struck by its clock-like regularities. The planets revolve about the sun in the same direction, and in the same plane—the sun’s equatorial plane known as the ecliptic. And as the planets race around the track they also spin like tops, and in the same direction. And their moons show the same patterns. The solar system seems to be one big, precise, clock-like machine. Well, almost.

In fact, imbedded in the solar system’s clock-like regularities are a great many anomalies, some of which were known in Bernoulli’s day. The comets do not travel in the ecliptic, many moons go their own way, and Venus and Uranus don’t spin like the other planets. And beyond the obvious anomalies there is a steady stream of less obvious, but no less vexing, deviations. For instance, while the planets do appear to travel in the ecliptic, in fact their orbits all deviate from that ideal, in varying degrees.

This is the puzzle of the solar system. It reveals striking patterns but also myriad and significant anomalies. Bernoulli was sure a single cause was behind all this, but his certainty was to give way, years later, to a variety of complex ideas with multiple causes that would be needed.

A comet may have collided with the sun or a cloud of material may have condensed. Instabilities may have caused some planets to form rapidly, planets and objects collided, moons formed, icy dust collected, planets perturbed and raced around each other, moons were captured, objects were ejected to the far reaches, the solar wind cleaned house, and magnetic braking slowed the sun. These is a bit of the pinball-machine like chaos that has been envisioned to account for the solar system. Hardly the single cause Bernoulli had “proven.” And today’s discoveries of other solar systems, with their variety of patterns, has complicated the picture even more.

But if Bernoulli’s foray into cosmology was ill-fated, he did make a lasting, if unfortunately, contribution to the historical sciences. That would be his method of constructing and comparing different hypotheses. Hypotheses in the historical sciences tend to be dramatically underdetermined and so, it would seem, hardly able to be proven.

But if competing hypotheses could be constructed—and knocked down—then is not one’s hypothesis the obvious winner? In fact statistical probabilities could be calculated allowing us no option, as Bernoulli argued, but to accept the hypothesis unquestioningly. His was not the first use of such contrastive thinking, but the son of math’s first family brought the authority of numerical calculations and to the historical sciences.

Bernoulli’s mathematical version of contrastive proofs soon became standard fare in eighteenth century cosmology, and then no less so in the nineteenth century’s theory of evolution. After Darwin it continued to provide many of the key justifications of evolutionary thought. Now a new paper out this week in the elite journal Nature continues the tradition.

The new paper constructs several hypotheses for the early phases of evolution history and shows how universal common descent, in one variant or another, is the clear winner. And in the now well-established Bernoullian tradition, the results are grossly misinterpreted in favor of evolution. After showing that a comparison of 23 proteins—similar versions of which are found in many species—fit the universal common descent hypothesis far better than the hypothesized alternatives, the paper erroneously states that the results are “very strong empirical evidence” for universal common descent.

Not surprisingly the paper is an instant hit with evolutionists, celebrated everywhere from journals and popular science magazines to the blogosphere. One science newsletter proclaims:

First Large-Scale Formal Quantitative Test Confirms Darwin’s Theory of Universal Common Ancestry

Scientific American has informed its readers that “The Proof Is in the Proteins: Test Supports Universal Common Ancestor for All Life,” and National Geographic adds that:

All Species Evolved From Single Cell, Study Finds
Creationism called "absolutely horrible hypothesis"—statistically speaking.

In his blog PZ Myers, who with his Lutheran background believes god would never have created this world, applauds the big numbers that “support evolutionary theory.” And Nick Matzke, who also believes in the evolutionary metaphysics that god would never have designed what we observe in the biological world, is delighted that the new work debunks creationism.

Of course all of this is false. It is junk science at its worst. In a public discussion I asked the paper’s author about these problems. I reminded him that one hypothesis comparing well against others does not translate into very strong empirical evidence for the hypothesis. But he disagreed. He assured me that his analysis is fundamentally based on modern, cutting edge statistical methods, and that he firmly stands by his conclusions. Indeed, no scientist or statistician would find them to be controversial, he added.

I explained to him that the problem lies not with the statistical methods. Daniel Bernoulli also used cutting edge methods of the day (he was the first that I know of to use a null hypothesis based on random distributions). But when comparing such scores a scientist or a statistician would merely claim that the hypothesis with the significantly higher score is the winner of the group. That is entirely different than his high claim that the results constitute very strong empirical evidence for the hypothesis. That conclusion is simply false. The hypothesis may be true, it may not be true, but the study does not provide such powerful empirical evidence for it. Unfortunately, such misinformation fuels the kind of reporting we saw above.

But again the evolutionist continued to disagree. You are simply incorrect, he replied. From a model selection perspective, from a likelihood perspective, and from a Bayesian perspective, empirical evidence can only be evaluated relative to other hypotheses. That’s all we have. No hypothesis can be evaluated in isolation—such an idea is impossible and incoherent. This view is not from evolutionary biology—this is the standard non-frequentist statistical view (and even most frequentists have the same view). He suggested I read some introductory books on likelihood and Bayesian statistics.

Evolutionary thought, including its history, metaphysics and abuse of science, is a fascinating study. I replied that I was amazed. The lengths to which evolutionists must go is incredible. It is always striking to see the certainty with which evolutionists promote their philosophies and metaphysics. You can see it in the history of evolutionary thought, and today it just keeps on coming. They impose their philosophies, as though they were facts, on the world. Their faulty logic is exceeded only by their boldness.

I again explained that when one hypothesis beats out others you cannot make the claims you are making. What you have is very strong evidence that the hypothesis beats out the other hypotheses, period. You do not have very strong evidence for the hypothesis, as you are claiming.

And your appeal to the limitations in your confirmation methods doesn’t change the fact that you are making false claims, and celebrating them as valid findings. The fact that “That's all we have” hardly justifies the publishing and promotion of misinformation. The fact that “That’s all we have” ought to serve to temper the claims, not exalt them.

But contrastive thinking has been at the heart of evolutionary thought for centuries. From Kant to Darwin, and on up, what has always been rather revealing is how evolutionists have presented their proofs as though they were objective, undeniable findings. It is always a bit shocking to see such bold claims made on such faulty logic.

At this point the evolutionist turned the blame on me. We have, he explained, overwhelming evidence that universal common ancestry beats out competing multiple independent ancestry hypotheses. If you don’t consider that as evidence for universal common ancestry, then you are certainly entitled to that opinion. But the rest of us are not required to believe that your opinion makes any sense. Yours is a strange philosophy, to my mind, and I’m sure to most people who will read your words.

Repeatedly I have found that evolutionists are unable to see the problems and fallacies with their theory. And so when you point out those problems, the evolutionist ultimately can only conclude that the problem lies with you. You are an obstructionist, or biased, or anti science, or something.

This evolutionist was not being judgmental in any personal way. He threw up his hands and concluded that I am the problem, but his response was genuine, not contrived. It was not mean spirited. Just as Bernoulli proclaimed that anyone who would deny the obvious evolutionary conclusions “must reject all the truths, which we know by induction” so too evolutionists ever since can only understand skepticism as, itself, problematic.

Evolution is a metaphysically-driven tradition and like most such traditions has built-in protections against objective critique. The result, unfortunately, is junk science. This new paper will be erroneously celebrated far and wide as yet a new level of certainty for evolution. Let the worship begin.

93 comments:

  1. "But again the evolutionist continued to disagree. You are simply incorrect, he replied. From a model selection perspective, from a likelihood perspective, and from a Bayesian perspective, empirical evidence can only be evaluated relative to other hypotheses. That’s all we have. No hypothesis can be evaluated in isolation—such an idea is impossible and incoherent. This view is not from evolutionary biology—this is the standard non-frequentist statistical view (and even most frequentists have the same view). He suggested I read some introductory books on likelihood and Bayesian statistics."

    Here you've made it clear that your real argument is not with evolution, it's with statistics. Which is something we already knew, but it's nice to have you say it explicitly.

    Your arguments against evolution, if taken seriously, would actually rule out vast amounts of inferential science which are based on statistical hypothesis testing. If you ever turned the mirror on yourself, you'd discover that you, like many fundamentalists, are just a primitive 1600s-style Baconian who believes that nothing should ever be believed unless it is directly witnessed -- well, unless it's in the Bible, of course.

    That's all fine, it's a free country, but don't pretend you've got some specific disagreement with evolution; actually you've got a vast disagreement with scientific inference in general, and you have this because you believe God can and does do whatever he wants, whenever he wants, and thus people should just believe the Bible and stop there.

    This is exactly why you'll never tell us how old you think the Earth is, for example.

    Cheers, Nick

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  2. “very strong empirical evidence” - and any of this is produced in support of there being a god where?

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  3. Nick,

    I'd add one thing-if Hunter is going to hold up THIS work of all things, without proposing an alternative, than exactly what path is the supposed science of ID going to take?

    If a study selecting the best models from all possible hypotheses (and Hunter can test his own!) without preconceptions or forced conclusions is ruled out, what is there?

    Are scientists we allowed to make observations, but never to draw conclusions?

    At this point Hunter's critique stops being useful, and feels like a infinitely regressive dive into what it means to conclude something is true.

