Thursday, September 20, 2012

Boudry vs Plantinga

Alvin Plantinga is a famous philosopher who is widely respected and seems to be able to publish in all the right places. He is a theist (Calvinist) and for a long time he was at the University of Notre Dame in Indiana (USA). Since his retirement from there, he has taken a position at Calvin College.

Plantinga has long advocated the accommodationist position from the perspective of Christian apologetics. I bought his latest book, Where the Conflict Really Lies, because I'm interested in the conflict between science and religion.

I've been struggling for weeks with how to explain Plantinga's case. My problem was that I found the whole book quite ridiculous and it seemed to me that Plantina's idea of logic and rationality was much closer to kindergarten philosophy than to something one might expect from a distinguished scholar. I hesitated to say that out loud because it sounds very condescending coming from a scientist.

I had to be missing something. There must be some sophisticated philosophy in there somewhere and I just wasn't getting it. I couldn't post.

Now I don't have to. A very bright young philosopher from Belgium, Maarten Boudry, has reviewed the book at: International History, Philosophy and Science, Teaching Group NEWSLETTER. This is a head-to-head philosopher battle so nobody can accuse Boudry of being an outsider who doesn't get philosophy. It's an interesting review because Maarten doesn't seem to have gotten the message that Plantinga is a highly respected philosopher. I've had a few beers with Maarten at a pub in Gent (Belgium) and I can assure you that he's a formidable opponent. You don't want to argue with him unless you know what you're talking about.

I was pleased to see that Maarten's opinion of Plantinga's philosophy is very similar to mine. You really should read the whole review. Let me entice with a few excerpts.
Plantinga’s effort to stave off the conflict between theism and evolution is a failure. Either he is buying into creationist fantasies that have been put to rest long ago, or he is hammering on the excessively weak claim that it is logically and metaphysically possible that, all evidence to the contrary, evolution unfolds under supernatural guidance.1 But if the bar for rational belief is lowered to mere logical possibility, and the demand for positive evidence dropped, then no holds are barred. Evolution (or gravity, plate tectonics, lightning, for that matter) could as well be directed by space aliens, Zeus or the flying spaghetti monster. (I was going to include the devil in the list, but then it turns out that, on page 59, Plantinga has no qualms at all about treating the horned one as a serious explanation. There goes my reductio.) ...

Miracles are perfectly possible, Plantinga claims, because there is nothing that prevents God from suspending the natural order and intervening in the world. But even if we grant that supernatural intervention is logically possible, the conflict between science and religion strikes back with a vengeance: there is no empirical evidence for the supernatural that stands up to critical scrutiny, and plenty of failed attempts to find such evidence (Boudry, Blancke, & Braeckman, 2010; Dawkins, 2006; Fishman, 2009). But that mighty elephant in the room gets no attention from Plantinga, who instead belabors the logical possibility of miracles with a 60-page digression into the different interpretations of quantum physics and lots of fancy formalizations ... on the logical and conceptual problems plaguing divine intervention. At this point we’re no longer talking about a conflict between science and religion, but one between theology and more theology. ...

This is the philosophical equivalent of doing brain surgery with an axe....

The extensive use of logical trickery is one of the most irritating aspects of this book. At some point in chapter 3, Plantinga pretends to prove that determinism is “necessarily false”, but the formalization of determinism he starts out with is obviously wrong. The trick is pulled off with two nested conditionals in the first premise: at that point, the rabbit is already smuggled in the hat, and what follows is just formalistic window dressing. Formalization can be a means to provide clarity and rigor to an argument, and thus to enhance a philosophical debate. Alas, it can also be misused as a rhetorical ploy to disguise non-sequiturs under a tapestry of symbols. This is analytic philosophy at its worst.

The upshot of the argument in this book, according to Plantinga, is that theism is “vastly more hospitable to science than naturalism” and that this belief in an invisible creator “deserves to be called ‘the scientific worldview’” (no worries about “metaphysical add-ons” this time). This is sheer rhetorical bluster. Naturalism emerges unscathed from Plantinga’s attack, and he has done nothing that comes even close of averting the conflict between science and religion. This book will not impress anyone except those who were already convinced that science and religion can live in peaceful harmony, and even in those accommodationist quarters, it seems to have put some people off (Ruse, 2012). If this is the best that sophisticated defenders of theism can come up with, God is in very dire straits indeed.
Why aren't there more philosophers who are willing to declare openly that the Emperor has no clothes?


119 comments:

  1. I'm still struggling to understand the implied distinction between guided and unguided processes - no one (at least not Boudry, and presumably not Plantinga either) ever seems to define or explain what is meant by these terms.

    Suppose I observe two apples falling from a tree; one falls in a "guided" and the other in an "unguided" way. Will their trajectories be different? If so, how? Is the way in which apples ordinarily fall "guided" or "unguided"? What does it mean for a process like evolution to be "guided"? What on earth is the guided/unguided debate actually about - is it more than just semantics?

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    1. For the people who care, it's about whether or not God exists. For the rest of us, it's about whether or not science and evolution, and education about these, can/should be dragged into battles between theist apologists and atheist apologists.

      The atheist would say that the "random" fall of the apple is evidence against God (a little bit of evidence). The theistic evolutionist would say the apple fall could be truly random, or could be guided in some metaphysical sense that God guides everything, while unguided in a statistical or physical sense. The creationist would say God specifically, physically intervenes, at least sometimes, in apple falls.

      The agnostic (me) would say it's all a big pile of unresolvable, unanswerable angels-on-the-heads-of-pins type question, and the various answers should be left out of science and science education entirely.

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    2. But the apple's fall is not random - it falls toward the earth in a very predictable way. Is this guided or unguided falling? I'm just asking what these words _mean_, in an attempt to understand the discussion.

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    3. Hi Konrad,

      I believe that the apple's trajectory can be predicted by the Newtonian laws of physics. But now say a gust of wind makes the apple fall a little to the north of where it would have fallen if there had been no wind. Does that falsify Newtonian physics? Of course not. It means that additional forces caused our prediction to be incorrect. Now let's assume (for the sake of argument) that God had wanted the apple to fall slightly to the north of where it would fall and created the gust of wind. In that case we would say that God's intervention into the nature caused a different outcome. And we could say that the apple's fall was guided.

      If physical determinism is true, then it might be possible that God set up the Big Bang so that all future events happened in a very specific way. And we could say that it was all guided. If physical determinism isn't true, an quantum indeterminacy is true, then I think if God wants to guarantee that certain specific events occur, then it would require that God intervene to guide those events.

      Would God's intervention be detectable? Not necessarily, since we have no way of observing each and every event that happens in this universe.

      And that is Plantinga's point: Scientists may insist that all of natural history is the result of unguided events, but they have no way of confirming that this is the case. So there is no conflict between science and religion regarding this point.

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    4. All available evidence indicates that evolution is unguided and has no purpose or goal. But if a scientist says this out loud it rankles theists who claim that scientists are stepping outside the limitations of science into the realm of metaphysics. Accommodationists, like Nick Matzke, agree with them.

      Apparently, scientists are supposed to avoid stating an obvious scientific fact since it might offend theists who want to believe that God guided evolution so that it would results in humans.

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    5. I think (from these second-hand accounts) that Plantinga's argument is not just that you can never rule out a little bit of unnoticeable divine intervention but that adding that in somehow enriches the science. Martaan has quite properly "called bullshit" on that argument.

      However the one unanswered question, perhaps calling Martaan's whole argument into question, is what that black cloth thingie is in his portrait. Is it some bunting on the window, which he just happens to be standing in front of, or is he outside and it is a scarf blowing in the wind, attached to his left shoulder? Is there any known way of gathering evidence to decide this? Could it be Divine Intervention?

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    6. Bilbo: ok, and presumably if god wanted the apple to fall where it would without wind He would cause an absence of wind and through this intervention again control the outcome - thus also guided. So under this meaning of "guided", all processes are guided. What, then, is the purpose of introducing the terminology?

      Larry: when you say "evolution is unguided", what do you mean by that? How would it be different if it were guided? Is it different from the apple example?

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    7. Joe: Yes, the scarf(?) puzzles me ever time Larry posts the picture. But to address your other point, I don't see anyone arguing that. I do see the (correct) argument that God could direct all physical events, including evolution, without violating (the Copenhagen interpretation of) quantum physics. This is compatible with all our observations if we assume that He makes a point of avoiding detection by fairly sophisticated statistical methodology and that He does not prioritize the avoidance of suffering (theologians do attempt to justify both of these assumptions).

      Unfortunately I do not see evidence that Plantinga understands the concept of Occam's razor or any of the several ways it is formalized in statistics (e.g. hypothesis testing, model selection, multi-model inference, Bayesian model comparison, posterior predictive checking) - or perhaps he doesn't admit these as part of science. This is sad because it's the part of science where the actual conflict lies.

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    8. The scarf: If you look carefully, the end is resting on a part of the window pillar that is jutting out. It is as though Boundry stood there for the photo, then threw his scarf over his shoulder and the end caught on this jutting bit.

      As for the guided vs unguided apple. The direction of the fall of the apple is not what this debate is about here. No-one expects the apple to fall up. It will always take the most direct root down, until an object blocks it's fall, be that a bucket or the ground.

      The debate about guided vs unguided is refering to the timing of it's fall. At what point in its development, will the apple fall? It could be said that every apple falls at exactly the same point in development - when they reach X. But how does the apple 'know' when it has reached X? Is there some inherent wisdom in apples to know 'now' is the time to fall and not 5 minutes before or after? Or is it simply the apple continues to grow until the stem which attaches it to the branch can no longer take its weight?

      One the one hand, every apple falling when they reach that X factor could be said to be guided, as in it was designed or programmed into apples at the beginning. On the other hand, the fact no-one can really know when the apple will fall can be said to be unguided and therefore, random.

      I'm not a scientist, philosopher or any boffin, just someone who can think and see both sides of an argument.

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    9. frankly, the scarf resting on the pillar looks as if it was posed that way..but why? It would be a strange pose to arrange. Maybe I am seeing design where none exists. The distal end looks like a reclining black cat peering out the window.

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    10. The placement of the scarf is no accident, it was guided.