    If we add an asterisk to the New Scientist article defining what we mean by scientific truth and theory, and state that no, some possibilities (in this case, I guess a Creator making separate unique creations that are created with the same proteins with small alterations in sequence related in exactly the manner that gives the appearance of descent, a tree of life, and a UCA, or that a demon did and always will alter the output of the computer running the programs to trick us) maybe aren't really scientific --falsifiable or even testable--hypotheses, does that make everything better?

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  4. I'm curious, Corny: If you applied your reasoning in this post to scientific theories that you do not have a dogmatic religious objection to -- sorry, I meant "scientific theories other thanevolution" -- which of those other theories would you conclude are "junk science' on the same grounds that you now use to conclude that evolution is 'junk science'?

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  5. Posted elsewhere, and now again here, in modified form:

    George has made a very significant error in comparing my methodology to Bernoulli's. And the error is extremely ironic (and pretty darn funny, if you're a statistics geek like me).

    The results in my paper are explicitly based on model selection theory, likelihoodist and Bayesian statistics -- not on classical frequentist null-hypothesis testing, which in fact I criticize in the main text of the paper and in the supplementary materials. Bernoulli's solar system argument, however, is a classic example of a null-hypothesis test -- it is often cited as the first one known.

    The irony here, of course, is that I don't use Bernoulli's methods, for the very reason that disproving the null hypothesis is not evidence for your favored hypothesis. Bernoulli's argument was fallacious because all he did was show that the random hypothesis (the null hypothesis) did not explain the data well. That says nothing about Bernoulli's favored hypothesis of a single solar cause. So in this sense George is correct about Bernoulli, that "disproving" the null hypothesis is not evidence for the favored hypothesis.

    But this criticism does not apply to Bayesian statistics (or to likelihoodist and model selection methods). There is a rich history in Bayesian statistics of criticizing null-hypothesis tests. Bayesians consider null-hypothesis tests to be illogical.

    Bernoulli's error was that he never considered how well his favored hypothesis (a single solar cause) explains the data. Bernoulli's favored hypothesis could have even been worse than the null hypothesis, for all he knew. Or not all that much better.

    And this is the strength of the Bayesian methods I used -- with these methods, you have to explicitly calculate how well all the different hypotheses explain the data, not just how well the "null" does. In fact, in my methodology there is not even such a thing as a "random null hypothesis".

    And by calculating the probability of the observed data under each of the different competing hypotheses, you are in fact able to calculate the evidence for the different hypotheses -- the very thing George claims is impossible. That is exactly what Bayesian methods allow you to do, and it's why they have become so popular throughout science in the past 15 years.

    Cheers,

    Douglas

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  6. "He who would deny this, concluded the scientist-mathematician, “must reject all the truths, which we know by induction.”"

    But, of course, while deduction may give us truths which we can know to be true, induction cannot.

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  7. Nick:

    "you believe God can and does do whatever he wants, whenever he wants"

    Yes, including using evolution as his creation tool.

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  8. This comment has been removed by the author.

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  9. "After showing that a comparison of 23 proteins—similar versions of which are found in many species—fit the universal common descent hypothesis far better than the hypothesized alternatives, the paper erroneously states that the results are “very strong empirical evidence” for universal common descent."

    Oh, hell! These people will say *anything* -- and just as quickly unsay it (and sweep having ever said it under the rug).

    Back when it was assumed that the DNA code (codon triplet -> amino acid transcription) was universal, *that* was asserted to be undisputable proof of "universal common descent" and disproof of all other competing hypotheses.

    Now that it is known that the "canonical" DNA code (as it is now called) is not universal, the former claim has been quietly retired and forgotten.

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  10. I thought that Bernoulli was famous for calculating the probability of the orbits of the known planets being as closely aligned as they are assuming that any alignment is equally likely. He came out with a very low number and concluded that there must have been a reason for their being aligned.

    1) Bernouilli's method is not contrastive. As Douglas says it is classical null-hypothesis testing.

    2) While this approach has many problems it turns out he was right. The planets are not aligned by chance.

    3) Null-hypothesis testing is not leading edge nowadays. It is much contested (ironically a supporter is William Dembski who adapts it when trying to justify complex specified information).

    4) Douglas is not using Fisherian hypotheis testing.

    Otherwise fine.

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  11. @Cornelius:

    I wonder what in your eyes would constitute strong evidence for universal common descent?

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  12. "Now that it is known that the "canonical" DNA code (as it is now called) is not universal, the former claim [universal code == indisputable proof of UCD] has been quietly retired and forgotten."

    Really now? That's not quite the case. In fact, the same Dr. Theobald who is the subject of this post addressed this topic in an article on the Talk.origins site written in 2002:

    "First, common descent does predict that the genetic codes should be similar a priori. Hunter is speculating about how biologists would have reacted in a hypothetical historical scenario in which we did not find highly similar codes between organisms. In reality, we can never know how biologists would have reacted to that, since that hypothetical scenario did not happen. What is known, however, is that the scientists who cracked the genetic code in the 1950's and 1960's worked under the assumption that the code was universal or nearly so (Judson 1996, p. 280-281). These scientists, which included Francis Crick, Sydney Brenner, George Gamow, and several others, all made this assumption and justified it based upon evolutionary reasoning, even in the complete absence of any experimental evidence. In fact, this assumption was instrumental in their success in solving the code. For instance, in 1957, nearly ten years before the genetic code was finally solved, Sydney Brenner published an influential paper in which he concluded that all overlapping triplet codes were impossible if the code was universal (Brenner 1957). This paper was widely considered a landmark work, since many researchers were leaning towards an overlapping code. Of course, it turned out that Brenner was correct about the nature of the true code. In 1961, five years before the code was deciphered, Crick and others also concluded that the code was (1) a triplet code, (2) non-overlapping, and (3) that the code is read from a fixed starting point (i.e. the "start" codon) (Crick et al. 1961). These conclusions were explicitly based on the assumption that the code was essentially the same in tobacco, humans, and bacteria, though there was no empirical support for this assumption. These conclusions turned out to be correct. In fact, in 1963—three years before the code was finally solved—Hinegardner and Engelberg published a paper in Science specifically explaining why the code must be universal (or nearly so) if universal common descent were true, since most mutations in the code would likely be lethal to all living things. Note, Hinegardner and Engelberg did allow for some variation in the genetic code, and predicted how such variation should be distributed if found:

    '... if different codes do exist they should be associated with major taxonomic groups such as phyla or kingdoms that have their roots far in the past.' (Hinegardner and Engelberg 1963)

    Their evolutionary prediction was correct, since the minor variations in the standard genetic code are indeed associated with major taxonomic groups (vertebrates vs. plants vs. single-celled ciliates, etc.).

    Second, we now know from experimental research that many plants, many animals, and many bacteria all have extremely similar genetic codes. There is no known biological reason, aside from common descent, for why the genetic codes of different species should be similar. Any new discovery of a plant, animal, or bacteria with a radically different genetic code would be a highly unexpected result if common descent is true."

    Hmm. Seems you're just plain wrong on at least two counts: The assumption of a universal code was itself never universal, nor does it seem that people have forgotten about it (maybe this disciplinary amnesia only took hold after 2002?). A third is debatable: there very well may have been some people who asserted that it was "indisputable proof" but, well, that practice clearly wasn't universal either. At best, you can have that one on a technicality.

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  13. Nick:


    =====
    Your arguments against evolution, if taken seriously, would actually rule out vast amounts of inferential science which are based on statistical hypothesis testing.
    =====

    Gosh, yeah right. Either we buy phony arguments that evolution is an undeniable fact, or we are out and out skeptics. Evolutionists are just ruthlessly logical.


    =====
    If you ever turned the mirror on yourself, you'd discover that you, like many fundamentalists,
    =====

    I'm not a fundamentalist.


    =====
    are just a primitive 1600s-style Baconian who believes that nothing should ever be believed unless it is directly witnessed -- well, unless it's in the Bible, of course.
    =====

    Gosh more ruthless logic that really cuts to the heart of the issue. That's exactly it, either evolution is much a fact as is gravity, or we're just "a primitive 1600s-style Baconian who believes that nothing should ever be believed unless it is directly witnessed." (except that Bacon never said any such thing).


    =======
    That's all fine, it's a free country, but don't pretend you've got some specific disagreement with evolution; actually you've got a vast disagreement with scientific inference in general,
    =======

    Yeah, we're just science bashers.


    =======
    and you have this because you believe God can and does do whatever he wants, whenever he wants, and thus people should just believe the Bible and stop there.
    =======

    It's fascinating because, I know Nick is a smart guy, yet look what he is reduced to. Of course one sees sophmoric rants all the time which go unheeded. But Matzke is not a no-nothing anonymous chatter just throwing mud for the fun of it. He is a smart, intelligent, knowledgable, well-educated, life scientist. And yet this is indistinguishable from a sophmoric rant.

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  14. Thomas S. Howard:

    =================
    "Now that it is known that the "canonical" DNA code (as it is now called) is not universal, the former claim [universal code == indisputable proof of UCD] has been quietly retired and forgotten."

    Really now? That's not quite the case. In fact, ...

    Their evolutionary prediction was correct, since the minor variations in the standard genetic code are indeed associated with major taxonomic groups (vertebrates vs. plants vs. single-celled ciliates, etc.).