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    11. MJA: How is the timing of the fall conceptually different from the direction? The context of the discussion so far is that wind may or may not be involved, so the direction is not predictable. As you point out, one could argue that either "guided" or "unguided" applies - this is because we have no agreed-upon definition for these terms.

      My points are:
      1) the discussion makes no sense until there is clarity about the meaning of the words being used; in this case, clarity would imply that we know what it would take for a process to be "guided" vs "unguided", and
      2) the categories "guided" and "unguided" are worse than useless if we choose their meaning such that everything in the universe per definition falls in the same category.

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    12. In the sense that folks appear to be using the terms here, "guided" = teleology, "unguided" = natural processes with no need for (indeed, no evidence of) teleology.

      When saying "no evidence of teleology," this means no evidence of the sort of supernatural being popularly referred to as a deity. (Naturally occurring Masters of the Universe would merely change the venue of the evolution inquiry, not resolve it in a different direction.) That is, any deity worthy of the name is reputedly blessed with mighty (in many cases unlimited) powers and knowledge. A proponent of teleology per deus would then have to posit a deity with such powers employing them in part (1) to do the enormous work of causing the universe to operate the way it does, and in part (2) to cover up any least sign that it had done (1), and indeed any least sign of its own existence. Pathological shyness? An antic sense of humor ("la-dee-dah, think I'll bury some dinosaur bones here, then I'll stick a bunch of propellers on the back ends of several trillion bacteria, and let Adam and Eve's great-great-great-etc. grandkids go nuts trying to figure it all out...")? Seems pretty absurd, so I think I'll decide to live my life as if it isn't so.

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    13. This atheist would never claim, as NickM asserts, that the
      "random" fall of [an] apple is evidence against God."

      Nor is it evidence against the existence of leprechauns, unicorns, or Batman.

      It seems to me that there is a lack of clarity in these discussions with regard to the presence and absence of evidence.

      Platinga, NickM, and other accommodationists argue that since it is logically impossible to rule out the invisible hand of the leprechaun guiding the fall of an apple, we must give some credence to the idea.

      I argue that prior to giving that credence, there must be some objective, empirical evidence in support of it. I maintain that the utter absence of such evidence suffices as a reason to reject the notion.

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    14. Larry wrote: "All available evidence indicates that evolution is unguided and has no purpose or goal."

      What available evidence are you referring to, Larry?

      Larry also wrote: "Apparently, scientists are supposed to avoid stating an obvious scientific fact since it might offend theists who want to believe that God guided evolution so that it would results in humans."

      Apparently, Larry, you think it is "an obvious scientific fact" that evolution was not guided by God. What scientific experiments did you do to confirm this?

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    15. Konrad wrote: "...ok, and presumably if god wanted the apple to fall where it would without wind He would cause an absence of wind and through this intervention again control the outcome - thus also guided. So under this meaning of "guided", all processes are guided. What, then, is the purpose of introducing the terminology?"

      Let's say that if God had not intervened, then there would have been no wind. Then we could say that the apple falling and landing where we predicted it would land is a case of an "unguided" event. Of course, presumably either God wanted or didn't care if the apple fell at that predicted location.

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    16. Bilbo asks,

      Apparently, Larry, you think it is "an obvious scientific fact" that evolution was not guided by God. What scientific experiments did you do to confirm this?

      The same sorts of experiments that I did to prove there was no Santa Claus and no tooth fairy. You don't believe in the tooth fairy do you? :-)

      Seriously, one can't prove a negative. The onus is on those people who make the claim for God-guided evolution to provide (extraordinary) evidence for their claim. All we can say is that right now there is no such evidence.

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    17. Bilbo: "Let's say that if God had not intervened, then there would have been no wind." Er, in other words we can't have wind without divine intervention? Really?

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    18. Re Bilbo

      I think that Mr. Bilbo is missing the point. If god subtly guiding the evolutionary process so that his intervention is undetectable is posited, then what does such a proposition bring to the table. Via parsimony, the proposition is unnecessary. Or as Laplace put it in the early part of the 19th century, we have no need of that hypothesis.

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    19. NickM:
      "The agnostic (me) would say it's all a big pile of unresolvable, unanswerable angels-on-the-heads-of-pins type question, and the various answers should be left out of science and science education entirely."
      The problem is, however, that any attempt to explain how things work has implicit metaphysical implications that people are quick to jump upon. I don't think many atheists really worry about the logical possibility of God (or Zeus) guiding mutations, it might be possible but a lack of evidence or meaningful definition means it's a useless conjecture. If we don't have any evidence for pin-dancing angels, then why worry about how to count them?

      But the implicit metaphysical implications go the other way too. God's hand being absent from the scientific account does lead theists to reject the science or take the science as being anti-God. I think it's no surprise that there's a lot of work trying to resolve the logical compatibility with theism, and to emphasise the boundary between science and the metaphysical implications - it's not the atheists who are the problem. We make the problem about atheists overreaching out of what I can only assume is political expediency; God is what needs to be resolved, not the lack of God.

      In other words, I think that your view and the atheist views are pretty much the same. The contention is whether or not absence of evidence can mean evidence of absence, and in an empirical view the mere logical possibility doesn't give any resolution to the theistic point of view. God could have intervened, but there's no reason to think that God did. This vindicates the atheists, puts the theist on the back-foot, and the accommodationist tries hard to give consolation to the theist by chastising the atheist.


      "It's unknowable" is a cop-out! It's only unknowable in a way that's indistinguishable from irrelevance.

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    20. "Laurence A. MoranThursday, September 20, 2012 8:36:00 PM

      All available evidence indicates that evolution is unguided and has no purpose or goal."


      This is extremely debatable. Convergence under natural selection could dominate mutational randomness, and it could be if you re-ran the Big Bang 1000 times, you'd get intelligent humanlike critters 1000 times, simply because it's an adaptive peak that is eventually explored in any complex biosphere. It's fine if your gut tells you something different, but you can't pretend that it's established scientific fact.

      "But if a scientist says this out loud it rankles theists who claim that scientists are stepping outside the limitations of science into the realm of metaphysics. Accommodationists, like Nick Matzke, agree with them.

      Yep, although I stipulate by longstanding protest against the "accommodationist" label.

      Apparently, scientists are supposed to avoid stating an obvious scientific fact since it might offend theists who want to believe that God guided evolution so that it would results in humans."

      Not really. What I'm worried about mostly is this: if scientists and science educators took seriously Larry's advice, and taught in public schools that science has answered these cosmic age-old metaphysical questions, they'd get sued for violating the prohibition on government establishment of religion, and they would lose. Judges would like nothing more than an opportunity to show that they will apply the First Amendment just as strictly to atheist apologetics as to theist apologetics.

      The last thing science education and evolution education need are those sorts of entirely avoidable legal disasters.

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    21. In other words, I think that your view and the atheist views are pretty much the same. The contention is whether or not absence of evidence can mean evidence of absence, and in an empirical view the mere logical possibility doesn't give any resolution to the theistic point of view. God could have intervened, but there's no reason to think that God did. This vindicates the atheists, puts the theist on the back-foot, and the accommodationist tries hard to give consolation to the theist by chastising the atheist.

      As a Bayesian, I know that absence of evidence is only evidence of absence in the context of a model that says presence=high probability of evidence. But, many models of God say that if God exists, what should be expected is entirely or virtually entirely the reliable action of natural laws.

      Likelihood is the probability of data on the model

      data=things work by natural laws

      likelihood(data | God doesn't exist) = ~1
      likelihood(data | God exists) = ~1

      If the likelihoods are the same, any difference in the posterior probability is due to the difference in the prior probabilities that people put on the models. Which is fine, but, scientifically, we want the data to determine our conclusions, not the priors. If the data is unable to do that, then all you've got is personal opinions about the priors, which doesn't get us anywhere.

      "It's unknowable" is a cop-out! It's only unknowable in a way that's indistinguishable from irrelevance.

      I'm sorry, I learned somewhere that science was about being careful and restrained and staying close to the data and testable hypotheses, not about making dramatic declarations about ineffable and poorly-defined metaphysical matters on the basis of ambiguous data and assertions of bravery.

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    22. "But, many models of God say that if God exists, what should be expected is entirely or virtually entirely the reliable action of natural laws."
      "I'm sorry, I learned somewhere that science was about being careful and restrained and staying close to the data and testable hypotheses, not about making dramatic declarations about ineffable and poorly-defined metaphysical matters on the basis of ambiguous data and assertions of bravery."
      This is what I don't get, Nick. In the first instance, you chastise me for not considering an interventionist God that is indistinguishable from non-interventionist God. Then in the second, you chastise me for pointing out that scenario.

      Nowhere did I say that it was a scientific conclusion, but made clear that it was about how people take the science to metaphysical conclusions about their position. That is to say, the logical possibility of certain gods and certain interventionist acts doesn't change the atheist point one bit, the unanswerable that you laid out as your "agnosticism" would be the same point atheists make. A conception of God that's empirically indistinguishable from naturalistic observations makes such a conception useless.

      I repeat, I'm not talking about scientific conclusions here. I started my response to you by explicitly talking about metaphysical implications and how the issue inevitably brings them up. The atheist position (metaphysical, not scientific) is vindicated by the science, while many theisms (metaphysical, not scientific) struggle. The reconciliation of any given theism with evolution is an exercise in theology, and is best left to the believer. It's not the atheist who has a problem with the science, it's certain religious believers.

      If any atheist says "Evolution must mean all gods couldn't possibly exist", then I can agree that the atheist is overstepping their bounds. But who is doing that?

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    23. Larry wrote: "The same sorts of experiments that I did to prove there was no Santa Claus and no tooth fairy. You don't believe in the tooth fairy do you? :-)

      Seriously, one can't prove a negative. The onus is on those people who make the claim for God-guided evolution to provide (extraordinary) evidence for their claim. All we can say is that right now there is no such evidence.
      "

      So in other words, Larry, your claim that there was obvious scientific evidence that God did not guide evolution is false. At best, all you can say is that there is no scientific evidence that God did guide evolution. The point is that the lack of scientific evidence does not prove that God did not guide evolution. This means there is no conflict between the scientific evidence and the belief that God guided evolution. Hence, there is no conflict between science and religion on this point.

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    24. Konrad: "Er, in other words we can't have wind without divine intervention? Really?"

      I was making an assumption for a particular occurrence of wind at a particular place and time. I thought that was obvious.