    Second, we now know from experimental research that many plants, many animals, and many bacteria all have extremely similar genetic codes. There is no known biological reason, aside from common descent, for why the genetic codes of different species should be similar. Any new discovery of a plant, animal, or bacteria with a radically different genetic code would be a highly unexpected result if common descent is true."

    Hmm. Seems you're just plain wrong on at least two counts: The assumption of a universal code was itself never universal, nor does it seem that people have forgotten about it (maybe this disciplinary amnesia only took hold after 2002?). A third is debatable: there very well may have been some people who asserted that it was "indisputable proof" but, well, that practice clearly wasn't universal either. At best, you can have that one on a technicality.
    ==================

    Except that Matzke said this, not me.

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  15. Corny, your argument is that we should not regard the hypothesis of universal common descent as being empirically confirmed just because it's a better fit to the data than any other hypothesis we've got. What, exactly, does this "empirically confirmed" phrase even mean if your argument is valid? Can you name any hypothesis which you regard as "empirically confirmed", that isn't also a better fit to the data than any other hypothesis we've got?

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  16. Just a couple of quick questions.

    "Universal common descent" is compared to "creationism" here. But there are plenty of ID boosters and religious believers who accept UCD, and who also believe God directed evolution or even intervened at certain points (without necessarily introducing some sudden and utterly precursorless organism within the chain).

    Should I take this discussion to mean that those people aren't creationists?

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  17. I'm a little confused. First they said that the universal genetic code was proof of evolution. Now they are saying that the fact that the code is not universal is proof of evolution? I could use some clarity.

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  18. Mark Frank:

    =======
    I thought that Bernoulli was famous for calculating the probability of the orbits of the known planets being as closely aligned as they are assuming that any alignment is equally likely.
    =======

    Well to be fair to his legacy, I wouldn't say this is what he is famous for. I'd say his fluid flow equation ranks much higher, for example.

    ===========
    He came out with a very low number and concluded that there must have been a reason for their being aligned.

    1) Bernouilli's method is not contrastive. As Douglas says it is classical null-hypothesis testing.
    ===========

    Hm, I think of it as contrastive. Isn't setting up two hypotheses and contrasting them "contrastive"? Or am I using the term incorrectly?

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  19. "... I could use some clarity."

    You'll never get it from the DarwinDefenders.

    For that matter, one is lucky to get them to not misrepresent what one has said when they've taken a mind to assert it is false ... as witness Mr Howard's original contribution in his lengthy (and mostly not-terribly relevant copy-and-paste) "refutation" of what I'd said.

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  20. Cornelius:

    "Except that Matzke said this not me"

    He didn't say it either. Theobald did, or at least he said most of it, as I was in fact quoting him in response to something else that Ilion, who is neither you nor Matzke, said. IOW, I wasn't talking to you.

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  21. I have a couple of questions:

    1) Is Dr. Hunter now satisfied with the methodology in the paper? It seems any competitive scientific hypothesis can be tested using Dr. Theobald's methods. If Hunter has an alternative, perhaps he should propose it, and it can be tested. My guess is he does not (or, it is non-scientific).

    Of course, this would mean proposing something, and Hunter seems to resists taking stands.
    e.g.: How old IS the Earth, Dr. Hunter?

    2) If Dr. Hunter accepts this study is, on some level, evidence for UCA, as he has stated above, how would he report it? Can he give us a paragraph summarizing the conclusion? This might clarify how he thinks science should operate.
    I'm still a bit confused on the difference in reporting UCA emerged as the best model from an empirical study, and what has been reported. Is this not this a key test that could have produced evidence falsifying UCA? Separate origins could have been detected.

    Some of the offending tag lines you've presented:

    "Test Supports Universal Common Ancestor for All Life,"
    ""Creationism called "absolutely horrible hypothesis"—statistically speaking.""
    "First Large-Scale Formal Quantitative Test Confirms Darwin’s Theory of Universal Common Ancestry"

    Seem absolutely benign. The test does support UCA. Statistically, separate creation of humans scored very poorly. Confirm (com- + firmare to make firm), can mean to corroborate or substantiate. Does this study not give evidence to common ancestry? Not only evidence, but a technique to test all other hypotheses.

    3) To clarify how science SHOULD be conducted, can Dr. Hunter give us a primary ID study (not review), with proper methodology that doesn't overstate its conclusions? Please describe how it is empirical, non-contrastive, Baconian?, and proper in all ways, perhaps including its depiction in the ID/creationist literature, while this one is not.

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  22. Ilion: quoting a source that deals directly with a topic you raised in your post of your post and that demonstrates more than adequately that your assertions about what claims have been made by evolutionary biology as a whole are simply flat-out wrong is somehow irrelevant?

    Um.....OK? That's a rather strange mental space you inhabit, but you seem to like it that way, so I'll leave you to it then.

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  23. This comment has been removed by the author.

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  24. For example, take the "tornado in a junkyard" calculations that test a SINGLE hypothesis, the spontaneous formation of an modern, mature protein from amino acids, in water, sans any chemical evolution.

    The probability from this calculation is then reported as not only evidence against abiogenesis, but all of evolutionary theory.

    Why is that claim better than this paper?

    If it is not, would you care to write a post correcting this?

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  25. Cornelius,
    "I said your claim that your results are very strong empirical evidence for the universal common descent hypothesis is false. You later agreed, but with the caveat that pointing out that your claim is false amounts to skepticism"

    Where exactly did THeobald agree to this? Telling you that you're entitled to your own opinion is hardly the same as agreeing with you.

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  26. """Creationism called "absolutely horrible hypothesis"—statistically speaking."""

    Again, I'd like to know if that means that UCD-accepting ID proponents and religious believers (Like Behe, etc) are therefore not creationists? If they aren't, that's great. If they are, the quote is flat-out wrong.

    ""First Large-Scale Formal Quantitative Test Confirms Darwin’s Theory of Universal Common Ancestry""

    Is it really "Darwin's Theory" after 150 years, and with all manner of caveats and changes to the theory added (symbiogenesis, HGT, etc)? Would additional research supporting the Big Bang hypothesis rightly be reported as "Latest Scientific Research Confirm's St. Augustine's Theory of Creation"?

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  27. Crude-

    Those lines are referencing specifics.

    "Creationism called "absolutely horrible hypothesis"—statistically speaking."

    The statistical test of 'Creation' was of Humans as an independent lineage. You should ask an actual ID supporter whether UCA is ok with them, or if they've been thrown under the bus along with believers in theistic evolution. I've seen some pretty visceral reactions to UCA around here-even denying that phylogeny exists at all.

    "Is it really "Darwin's Theory" after 150 years, and with all manner of caveats and changes to the theory added (symbiogenesis, HGT, etc)?"

    In Origins Chapter 14, Darwin specifically predicted UCA. These articles credit that. A lot has changed, and most of us don't call ourselves 'Darwinists,' (some Brits do), but in this case it is giving credit where credit is due for a specific prediction.

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  28. RobertC,

    The statistical test of 'Creation' was of Humans as an independent lineage. You should ask an actual ID supporter whether UCA is ok with them, or if they've been thrown under the bus along with believers in theistic evolution. I've seen some pretty visceral reactions to UCA around here-even denying that phylogeny exists at all.

    I've already inquired what "actual ID supporters" think of this, and gotten my answer from them time and again - from the mere existence of Behe to Bill Dembski's own take. Nor have ID proponents "thrown theistic evolutionists" under a bus.

    I'm asking you, because you're the one who said those tag lines "Seem absolutely benign."

    So again: Are ID proponents or religious people who accept common descent "creationists" or not?

    In Origins Chapter 14, Darwin specifically predicted UCA.

    And Augustine specifically predicted a beginning to the universe. Again: Would additional research supporting the Big Bang hypothesis rightly be reported as "Latest Scientific Research Confirm's St. Augustine's Theory of Creation"? If not, why not?

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  29. nanobot74:

    "Where exactly did THeobald agree to this? Telling you that you're entitled to your own opinion is hardly the same as agreeing with you."

    Has Theobald agreed with anything Hunter has said? Hang on.

    *Goes and looks through various comments by Theobald*

    Um, yeah, not seein' it. Found a highly relevant exchange, though. Theobald quoted this:

    Cornelius:"That is entirely different than your claim that the results constitute 'very strong empirical evidence for the hypothesis.' That is simply false. "

    His response?

    Theobald:"And you are simply incorrect. [more disagreement follows]"

    So, Cornelius...do words just mean whatever you chooose them to mean, neither more nor less? 'Cause you have an awfully strange definition of "to agree".

    *keeps looking*

    Perhaps you meant this?

    Theobald:"Fine, so from my analysis we have overwhelming evidence that universal common ancestry beats out competing multiple independent ancestry hypotheses. If you don't consider that as evidence for universal common ancestry, then you are certainly entitled to that opinion. But the rest of us are not required to believe that your opinion makes any sense"

    Cornelius, I'm really starting to feel distinctly misinformed here, and NOT by Dr. Theobald.

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  30. Come to think of it, I have another question on the 'creationist' line:

    Theobald also tested the creationist idea that humans arose in their current form and have no evolutionary ancestors.

    The statistical analysis showed that the independent origin of humans is "an absolutely horrible hypothesis," Theobald said, adding that the probability that humans were created separately from everything else is 1 in 10 to the 6,000th power.