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    25. SLC: "I think that Mr. Bilbo is missing the point. If god subtly guiding the evolutionary process so that his intervention is undetectable is posited, then what does such a proposition bring to the table. Via parsimony, the proposition is unnecessary. Or as Laplace put it in the early part of the 19th century, we have no need of that hypothesis."

      I didn't miss the point at all, SLC. Plantinga wrote a book, one of whose purposes was to show that there was no conflict between science and religion regarding the question of evolution. So far, neither Larry nor you have shown that there is a conflict. One could believe that God guided evolution, and there is no scientific evidence that indicates that God didn't do so. No conflict.

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    26. Nick "The Acommodationist" Madzke says,

      This is extremely debatable. Convergence under natural selection could dominate mutational randomness, and it could be if you re-ran the Big Bang 1000 times, you'd get intelligent humanlike critters 1000 times, simply because it's an adaptive peak that is eventually explored in any complex biosphere. It's fine if your gut tells you something different, but you can't pretend that it's established scientific fact.

      Nick, Nick, Nick, ... it's not my "gut" that tells me that evolution looks unguided. And it's certainly not established scientific fact, either. Nobody says that unless it's being proposed as a strawman argument.

      Nothing that *I* know about evolution indicates that life HAD to arise given the right conditions. Nothing that *I* know about evolution says that complex cells with mitochondria and chloroplasts HAD to form. As far as I know there's no evidence to suggest that most phyla of animals HAD to arise during the Cambrian explosion. Nobody says that our ancestors were pre-destined to survive multiple mass extinctions. I've never seen a scientific theory that say highly intelligent brains HAD to evolve.

      The history of life on earth covers about 3.8 billion years of evolution. There were no intelligent beings for at least 3.4 billion years and none that could worship god(s) for the first 3.79 billion years. Does that look guided to you? Does it look like evolution aimed toward filling a particular niche that only intelligent animals could fill?

      If you think there's something that *you* know about evolution that *I* don't then please share it.

      You are free to make up extraordinary just-so stories if you like but the reason you have to do that is precisely because everything we know about science points in the opposite direction. We are the product of a long series of accidents and if the tape of life were replayed there's no evidence that intelligent life would HAVE to evolve.

      Why don't you try defending the idea that evolution was destined to produce lilacs or lobsters and see if anyone takes you seriously? After all, it's the same logic you use to defend the theists.

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    27. Re Nick Matzke

      This is extremely debatable. Convergence under natural selection could dominate mutational randomness, and it could be if you re-ran the Big Bang 1000 times, you'd get intelligent humanlike critters 1000 times, simply because it's an adaptive peak that is eventually explored in any complex biosphere.

      Not even Ken Miller argues for this position any more. I have pointed out on Panda's Thumb that an argument can be made that intelligence might have a selective advantage and thus the evolution of intelligent life might be inevitable. However, such intelligent life need not bear much resemblance to humans. Had the asteroid collision 65 million years ago not taken place, the Troodons might have eventually evolved into intelligent birdlike creatures as described by paleontologist Dale Russell.

      Re bilbo

      According to Plantigna, the hypothesis that god is guiding evolution is untestable. Therefore, it is not a scientific proposition. Plantigna is just making shit up by proposing an untestable hypothesis.

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    28. Nothing that *I* know about evolution indicates that life HAD to arise given the right conditions. Nothing that *I* know about evolution says that complex cells with mitochondria and chloroplasts HAD to form.

      But, it's an empirical fact that endosymbiosis has evolved many times. Mitochondria and chloroplasts are just the most famous examples.


      As far as I know there's no evidence to suggest that most phyla of animals HAD to arise during the Cambrian explosion.

      Well, the word "phyla" is best dispensed with, but it's clear that any number of complex adaptations evolved not once but multiple times mostly-independently during the Cambrian. E.g. legs, camera eyes, complex brains, etc. If we went back in time and killed off all but one of the wormlike ancestors of the major Cambrian clades, probably what would have happened is that a bunch of new clades would evolve. They wouldn't be "the same" animals as we have now, but they would have had legs, eyes, brains, etc. And we wouldn't know the difference hundreds of millions of years later.


      Nobody says that our ancestors were pre-destined to survive multiple mass extinctions. I've never seen a scientific theory that say highly intelligent brains HAD to evolve.

      That's the point of the convergence argument -- if it's correct, then this stochasticity doesn't matter much in the long run, various adaptive peaks will eventually be explored given enough time. Pterosaurs went extinct in the K-T, but birds diversified and bats evolved. Maybe if there had been no K-T extinction, some dinosaur group would have evolved a group of social hunters, and a subgroup of them would have specialized in an even more intelligent direction (as someone mentions below). Those guys would then sit around thinking how special and unique THEY were.

      The history of life on earth covers about 3.8 billion years of evolution. There were no intelligent beings for at least 3.4 billion years and none that could worship god(s) for the first 3.79 billion years. Does that look guided to you? Does it look like evolution aimed toward filling a particular niche that only intelligent animals could fill?

      That's not the argument. The argument is that a niche for intelligent, social organisms would exist in any complex biosphere, and given enough time, evolution would explore it. This allows the possibility (but doesn't prove, of course) that some Universe-creating agent could create a Universe with the purpose of producing intelligent life, and yet never have to lift a finger beyond just letting natural laws work.

      It's all wild speculation, of course, but so is the opposite opinion.

      If you think there's something that *you* know about evolution that *I* don't then please share it.

      Sure. The view I've highlighted above is put forward by Simon Conway Morris. Conway Morris developed it explicitly in response to Stephen Jay Gould. Gould used Conway Morris's work on the Cambrian "phyla" to suggest (in _Wonderful Life_) that evolution was dominated by random, stochastic events, and not-so-subtly suggested that this was evidence that we lived in a world free of any higher power.

      But Conway Morris, who, unlike Gould, is an actual expert on the Cambrian, disagreed, and has elaborated the convergence argument in response.

      As it happens, Kenneth Miller agrees with Gould's scientific position, but disagrees with Gould's metaphysical position. Dawkins, on the other hand, agrees with Conway Morris scientifically, but reaches opposite metaphysical conclusions.

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    29. Lessons:

      (1) Respected scientists are on both sides of the scientific question. You don't get to just assert that the Gouldian view is the only plausible scientific position.

      (2) The assertions that people make connecting some scientific position to some metaphysical conclusion are actually incredibly dubious, and mostly expressions of gut feelings.

      Just remember:

      Gould: evolution dominated by randomness; atheist
      Miller: evolution dominated by randomness; theist
      Conway Morris: evolution dominated by convergence; theist
      Dawkins: evolution dominated by convergence; atheist

      You are free to make up extraordinary just-so stories if you like but the reason you have to do that is precisely because everything we know about science points in the opposite direction. We are the product of a long series of accidents and if the tape of life were replayed there's no evidence that intelligent life would HAVE to evolve.

      A good summary of Gould. But the convergence position doesn't have to assert that it would have HAD to have happened, just that it would be reasonably probable.

      Why don't you try defending the idea that evolution was destined to produce lilacs or lobsters and see if anyone takes you seriously? After all, it's the same logic you use to defend the theists.

      Both pollination-attractors and legged crawly guys have evolved multiple times, that hardly is an argument that they are improbable events over geological history.

      There were no intelligent beings for at least 3.4 billion years and none that could worship god(s) for the first 3.79 billion years. Does that look guided to you?

      Not particularly, but I suspect a Universe-creator would have a rather different sense of time than us.

      I just don't see anything convincing that brings science down on one side or the other of the God question. The arguments that attempt to do this, on either side, are dubious and weak. If one is really rigorously committed to applying science to metaphysical questions, then agnosticism is the correct answer at the moment.

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    30. "I just don't see anything convincing that brings science down on one side or the other of the God question."
      What about HADD?

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    31. Nick Matzke says,

      I just don't see anything convincing that brings science down on one side or the other of the God question. The arguments that attempt to do this, on either side, are dubious and weak.

      Come on, Nick. I know you don't believe that. Theists have been making claims about their god(s) for millennia and science has been steadily whittling away at those claims for just as long. Today, in the 21st century, it takes entire books by "sophisticated" theologians to defend even the most fundamental "God questions" and, even then, they are hard-pressed to come up with something that passes simple tests of logic and common sense.

      Science has had, and continues to have, a great deal to say about the claims on behalf of personal god(s).

      It's okay to be an accommodationist, Nick, but for you to dismiss the impact of science on religion by saying that their arguments are "dubious and weak" seems a bit of a stretch, even for you!

      If one is really rigorously committed to applying science to metaphysical questions, then agnosticism is the correct answer at the moment.

      The scientific way of knowing is being applied to testable claims such as whether life looks as though it has been designed by supernatural beings. It is being applied to claims that there is a universal Moral Law. It is being applied to claims that prayer works, or that we have a soul, or heaven exists, or that certain miracles have happened.

      It is disingenuous of you to declare all these investigations out-of-bounds simply by declaring that they are "metaphysical questions." That's nonsense. Even the theists are feeling the heat as their cherished "facts" are being destroyed by the scientific approach to knowledge. Up until now, they have always maintained that their beliefs are rational and based on evidence. They can't do that any more.

      BTW, if you really don't see anything convincing then why don't you believe in one of the gods?

      Delete
    32. Nick Matzke says,

      Lessons:

      (1) Respected scientists are on both sides of the scientific question. You don't get to just assert that the Gouldian view is the only plausible scientific position.


      Good point. This is obviously a controversial topic with respected scientists on both sides. Unfortunately one side (yours) also has a fair number of the other kind of scientist. :-)

      So, Nick, if we agree that some of these issues are controversial, can I look forward to you pointing this out every time you make the claim that science is restricted to "methodological naturalism" and that all conflicts between science and religion are "metaphysical"?

      If there's ever another Dover trial, will you do your best to make sure the judge knows the truth about the controversy rather than just presenting one side as though it was acknowledged as a universal consensus among philosophers and scientists? Will you call Maarten Boudry and Jerry Coyne to the stand along with Robert Pennock and Ken Miller?

      I don't think you will do this because you really don't believe that there's another legitimate side to the debate.

      Delete
    33. Larry wrote: " ... it's not my "gut" that tells me that evolution looks unguided. ...Does that look guided to you? Does it look like evolution aimed toward filling a particular niche that only intelligent animals could fill?"