    Here's my problem: The "creationist idea" is not that mankind simply popped into existence uncaused and unintentionally however-many years ago. Creationism is intimately tied up with the idea that God directly intervened for this development.

    Unfortunately, I don't have access to Theobald's paper, so I have to ask: Did his probability estimate include the possibility (or assumption) that God (or even a designer/designers) existed?

    Is the "1 in 6000 to the 10th power" estimate assuming 'undirected natural forces'? Because if so, I fail to see how this is at all a test of the supposed 'creationist argument' in question. It would be some bizarre test of whether an event vaguely similar to a creationist story took place, while removing the 'designer' factor.

    Of course, if this isn't assumed - if this scientific paper is explicitly querying the odds of an unnamed divine or pseudo-divine creator intervening in nature - well, that will be very interesting to see as well.

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  31. I found it! The (single) point of agreement:

    "So in this sense George is correct about Bernoulli, that 'disproving' the null hypothesis is not evidence for the favored hypothesis."

    Totally different from that which was claimed, but hey...what d'ya want? Accuracy? Pshaw!

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  32. Crude-

    Your comments are only serving to reinforce that 'creation science' is not, and never can be a science.

    This is not to say specific claims therein are not refutable.

    For example, we can present evidence aplenty that the world is not 6000 years old.

    A counter-claim that the world IS 6000 years old, but supernaturally made to look older cannot be falsified.

    Similarly, a single creationist hypothesis was falsified here.

    As even the National Geographic article, had you read it says,

    "Theobald also tested the creationist idea that humans arose in their current form and have no evolutionary ancestors.

    The statistical analysis showed that the independent origin of humans is "an absolutely horrible hypothesis," Theobald said, adding that the probability that humans were created separately from everything else is 1 in 10 to the 6,000th power."

    So a unique, independent origin for humans-one major creationist claim-is falsified. We evolved from other species. OK?

    This is not to say the counter-claim: that we were uniquely created, but in an exact manner, using proteins found in other organisms, modified in such a way to make them look related to ours by a precise way that suggests ancestry-is falsified or even falsifiable.

    Similarly, the claim of theistic evolutionists that we are evolved, but all is guided by God is not falsifiable, or a scientific claim. Even Theistic evolutionists admit this, and you don't see many trying to get the 'Theistic' part taught.

    Under the broad banner that Creationism is the belief that everything is the work of a supernatural, was that falsified? No. Is the belief that God created mankind in its present form without trickily making us appear evolved falsified? Likely.

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  33. RobertC,

    Your comments are only serving to reinforce that 'creation science' is not, and never can be a science.

    A shame I wasn't addressing that topic whatsoever. How do you know what I even think of "creation science"?

    So a unique, independent origin for humans-one major creationist claim-is falsified. We evolved from other species. OK?

    Nowhere did I ask whether or not humans evolved (and in fact, I believe humans did evolve.) As a theistic evolutionist of sorts, I find your reasoning here to be pretty shoddy, not to mention contradictory (You keep suggesting that the claim is both falsified and unfalsifiable), even when deployed against the view that 'Man was created in his present form without any biological precursors'. But it's also a red herring.

    I asked you two specific questions about taglines you said "seem benign". I'd really like direct answers to those questions. I'll repeat them again:

    Are ID proponents or religious people who accept common descent "creationists" or not?

    Would additional research supporting the Big Bang hypothesis rightly be reported as "Latest Scientific Research Confirm's St. Augustine's Theory of Creation"? If not, why not?

    As an aside, I will personally admit that the claim that, say, "an omnipotent God created man instantaneously a finite number of years ago" is not a scientifically falsifiable hypothesis. I've questioned the claim that an actual 'creationist hypothesis' has been adequately assessed by Theobald's paper, and implied that there may be a problem of giving a probability estimate for that very question and calling it "science".

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  34. Crude,

    I think I've clearly explained how this work falsifies A creationist hypothesis and allows for the testing of others, while others are unfalsifiable. On a side note, I mentioned many facets of creationism, ID, and Theistic Evolution are not falsifiable-especially as they regress into explaining away the data.

    "Are ID proponents or religious people who accept common descent "creationists" or not?"

    If Creationism is the belief that all things are the work of a supernatural creator, than yes. In usage, I suppose fuzzy line have been drawn between one and another. The brightest line to me, is whether an individual proposes it is science or not.

    "Would additional research supporting the Big Bang hypothesis rightly be reported as "Latest Scientific Research Confirm's St. Augustine's Theory of Creation"? If not, why not?"

    No. Augustine's hypothesis of creation has already been falsified. The world is more than 6000 years old:

    "They are deceived, too, by those highly mendacious documents which profess to give the history of many thousand years, though, reckoning by the sacred writings, we find that not 6000 years have yet passed."
    – Augustine, Of the Falseness of the History Which Allots Many Thousand Years to the World's Past, The City of God, Book 12: Chapt. 10 [419]

    Besides that, except for the concept of a beginning of time, I cannot conceive any way Augustine would have proposed the Big Bang, in all its details. It is falsely ascribing more than he proposed to him.

    Darwin's prediction of a Universal Common Ancestor, on the other hand, was very specific.

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  35. Doug:

    [Edited for emphasis and clarity]

    ============
    George has made a very significant error in comparing my methodology to Bernoulli's. And the error is extremely ironic (and pretty darn funny, if you're a statistics geek like me).

    The results in my paper are explicitly based on model selection theory, likelihoodist and Bayesian statistics -- not on classical frequentist null-hypothesis testing, which in fact I criticize in the main text of the paper and in the supplementary materials. Bernoulli's solar system argument, however, is a classic example of a null-hypothesis test -- it is often cited as the first one known.

    The irony here, of course, is that I don't use Bernoulli's methods, ... So in this sense George is correct about Bernoulli, that "disproving" the null hypothesis is not evidence for the favored hypothesis ... But this criticism does not apply to Bayesian statistics

    ============

    You're reading this in as, of course, I never made such a criticism. What I noted is that Bernoulli used contrastive thinking and made unsupportable claims, as you do.


    ===========
    And by calculating the probability of the observed data under each of the different competing hypotheses, you are in fact able to calculate the evidence for the different hypotheses -- the very thing George claims is impossible. That is exactly what Bayesian methods allow you to do, and it's why they have become so popular throughout science in the past 15 years.
    ===========

    No, I did not claim that is impossible. I said your claim that your results are very strong empirical evidence for the universal common descent hypothesis is false. You later agreed, but with the caveat that pointing out that your claim is false amounts to skepticism -- an overly naunced, finicky interpretation of your results. You wrote:

    =========
    Fine, so from my analysis we have overwhelming evidence that universal common ancestry beats out competing multiple independent ancestry hypotheses. If you don't consider that as evidence for universal common ancestry, then you are certainly entitled to that opinion. But the rest of us are not required to believe that your opinion makes any sense. Yours is a strange philosophy, to my mind, and I'm sure to most people who will read your words.
    =========

    So you make a false claim and when it is pointed out by someone you say that person's view is unreasonable. Evidence needs to be carefully understood and treated for what it is. You do no such thing with your results. Rather, in an attempt to defend your false claim you put me in the position of skeptic, saying that my pointing out your false claim amounts to an unreasonable position -- technically correct but really just a technicality.

    You have made a false claim, and now having been apprised you resist correcting it. It is difficult to imagine how one could do more to abuse science or abuse one's privilege as a scientist. Not only have you made a false claim, but you have shouted it from the rooftop, and you have made the false claim about what is arguably the most influential theory in all of science. You're not arguing about how a particular enzyme works. This is not an arcane scientific debate that doesn't matter to people. In those cases, as bad as false claims are, at least their impact is bounded. In your case, your false claim has global consequences, both literally and figuratively.

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  36. George:

    You wrote:

    "I said your claim that your results are very strong empirical evidence for the universal common descent hypothesis is false. You later agreed, but with the caveat that pointing out that your claim is false amounts to skepticism -- an overly naunced, finicky interpretation of your results."

    This is false, George. I never agreed to that. The results reported in my paper are indeed very strong empirical evidence for the theory of universal common ancestry, and I have never said anything to the contrary.

    Evidence for hypothesis A relative to another hypothesis B necessarily means that there is evidence for hypothesis A. All we have is relative evidence -- all evidence is relative to other competing hypotheses. Because that is all we have, when we say "there is evidence for hypothesis A" we can only mean that "there is evidence for hypothesis A versus some other hypothesis B". Again, this is the standard model selection, likelihoodist, and Bayesian statistical interpretation of evidence. And it is a view I wholly subscribe to.

    Contrary to your assertions, I don't think you are "technically correct" -- I think your claim is absurd.

    Let's look again at what you wrote above in your blog post:


    "What you have is very strong evidence that the hypothesis beats out the other hypotheses, period. You do not have very strong evidence for the hypothesis, as you are claiming."


    I honestly have no idea what you mean. You agree that there is very strong evidence that universal common ancestry beats out all other competing hypotheses. Yet you claim that's not strong evidence for universal common ancestry. That makes no sense. No one here but you understands what you mean -- and nobody is rushing to your defense on this esoteric point.

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  37. Let's apply Hunter's logic in physics. We have strong evidence that general relativity beats out Newton's theory of gravity but we don't have strong evidence for general relativity. That's rather absurd, don't you think, George?

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  38. Shorter Corny: How dare you claim that you've demonstrated your hypothesis is empirically supported? All you've done is prove that it fits the data better than any other!

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  39. You can't argue with fools (it's logically impossible) ... and most DarwinDefenders choose foolishness and the protection of their emotional investment in Darwinism over reason.

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  40. Ilion, are you ever going to make an actual contribution here? Or just toss snide little comments into the mix.
    Most posts which don't add knowledge at least end with a question mark to make them worthwhile.
    Otherwise, just observe.

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  41. Bernoulli is a bit of a side show compared to Cornelius desire to reject the whole of modern statistics - but for completeness.

    Me:
    ==========

    1) Bernouilli's method is not contrastive. As Douglas says it is classical null-hypothesis testing.


    Cornelius
    ===========


    Hm, I think of it as contrastive. Isn't setting up two hypotheses and contrasting them "contrastive"? Or am I using the term incorrectly?

    ==========

    You coined the term "contrastive" so you can use it to mean whatever you wish. However, all Bernoulli contrasted was "null hypothesis is true" with "null hypothesis is false". If that is "contrastive" then as far as I can see all inferences about a hypothesis are contrastive.

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  42. Hunter, speaking of Doug's daring to claim he has provided strong evidence for common ancestry, says:

    "In your case, your false claim has global consequences, both literally and figuratively."

    And what are those consequences?

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  43. Oh, silly Tom! I simply cannot help it that you are unable (or unwilling) to see the worthwhile contribution of my snide comments. And, frankly, I don't care about your disability; it's not my moral responsibility to polish the fragile egos of DarwinDefenders, or of other irrational persons.

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  44. Ilion, there is only one thing you appear to be 'polishing'.

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  45. Tom, have you not heard? "You can't polish [what you are offering]"

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  46. Cornelius, I'd really like to know why you keep calling Theobald a liar? You've asserted more than once that he is knowingly making false claims, and yet you utterly fail to back that up with anything but pure, biased opinion and bitter whining. And then, YOU lie about him agreeing with you, are shown to be wrong by others, told you are wrong by Theobald and you...do nothing. No apology. No retraction. You blithely continue whining that Dr. Theobald refuses to apologize for making false claims when the only such documented claim is the one you made up and are still repeating. Lovely.

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  47. Of course, when a DarwinDefender accuses, "... and yet you utterly fail to back that up with anything but pure, biased opinion and bitter whining," the English translation of the accusation is generally: "You have failed to force me to admit the truth of what you have said."

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  48. Douglas,

    "No one here but you understands what you mean -- and nobody is rushing to your defense on this esoteric point."

    I must be a genius because I understand just what Cornelius is saying. He is saying that the best hypothesis is not necessarily correct. Science has a history of a plethora of such theories. One example: ether - no one understood how light could have waves without a medium. It was discovered that there is no ether. The best hypothesis was wrong. Another example already mentioned: the flat earth theory, also wrong. (Did you know that the ancient Greeks knew the world was spherical because they would see the tops of the masts of a ship first as it returned to port. This was also known by an ancient Alexandrian scholar from the difference in shadows at wells between two cities. This scholar made a remarkable estimate for his time.) And my last example is the infinite universe theory. According to Hoyle the universe has been around for ever. Science has shown that the universe is about 13.7 billion years old from the time of the big bang. All these theories were the best theories of the time, but evidence proved them to be wrong. I think what Cornelius is getting at is that your paper may show the best theory statistically (I am not a biologist), however, it does not prove the mechanism of evolution. That is, it does not explain how one species evolved into another, and how that could be possible for all species. It could be possible that your 23 proteins are essential proteins for all creatures that modify according to morphology.

    .

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  49. Well, Ilion, why should I believe it's the truth when, you know, he's utterly failed to back it with anything other pure biased opinion and bitter whining? If you'd prefer a "translation": "Please provide some actual evidence showing you're not just making this crap up."

    Oh, and "DarwinDefender"? Who's defending Darwin here? I mean, for one, he's dead. For two, Darwin is not the subject of discussion. For three, as an insult, that sucks. It utterly lacks zazz.

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  50. Hundreds of thousands of scientists keep working on refining or improving TOE. What have they accomplished but writing academic papers? As long as the processes (if any) of evolution is not defined or cannot be defined, it's tough to repeat any experiment in TE. "Natural selection" includes just about anything man can think of to make animals propagate their "better genes". That would be synonymous to random.

    The world could be a better place if all the time, money, and energy spent on TOE were put to work in another endeavor.

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  51. Peter,

    You wrote:

    "He is saying that the best hypothesis is not necessarily correct. "

    Surely that's not what he means, because that is not his argument. Obviously the best hypothesis is not necessarily correct. However, just because a hypothesis might be false does not imply that we can't have strong evidence for it. We can and do have strong evidence for false hypotheses. For example, we are fairly sure that Newton's theory of universal gravitation is false, yet there is extremely strong evidence for it. There happens to be even stronger evidence for Einstein's general theory of relativity. We have extremely strong evidence for the general theory of relativity, but that does not mean it is correct.

    Hunter's claim is quite different -- he says that having evidence for hypothesis A over hypothesis B does not mean we have evidence for hypothesis A. And he thus accuses me of lying when I say that my paper reports strong evidence for the theory of universal common ancestry. That accusation is baseless.

    This is science -- no hypothesis is "sacred", everything is open to doubt and improvement and re-examination as new data is gathered. Of course universal common ancestry might be false. That's why I tested it.

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  52. Douglas,

    "Hunter's claim is quite different -- he says that having evidence for hypothesis A over hypothesis B does not mean we have evidence for hypothesis A."

    Thanks for that clarification. Verbal communications can be very difficult. It seems this may be a matter of semantics. In this case there is the difficulty understanding what 'evidence' means. Does evidence refer to empirical studies showing how one creature evolved into another, or does it refer to your work using proteins rank various hypothesis? The two are different I think.

    I don't want to speak for Dr Hunter, or put words in his mouth, the way I interpret Dr Hunters objection is that the evidence in your paper is not evidence which explains how one creature evolves into another. Dr Hunter is an empiricist. In my opinion that is the evidence he expects for a theory to be supported. From this perspective a statement saying UCD has been proven would be false.
    .

    ReplyDelete
  53. Peter,

    Again I don't think that is George's argument -- he has never said anything in about mechanism in reference to my paper. And anyway evidence for a theory and its mechanism are two different things.

    My study is not primarily about mechanism, but it does address it. Here is the final sentence of my paper:

    "Hence, the large test scores in favour of UCA models reflect the immense power of a tree structure, coupled with a gradual Markovian mechanism of residue substitution, to accurately and precisely explain the particular patterns of sequence correlations found among genealogically related biological macromolecules."

    The winning models (the universal common ancestry models) all explain the genetic connections between species by a gradual mechanism of mutation and residue substitution. So in this sense my results are evidence for that. However, there are many different mechanisms that are consistent with gradual residues substitution, and my results do not distinguish among them.

    Furthermore, one could consider the tree structures to be another component of the mechanism of UCA. And I do test those -- my results show evidence that proteins have different tree structures, rather than a single "tree of life". This can be interpreted different ways, since from population genetics we do not expect gene/protein trees to exactly match organism trees, and similarly we do not expect organism trees to exactly match species trees (a simple example is that your family tree is different from the human phylogeny or even the relationships among different human "races", cultures, and ethnicities).

    In any case, having a mechanistic explanation is not necessary to have strong evidence for a theory. A prime example is again gravity. We have extremely strong evidence for both Newton's universal theory and Einstein's general theory of relativity, both of which explain gravity. Yet we still to this day have no empirical support for a mechanism for gravity. It is widely thought that gravitational force is imparted by exchange of gravitons, in analogy with the other three fundamental forces, yet we have never observed one, not even indirectly.

    Theories in science as like nested Russian dolls -- there is always a lower level theory to explain a higher level theory, and the lower level theory is a "mechanism". Classical thermodynamics was well-established before statistical mechanics provided a mechanism. And quantum mechanics supplies an even lower-level mechanism for that. In all cases it's possible to gather evidence for a theory in the absence of an explanatory mechanism -- though of course it helps to have one.

    Cheers,

    Douglas

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  54. Peter,

    One further comment. You wrote:

    "From this perspective a statement saying UCD has been proven would be false."

    I would never claim that UCD, or any other theory, has been proven. My views on this are well-known and public:

    http://www.talkorigins.org/faqs/comdesc/sciproof.html

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  55. NickM:

    ====
    And what are those consequences?
    ====

    I can think of two consequences of this sort of junk science that concern me. On the one hand, it further diminishes the legitimacy of science in the opinion of many. Simply put, junk science leads to science bashing--ironically the very thing you accuse me of.

    On the other hand, at the other extreme the tremendous appeal of this junk science attracts many others. Look how this paper is celebrated. So it creates its own momentum.

    So you can have a bifurcation where the unhealthy extremes gain at the cost of moderate middle positions.

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  56. Dr Hunter,

    I see a lot of resistance to your thesis here because, as you say, people see your point as a technicality without much practical force. I think you would get a lot more understanding from your audience if you made clear why, in a practical way, Dr Theobald's conflation of "this evidence shows that the UCA hypothesis beats out the alternatives" and "this evidence supports the UCA hypothesis" makes a real difference.