      That sounds like your "gut" talking, Larry. Certainly not your science.

      Delete
  2. "You don't want to argue with him unless you know what [you're] talking about."

    I won't argue with Maartan because I am not qualified to do so, but I do know the difference between "your" and "you're."

    ReplyDelete
    Replies
    1. Veronica,

      I don't mind that you correct my spelling and grammar but I do mind, greatly, that you don't do it gracefully by simply noting that I made a typo that needs correcting.

      I also know the difference between "your" and "you're" and it's very insulting for you to imply that I don't.

      Do you deliberately peruse my posts looking for these minor mistakes or does it come naturally to you because you are perfect and never make such mistakes, ever?

      Delete
    2. Some fans of your blog (including this one) might feel that the large numbers of these kinds of typos (even spelling the subject of this article wrong twice) indicate a lack of respect for readers. Maybe more proofreading would be helpful.

      Delete
    3. @anonymous

      Thanks. The idea that my typos might be interpreted as a lack of respect for readers is something that I never thought of. It certainly would explain Veronica's attitude. As for proofreading, I can assure you that it's not that simple. Some people have a talent for spelling and they instantly pick out all errors whenever they see them. I am not one of those people. It's hard work for me. I wish I were like you and didn't have to worry about such things.

      Delete
    4. Larry: The idea that my typos might be interpreted as a lack of respect for readers is something that I never thought of.

      Yahhh!!! Larry, that’s why you went out your way to misspell my name a couple of days ago, when you were confronted with a scientific issue that you could not handle (pun intended!!! ; I emphasize this because I made few jokes before that you did not take them as such):

      (Laurence A. Moran, Wednesday, September 19, 2012 9:34:00 AM

      “Claudi Bandewa says”

      ”However, this study needs to be done very carefully because of the variable rate of selection at different loci.

      Natural selection plays almost no role in the construction of phylogenetic trees from sequence data. We can safely ignore it.”


      Seriously, Larry, how can you say that:

      Natural selection plays almost no role in the construction of phylogenetic trees from sequence data. We can safely ignore it

      I think that goes against the foundation of the entire theory of evolution?

      Also, what about the questions in the previous post:

      Back to the paper in discussion here, do you think it is valid? I mean, was the rate of mutation directly associated with the rate of transcription?

      Delete
    5. "Some people have a talent for spelling and they instantly pick out all errors whenever they see them."

      That's me. And I am always willing to share my gift with the world.

      Delete
  3. Larry,

    I suggest a better review by the philosopher Paul Draper (one of the editors of Philo):

    http://ndpr.nd.edu/news/31324-where-the-conflict-really-lies-science-religion-and-naturalism/

    ReplyDelete
    Replies
    1. Aha, Draper offers a definition of "guided": "planned or otherwise directed or shaped by some personal agent". Under this definition, guided evolution is just a synonym for Intelligent Design. So is Plantinga really just discussing whether Intelligent Design conflicts with science?

      I wonder whether ID advocates will be upset (because of the clear distinction this makes between ID and science) or happy (because of Plantinga's conclusion of no conflict)?

      Delete
    2. Draper: But even if the sensus divinitatis is not in play, Plantinga thinks that design beliefs resulting from [intelligent] design discourse like Behe's are rational and that evolutionary biology provides only a partial defeater because it has not established the biological possibility of unguided evolution leading to the sorts of biochemical systems Behe discusses. Plantinga concludes that such discourse supports theism, but that it is hard to say how much.

      I might be more inclined to agree with this if my exposure to discourse about the nature and history of life on earth were limited to books and articles written by advocates of intelligent design. But when I consider discourse about imperfect design in nature and discourse comparing the extremely slow process leading to biological complexity to the much faster process by which human beings have produced machines of great complexity; when I also take into account the fact that while both human design and natural selection, unlike divine design, involve a trial and error process of "selecting" what works and discarding what doesn't; and when I further consider discourse about the reproductive cycle of the guinea worm and the often grotesque and horrific effects of that cycle on human beings who host that parasite; then I feel an inclination to reject design, and a very strong inclination to reject divine design (i.e., benevolent design supported by power and wisdom limited only by logic). Indeed, I would consider anyone who responds to such discourse by increasing the credence they give to theism to be in a state of suboptimal cognitive health.

      Delete
    3. Diogenes,

      ...anyone who responds to such discourse by increasing the credence they give to theism to be in a state of suboptimal cognitive health.

      Indeed.

      How can Platinga distinguish his sensus divinitatis from delusional disorder?

      Delete
  4. If one has faith in god and/or Genesis then its up to people to demonstrate God/Genesis is the the origin of anything that exists.
    They must show, prove, processes and results.
    Have they done so?
    Saying they have isn't proof they have?
    Its up to evolutionists to prove their case since there is and always was another case for origins.
    for hundreds of millions in North America they have not proven it and for much of the rest they just have faith in evolutionists.
    The case for evolution has reached very few people in any substantial way.
    !
    Saying there's a conflict between science and religion is really saying one's side conclusions are based on science and the other side isn't.
    It's already a not well done opening statement for origin contentions.