    It seems to me, as Crude has pointed out (but we don't have access to the Nature article, and the press articles don't provide much detail...), the problem with Theobald's argument is that he didn't evaluate competing hypotheses fairly. If you were to make that argument in more detail and convincingly, I think a lot more people would see why this matters.

    For example, Theobald claimed to have falsified creationism, formulating it as the "probability that humans were created separately from everything else". If in doing so he assumes that humans will therefore share no genetic information with other species except by chance, then his evaluation is founded on unwarranted assumptions; he makes the classic error of excluding common design as a hypothesis. I don't know if he makes that assumption.

    But if you could point out how Dr Theobald failed to fairly evaluate alternative hypotheses, it would make a lot more sense to me why his claims are in error. Otherwise, it's not really clear why a "evidence shows that UCA is the best hypothesis we have" claim is so far from "evidence supports UCA". I think it's not just evolutionists who need to have the difference spelled out for them.

    Sincerely,
    Lars

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  57. Cornelius,
    "junk science"- just so we are clear: do you consider any study that compares two or more hypotheses, whether using frequentist or Bayesian statistics, and states that those statistical results provide evidence for their hypothesis, is "junk science"?

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  58. Lars,
    "he makes the classic error of excluding common design as a hypothesis"

    If this is your hypothesis, you are free to incorporate it into the model provided by THeobald. I'm sure he would even do it for you if you liked. First, you need to spell out what exactly you mean by common design and what the empirical predictions of that hypothesis would be. the ball is in your court.

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  59. Douglas,

    "having a mechanistic explanation is not necessary to have strong evidence for a theory."

    True, but without a strong mechanistic explanation, and laboratory verification there will continue to be debate about evolution. No one debates the flat earth hypothesis anymore because we can see pictures of the earth from space. Judging from the complexity of the biology of life, the difficulties in testing evolution, and the strong theological responses it arouses, I don't see an end to the debate for at least another 150 years.

    .

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  60. I assume, Peter, that for the sake of intellectual consistency, you hold similar views about universal gravitation.

    ReplyDelete
  61. Lars,

    You wrote:

    "Theobald claimed to have falsified creationism"

    I have never made that claim, and I certainly did not make it in my paper. That was National Geo's take on it, and I let them know my disapproval in no uncertain terms.

    I will comment on this in more detail when I post on my paper at the Panda's Thumb, but for now here is what I wrote Ker Than at NG:

    ***************
    I want to be very careful here -- "Creationism" means different things to different people. For instance, the noted evolutionary biologist Theodosius Dobzhansky, who coined the phrase "Nothing in biology makes sense except in the light of evolution", made this statement in the same article: "I am a creationist and an evolutionist. Evolution is God's, or Nature's, method of creation". I take a similar view.

    For the record, I do not think that creationism is an absolutely horrible hypothesis -- at least not creationism broadly construed, which I think is in fact a proposition outside of science's ability to test. I like how you phrased it in the previous section, "the hypothesis that the biological origins of humans are different from other organisms" -- that is what my analysis showed is a "horrible hypothesis".
    *****************

    Cheers,

    Douglas

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  62. Thomas,

    "I assume, Peter, that for the sake of intellectual consistency, you hold similar views about universal gravitation."

    I do. I know that every time I drop a hammer it falls to the ground. Every year the earth rotates around the sun. I do not know however if every creature that ever existed in every epoch morphed from a previous creature. Likewise, I do not know if a random collections of organic molecules coalesced into a replicating life form.

    Being a Theist I could easily believe that God created through evolution. However, I need to see a verifyable mechanism first. Until that time 'God did it' is still a possibility.


    .

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  63. Well, then actually, you do not. We don't have a mechanism for gravity. Yes there's the warped spacetime of relativity but:

    a. there's no explanation provided for how mass does this to spacetime. It just sort of does. So, not much of a mechanism, really.

    b. everyone knows that it has yet to be fully reconciled with QM, which treats forces in a very different way.

    So, you may observe all the falling hammers you like, but that won't make you consistent. You're still giving a pass to one theory while demanding a mechanism be provided by the other.

    What's makes this odder is that on this count, evolution has actually met your demand (I'm simply ignoring the conflation with the field of abiogenesis, BTW). I assume you're aware of natural and sexual selection and genetic drift? Mechanisms. Observed and quantified mechanisms, to boot. Not to mention all the extremely well-documented mechanisms of genetics, which collectively provide the required "raw materials" needed by those evolutionary mechanisms.

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  64. It's kind of humorous to see Darwinists and/or logical positivists demanding of others intellectual consistency, isn't it? I mean, considering that they have no comprehension of either intellectual consistency or intellectual honesty.

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  65. Peter has never observed hammers falling on Pluto either -- or Alpha Centauri A, or on any of the countless planets/stars in the Andromeda galaxy. Or 10,000 years ago in New Zealand. The claim of Newton's theory of universal gravitation is that gravity is universal: every massive particle in the universe attracts every other massive particle. Einstein's theory make a similar claim, where every massive particle in the universe distorts space-time. And there's no known mechanism (very unlike the case in evolution, where there are several readily observable mechanisms with good empirical support).

    For some reason I have yet to see people get up in arms whenever a new formal test of relativity is published, one that claims new strong evidence for relativity.

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  66. Hunter replied,

    "Gosh, yeah right. Either we buy phony arguments that evolution is an undeniable fact, or we are out and out skeptics. Evolutionists are just ruthlessly logical."

    Oh please. Your argument boiled down to saying that things like likelihood ratio tests and model selection theory don't provide strong evidence for a model when the data favors that model by thousands of orders of magnitude. But these tests and their interpretation are standard throughout statistics and throughout science, and not just historical science, either. You are basically complaining about the fact that evolutionary biologists are using data to test their theory in the same way that everyone else in science and statistics does. And yet you accuse us all of lying and of "worship" when we do these statistical analyses.

    It doesn't mean you're a philosophical skeptic doubting everything -- pretty obviously you're willing to believe in traditional creationist miracles without the slightest skeptical analysis, because you think God creates according to his good pleasure and it's not the place of human intellect to doubt or question how or why he would do things that way. But it does mean your fight is with the modern scientific project in general, not just evolution or historical science.

    "I'm not a fundamentalist."

    I don't believe you. First, young-earth creationists are pretty much fundamentalists by definition, and it's pretty clear from your theological statements that you are YEC or one of those "I'm agnostic on the age of the Earth" people, although for some reason you appear to not have the courage of your convictions to admit it outright.

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  67. Second, even old-earth creationists are fundamentalists in the original sense of the term -- believing in Biblical inerrancy, privileging the Bible over scientific evidence come hell or high water, etc.

    Third, your theology quite closely fits what historians describe as the key attitudes of fundamentalists with regard to science. Ranting and raving against speculation, opposing any statistical or inferential argument that goes against your personal "common sense", the assumption that scientists are against you because of nefarious biases rather than because they are deeply familiar with the evidence, a desire to return science to the "Baconian", "empiricist" ideals of early modern science in the 1600s before annoying people like Kant and Lyell messed it up, etc., etc. It's all very specifically laid out by historians like Mark Noll and George Marsden, in books like "Understanding Fundamentalism and Evangelicalism." And you fit their profile perfectly.

    So, sorry, based on the evidence in front of me, especially reading your books, you're a fundamentalist.

    "Gosh more ruthless logic that really cuts to the heart of the issue. That's exactly it, either evolution is much a fact as is gravity, or we're just "a primitive 1600s-style Baconian who believes that nothing should ever be believed unless it is directly witnessed." (except that Bacon never said any such thing)."

    What Bacon actually said is a complex matter, but regardless, the equation of theory and inference with pointless speculation, the distrust of anything but direct observation, etc., are precisely what historians regularly call the "Baconian" position of early modern science.

    This isn't something I made up, it's something lots of historians of religion, including evangelical historians, say:
    [no links: search Google Books on "Baconian fundamentalism"]

    And why, look at what Hunter's very first suggestion was when asked what he would like science to be like:

    [No links. See "Oracle of Reverend Jerry Coyne", January 2010, search on "Fracis Bacon"]

    "'What would an example of this kind of science look like?'

    For starters, you can look at Francis Bacon. Also the semi empiricists, such as modeled by Boyle, Newton and others of the 17th c Royal Society."

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  68. Finally:

    "'and you have this because you believe God can and does do whatever he wants, whenever he wants, and thus people should just believe the Bible and stop there.'

    It's fascinating because, I know Nick is a smart guy, yet look what he is reduced to. Of course one sees sophmoric rants all the time which go unheeded. But Matzke is not a no-nothing anonymous chatter just throwing mud for the fun of it. He is a smart, intelligent, knowledgable, well-educated, life scientist. And yet this is indistinguishable from a sophmoric rant."

    Yeah, this means a lot coming from a guy who accuses evolutionary biologists of lying and of religious dogma with essentially every single breath, up to and including when they apply to evolution the various objective, rigorous, scientifically universal methods of statistical hypothesis testing that are available in modern science.

    As for why get into this -- I think it would save everyone a lot of time if we just cut to the heart of the issues. You think the ultimate arbiter of truth is the Bible. We think it's empirical evidence. But, probably because you know you'd lose if you just said what you actually thought about the Bible and its role in all of this, you come up with meandering, unconvincing, and totally arbitrary and self-inconsistent ways to attempt to accuse evolutionists of being unempirical and based on religion. But it's all just a silly game you're playing to distract from the real issues. All I can do is point it out.

    PS: An aside: "And Nick Matzke, who also believes in the evolutionary metaphysics that god would never have designed what we observe in the biological world, is delighted that the new work debunks creationism."

    Not true. I have no idea what God would do. Thus, I think the hypothesis that God intervened in biology or geology is totally unconstrained and thus totally empirically empty and not testable, and thus has to be excluded from science unless and until someone comes up with a well-constrained God model that can be tested with evidence like everything else in science has to be. However, creationists do think they have a pretty good idea about how God would do things -- although the ID sort of creationists sometimes try half-heartedly to pretend that they don't make these sorts of assumptions -- and I am perfectly happy to put their specific notions to the test of empirical evidence. And this is a totally legitimate activity.

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  69. NickM:
    "You think the ultimate arbiter of truth is the Bible. We think it's empirical evidence. But, probably because you know you'd lose if you just said what you actually thought about the Bible and its role in all of this..."

    Well, we don't actually need Cornelius to say anything. He is on the faculty of Biola after all, and they of course have a doctrinal statement. The explanatory note of which includes this (bolding mine):

    "The existence and nature of the creation is due to the direct miraculous power of God. The origin of the universe, the origin of life, the origin of kinds of living things, and the origin of humans cannot be explained adequately apart from reference to that intelligent exercise of power. A proper understanding of science does not require that all phenomena in nature must be explained solely by reference to physical events, laws and chance.

    Therefore, creation models which seek to harmonize science and the Bible should maintain at least the following: (a) God providentially directs His creation, (b) He specially intervened in at least the above-mentioned points in the creation process, and (c) God specially created Adam and Eve (Adam’s body from non-living material, and his spiritual nature immediately from God). Inadequate origin models hold that (a) God never directly intervened in creating nature and/or (b) humans share a common physical ancestry with earlier life forms."

    As you might guess, it also includes a very firm endorsement of biblical inerrancy.

    So what it comes down to is that Cornelius either fully adheres to the doctrinal statement or he does not. Obvious, I know, but it's what those options imply that is interesting:

    If it's the former option, then you're right and for him the Bible really is the ultimate arbiter of truth, and thus religion drives Cornelius, not science. What I find most interesting here, however, is that the doctrinal statement declares that universal common descent simply cannot be true, period, because humans have no ancestors other than Adam and Eve. The Bible says so, after all.

    It's a rather striking coincidence then that Cornelius is so dead set on declaring Dr. Theobald a liar and discrediting his paper, given the subject of said paper. Even more striking given that the model he is required to support by Biola's doctrinal statement performed so abysmally compared to the others that were tested.

    Cornelius is of course free to dispute this, and state he does not adhere to the doctrinal statement as far as these matters go. Problem is, that would mean he is employed by an institution which requires certain beliefs that he does not have. His position would have then been obtained under false pretenses and he would have to maintain those pretenses in order to remain employed. Which would make this part of his accusatory response to Dr. Theobald both supremely ironic and hypocritical (bolding again mine):
    "In your work you have promoted misinformation about evolution. But of course you've already been warned of that. At some point, it goes beyond a mere mistake, and you are well beyond that point. You are no longer merely making mistakes, and in your position the cost would be too great to retract."

    Now, I personally believe Cornelius does adhere to that statement, but he probably shouldn't admit to that. And if he doesn't, well, he probably shouldn't admit to that either. Not that staying mum is going to make him look all that great or do wonders for his credibility.

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  70. Nick:

    "Oh please. Your argument boiled down to saying that things like likelihood ratio tests and model selection theory don't provide strong evidence for a model when the data favors that model by thousands of orders of magnitude. But these tests and their interpretation are standard throughout statistics and throughout science ..."

    I see. So do you use a footnote that says "We note that our conclusions are based on fallacious reasoning but we believe this reflects standard statistical methods and practices." ?





    ==========
    "I'm not a fundamentalist."

    I don't believe you.
    ==========

    I know, you said that before. That was after you made your religious arguments and before your fallacious science.




    ==========
    First, young-earth creationists are pretty much fundamentalists by definition, and it's pretty clear from your theological statements that you are YEC or one of those "I'm agnostic on the age of the Earth" people, although for some reason you appear to not have the courage of your convictions to admit it outright.
    ==========

    No, I'm not a creationist. I have no theological preference on the age of the earth or evolution. But the two are often erroneously conflated. The evidence for an old earth is rock solid, but it does not help evolution. The age of the earth is simply not relevant.

    What is relevant is how evolutionist's are so driven by their convictions. This exchange is a classic example. Evolutionary thought comes out of Christian thought in the early centuries of modern science. Evolutionists have a metaphysical ax to grind. They claim evolution is undeniable, blackball anyone who finds problems with the science, and blame them for having the religious motives. Classic hypocrisy.

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  71. Nick:


    "Second, even old-earth creationists are fundamentalists in the original sense of the term -- believing in Biblical inerrancy, privileging the Bible over scientific evidence come hell or high water, etc."

    So Nick and the evolutionists use religious premises, mandate evolution, justify it with fallacious science, and then point the finger at you as "privileging the Bible over scientific evidence come hell or high water," even though I never made a religious or theological argument.





    "Third, your theology quite closely fits what historians describe as the key attitudes of fundamentalists with regard to science. Ranting and raving against speculation,"

    So evolutionists make religious mandates and claim evolution is a fact. When you point out the scientific absurdities they respond with just-so stories. When you explain that doesn't justify the fact claim, and is mere speculation, they blame you for "Ranting and raving against speculation." Sigh. Enter the asylum and this is what you get.





    "opposing any statistical or inferential argument that goes against your personal 'common sense', "

    No, opposing any statistical or inferential argument that is fallacious.





    "the assumption that scientists are against you because of nefarious biases rather than because they are deeply familiar with the evidence,"

    Ah, right, it's all about the evidence. Right. I keep getting confused with all the metaphysics. So let's see, with evolutionists even though the arguments are religious it's really all about the evidence. And with anyone who disagrees it's gotta be all about religion even though the arguments are about the evidence. Got it.




    "a desire to return science to the "Baconian", "empiricist" ideals of early modern science in the 1600s"

    Yeah! Now let's see, where are my induction tables again...




    "It's all very specifically laid out by historians like Mark Noll and George Marsden, in books like 'Understanding Fundamentalism and Evangelicalism.' And you fit their profile perfectly. So, sorry, based on the evidence in front of me, especially reading your books, you're a fundamentalist."

    Ah well, I guess that settles it. I guess I'll have to stop arguing with those fundamentalists. Oh, did you tell Denis Alexander and the other evolutionists that they are fundamentalists as well?





    =========
    And why, look at what Hunter's very first suggestion was when asked what he would like science to be like: ...

    "'What would an example of this kind of science look like?'

    For starters, you can look at Francis Bacon. Also the semi empiricists, such as modeled by Boyle, Newton and others of the 17th c Royal Society."
    ========================

    Its funny that mentioning Bacon can get you in trouble with both creationists and evolutionists. Hmmm. And Boyle and Newton? Shocking!

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  72. Nick:

    ===========
    "'and you have this because you believe God can and does do whatever he wants, whenever he wants, and thus people should just believe the Bible and stop there.'

    It's fascinating because, I know Nick is a smart guy, yet look what he is reduced to. Of course one sees sophmoric rants all the time which go unheeded. But Matzke is not a no-nothing anonymous chatter just throwing mud for the fun of it. He is a smart, intelligent, knowledgable, well-educated, life scientist. And yet this is indistinguishable from a sophmoric rant."

    Yeah, this means a lot coming from a guy who accuses evolutionary biologists of lying and of religious dogma with essentially every single breath, up to and including when they apply to evolution the various objective, rigorous, scientifically universal methods of statistical hypothesis testing that are available in modern science.
    ===========

    So your religious premises mandate evolution, you back it up with fallacious science, blacklist those who point it out, and accuse them of being outrageous and religious. Not a pretty picture.



    "As for why get into this -- I think it would save everyone a lot of time if we just cut to the heart of the issues. You think the ultimate arbiter of truth is the Bible."

    Umm, yeah like Denis Alexander and about a million other evolutionists.





    "We think it's empirical evidence."

    Good, we agree. Except, why then do you promote fallacious science? Why not just stick with the empirical evidence?





    "But, probably because you know you'd lose if you just said what you actually thought about the Bible and its role in all of this, ..."

    It's always about imputed motives. Evolutionists are good at labeling those who don't agree with imagined "ulterior motives" which they're constantly hiding away. Nick, you have made a dizzying array of heresy charges which have no basis in reality outside of your and evolutionist's heads. Your accusations are so off the mark it's humorous to read. I'm sorry, but this is another example of (dare I say it lest I be accused of ranting), speculation.







    "Not true. I have no idea what God would do."

    So all your religious arguments about how dysteleology, biogeography, etc, falsify creationism were merely testing creationism?

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  73. Thomas S. Howard:

    ========
    Now, I personally believe Cornelius does adhere to that statement, but he probably shouldn't admit to that. And if he doesn't, well, he probably shouldn't admit to that either. Not that staying mum is going to make him look all that great or do wonders for his credibility.
    ========

    If your intent is to imagine as many misdeeds as you can, and issue the usual canards, then I'll ignore. But if you genuinely want to learn something or have a specific question for me, I'll respond.

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  74. N.Matzke:I don't believe you [when you say you’re not a “fundamentalist”]. First, young-earth creationists are pretty much fundamentalists by definition, and it's pretty clear from your theological statements that you are YEC or one of those "I'm agnostic on the age of the Earth" people, although for some reason you appear to not have the courage of your convictions to admit it outright.

    C.Hunter:… The evidence for an old earth is rock solid, …

    Now, see, I *am* one of those “fundamentalists” Mr Matzke is so incensed about; and I quite disagree that “The evidence for an old earth is rock solid” (for I know that the adduced evidence is as assumption-laden, and circular, as evolutionism is); and, in fact, I *am* “ one of those "I'm agnostic on the age of the Earth" people ” he’s ragging on.

    But, take one guess, between he and I, which of us takes the rational and logical approach to these questions. Take one guess, between he and I, which of us is indeed open-minded … and properly skeptical, rather than selectively hyper-skeptical. Take one guess, between he and I, which of us respects your right (*) to be convinced by evidence which he himself doesn’t believe to be convincing.


    (*) I mock the Darwinists not *merely* because they choose to believe things I believe cannot be logically supported, but because of their foolishly misplaced triumphalism about things which cannot be rationally supported.

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  75. Ah well, I have to ask. Of course the evidence for an old earth is rock solid, because it's in the rocks -- but, Cornelius, do you actually accept the scientific conclusion that the earth is old? Say yes and I'll apologize for getting you wrong.

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  76. Nick:

    "Ah well, I have to ask. Of course the evidence for an old earth is rock solid, because it's in the rocks ..."

    Very good.

    " -- but, Cornelius, do you actually accept the scientific conclusion that the earth is old? Say yes and I'll apologize for getting you wrong."

    Yes, I certainly do. The only thing I would add is that I'm not particularly interested in the whole issue, and I don't have particularly deep knowledge beyond the usual dual isotope dating calculations. But that seems strong and, similarly, from what I understand of the history of thought, the whole age question seems to be much less metaphysically laden than evolution.

    I've read some of the primary literature, and some good historical works, but not a great deal. It seems to be the inverse of evolution. Whereas evolution is metaphysically laden and has substantial scientific problems (with positive evidences as well, of course), the science behind the age question seems to have only little metaphysical influence, and very strong empirical evidence.

    So I'm definitely on board with the scientific conclusion for the old earth, but if you want me to quantify my position more precisely I'd need to take a closer look as the scientific details.

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  77. Douglas,

    "Peter has never observed hammers falling on Pluto either -- or Alpha Centauri A, or on any of the countless planets/stars in the Andromeda galaxy."

    However, planets have been discovered around other suns thereby proving the univerrsality of gravity. It is a proof a claim by an observation. Seeing is believing. Evolution may be true, and I am certainly not qualified to comment on your work, or many of the details you raise. It is true that if you go deep enough into the Russian egg the theory of gravity will lack explanatory power, however, at least on one level - observations of planetary orbits - it does have observable verification of how it works. This is qualitatively different from evolution which has yet to show one creature evolving into another (not bacteria to bacteria|).

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  78. Fair enough. I was wrong and I apologize. I think once you've agreed that historical science works in the case of the age of the earth, your arguments against inference in historical science in other cases are sunk, but that's a different debate.

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  79. Nick:


    "Fair enough. I was wrong and I apologize."

    Apology accepted and I forgive you wholeheartedly. That was easy because I wasn't really offended, but I am disappointed when otherwise sharp people like yourself fail to transcend the traditional, parochial battle lines. There really is something more here than "evolution is a fact and those who disagree are dumb creationists," or "creation is a fact and those who disagree are dumb atheists."

    Unfortunately many folks gravitate toward these comfortable trenches, and in something of a Hegelian thesis-anti thesis, actively seek each other out, to justify their position. They'll even label anything "out there" as the enemy. Believe me, I'm not the enemy.


    "I think once you've agreed that historical science works in the case of the age of the earth, your arguments against inference in historical science in other cases are sunk, but that's a different debate."

    Sigh. You're smarter than that. Surely not all inferences (in the historical sciences, or otherwise) are equal. It would be quite an example of fallacious protectionism to claim legitimacy for your own inference based on the powerful evidence for ... *another* inference. Surely we haven't sunk that low.

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  80. Peter Wadeck: However, planets have been discovered around other suns thereby proving the univerrsality of gravity.

    A more accurate analogy would be the historical formation of the Solar System. We can observe the mechanisms involved, gravity, pressure, heat, and so on. We can observe distant nebula in what certainly appears to be various stages of collapse, stars at various places in their supposed aging cycles. And recently, centuries after Bruno hypothesized their existence, strong evidence of planets around other stars. Yet, we can't directly observe the formation of the Solar System.

    Similarly, we can observe the mechanisms of evolution, selection, variation, speciation, and so on. We can't directly observe the historical transitions — of course! — but we do have evidence of such a history. The world is not as it once was, and we have clear evidence of historical change. Fish to amphibians to reptiles to mammals to primates to hominids to you, just to trace a single lineage.

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  81. Zachriel,

    " We can't directly observe the historical transitions — of course!"

    We are in complete agreement up to this point. Nor can we replicate them in a laboratory.

    " — but we do have evidence of such a history."

    Yes, but not conclusive evidence, otherwise the debate would be over and the number of creationists would be akin to the flat earth society.

    .

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  82. Actually, the problem with those famous "mountains of evidence" is not that they are not conclusive, but that they are not real* evidence -- for the piling up of those imaginary mountains begins with assuming the very thing the non-existent mountains are claimed to have established.

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  83. Ilion -


    the piling up of those imaginary mountains begins with assuming the very thing the non-existent mountains are claimed to have established.


    Isn't that exactly how you test a hypothesis? Ask: 'what would we expect to find IF this were true...?' And then go and look/test to see if you find it. And if you do, then it is corroborating evidence.

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  84. Peter: Yes, but not conclusive evidence, otherwise the debate would be over and the number of creationists would be akin to the flat earth society.

    The scientific debate has been over for generations.

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  85. Zachriel,

    "The scientific debate has been over for generations."

    Only that evolution is a fact, but not regarding anything else, i.e. tree of life, relation between phenotype changes and dna, missing transitionary fossils, origin of life, etc.

    .

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  86. Ritchie: "Isn't that exactly how you test a hypothesis?"

    No; question-begging does not equal "testing a hypothesis."

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  87. It appears Ilion understands neither the concept of question-begging nor hypothesis testing.

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  88. One wonders: is Douglas intellectually dishonest, or simply too unintelligent to grasp the issue?

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  89. Peter Wadeck: Only that evolution is a fact, but not regarding anything else, i.e. tree of life, relation between phenotype changes and dna, missing transitionary fossils, origin of life, etc.

    As you say, evolution is a fact. Common descent is strongly supported. So we have descent with modification and divergence from common ancestors. That's pretty well Darwin's Theory of Evolution.

    Yes, the origin of life is still an open question.

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  90. Ilion -

    Then please enlighten us.

    How exactly do you test a hypothesis? And how does it differ from question-begging? And finally, what makes you say the theory of evolution is based on the latter rather than the former?

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  91. Johnjoe McFadden has given a Electromagnetic Field Theory of Consciousness/Mind. We all know that Physics describes four fundamental forces in the universe. They are Gravitational Force, Electromagnetic Force, Weak Nuclear Force and Strong Nuclear Force. They are responsible for the creation of particles, subatomic structures, atomic structures, molecules,elements etc. For natural things (life etc.)to be created, natural forces (God Forces) act in natural ways. When man operates and manipulates these forces and creates some new things or old one it is said ‘artificial’. For me everything is natural. Since man is the part of nature so everything created by him, in-vivo or in-vitro, using Forces of Nature is also natural and not artificial.

    I have given a theory of consciousness and mind as below:

    “Gravitation Force is the Ultimate Creator”, I presented this paper at the 1st Int. Conf. on Revival of Traditional Yoga, held at The Lonavla Yoga Institute (India), Lonavla, Pune in 2006. The Abstract of this paper is given below:

    “The Universe includes everything that exists. In the Universe there are billions and billions of stars. These stars are distributed in the space in huge clusters. They are held together by gravitation and are known as galaxies. Sun is also a star. Various members of the solar system are bound to it by gravitation force. Gravitation force is the ultimate cause of birth and death of galaxy, star and planets etc. Gravitation can be considered as the cause of various forms of animate and inanimate existence. Human form is superior to all other forms. Withdrawal of gravitational wave from some plane of action is called the death of that form. It can be assumed that gravitation force is ultimate creator. Source of it is ‘God’. Gravitational Field is the supreme soul (consciousness) and its innumerable points of action may be called as individual soul (consciousness). It acts through body and mind. Body is physical entity. Mind can be defined as the function of autonomic nervous system. Electromagnetic waves are its agents through which it works. This can be realized through the practice of meditation and yoga under qualified meditation instruction. This can remove misunderstanding between science and religion and amongst various religions. This is the gist of all religious teachings – past, present and future.”

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