    Creationists deny evolution is based on "science" or any more then our criticism!
    Evolutionism first must prove it is the result of science.
    Truly I find , since Darwin, its just lines of reasoning from small packets of data and then coupled to unrelated subjects to back up it's claims. Subjects like geology or genetics etc.

    Wrong ideas in science couldn't possibly be that scientific.
    Prove they are!

    ReplyDelete
    Replies
    1. "The case for evolution has reached very few people in any substantial way."

      A true point and always worth making. Critics might point out its complete lack of relevance to this thread, but I claim it as a beautiful demonstration of the infinite monkey theorem. A success for random typing!

      Delete
    2. Evolutionism first must prove it is the result of science.

      Even a wiki search could have answered that...

      http://en.wikipedia.org/wiki/Experimental_evolution
      http://en.wikipedia.org/wiki/Antibiotic_resistance

      Delete
  5. You don't want to argue with him unless you know what your're talking about. SB:

    You don't want to argue with him unless you know what you're talking about.

    I couldn't resist.

    ReplyDelete
    Replies
    1. While we're at it - Boudry's first name is spelled in three different ways.

      Delete
  6. Forget philosophy and start thinking about psychology. People who want to see agency in the world will see agency in the world, whether it's there or not. The question is: Why?

    ReplyDelete
    Replies
    1. They could be physiologically predisposed to see agency in the world. This could be an interesting research program in neuropsychology.

      Delete
  7. Another mixed review by Thomas Nagel, a philosopher is here http://www.nybooks.com/articles/archives/2012/sep/27/philosopher-defends-religion/

    Nagel's intrigued but not convinced by Plantinga.

    It's late and I'm too lazy to set up an account

    Willy

    ReplyDelete
  8. Larry,

    Minor correction: You wrote Maartan, and Martaan. As shown above his picture, his name is Maarten. You might want to correct that in your blogpost, as several people in the thread seem to be copying your spelling of his name.

    ReplyDelete
  9. Prof. Moran,

    You wrote: "All available evidence indicates that evolution is unguided and has no purpose or goal."

    But this is not correct. God may well have caused evolution to proceed exactly as it has, and we have no means of expecting that if God guided evolution then it would have proceeded differently. Meanwhile, we have no prior probability of God's existence. These missing pieces prevent us from ruling against God's guiding Hand on the grounds of evidence.

    Let me make a suggestion: It is painfully obvious that we should reject the idea that God guides evolution, at least in everyday practice. But this is not because the evidence somehow prevents us from accepting it. Instead, it's because the God hypothesis posits objects and events which, almost by definition, fall well outside the broadest-according regularities of our experience, and hence are inaccessible via the inductive reasoning on which evidence depends.

    So for instance, we should reject the idea that the world popped into existence last Thursday. It's not that we have evidence that the world is older than that---we don't! Rather, Last Thursdayism just isn't the sort of hypothesis that is accessible via inductive inference. The God hypothesis is a bit like that. We can't rule it out with evidence, nor can ever find evidence to support it; and so the hypothesis ends up being useless to us.

    But we must be cautious in our denouncing these useless hypotheses. I agree that we ought to denounce them; but we can't just say that there is all this evidence against them when clearly that is not the case. There is something far deeper which is wrong with them. They don't even qualify in the first place for evaluation with evidence!

    Regards,
    Ben

    ReplyDelete
    Replies
    1. @Ben Wallis It's not that we have evidence that the world is older than that---we don't!

      In general it is wise to steer clear of double negatives as the above statement very clearly demonstrates.

      What is not very clear about it is what it actually means but I parse it as a claim that there is no evidence for an old earth.

      A general observation on hypotheses, why should we privilege any particular non-evidence based hypothesis, be it guided evolution via supernatural agents or last Thursdayism ?

      There are an infinite number of such hypotheses and we as mere mortals have a finite amount of time to deal with them. Why would you want to waste precious time and resources dealing with such rubbish ?

      Delete
    2. Ben Wallis writes,

      But this is not correct.

      Yes it is. When I said that all available evidence indicates that evolution is unguided that is an absolutely correct statement.

      God may well have caused evolution to proceed exactly as it has, and we have no means of expecting that if God guided evolution then it would have proceeded differently.

      God, or the Flying Spaghetti Monster, may well have tricked us into believing that evolution is unguided when, in fact, he/she/it has secretly guided evolution in an undetectable manner. In that case my statement would still be correct because I have been successfully duped, just as God intended.

      I agree that we ought to denounce them; but we can't just say that there is all this evidence against them when clearly that is not the case. There is something far deeper which is wrong with them. They don't even qualify in the first place for evaluation with evidence!

      I understand your point but out there in the real world there are tons of people who disagree. They believe that there is solid evidence that God made humans. All of those beliefs conflict with science (expect strict Deism).

      Delete
    3. Prof. Moran,

      Thanks for the response. However, I was kind of hoping to convince you of my position. It's really not all that far from yours, at least insofar as it directs us to avoid taking hypotheses like the existence of God too seriously. So we've got that common ground, at least. But let me see if I can persuade you that the God hypothesis is even worse off than you make it out to be.

      Now, you APPEAR to insist that we really do have evidence against God's guiding Hand in evolution. (You only say this about guidance in general, but I'm talking about God's guidance in particular.) But I gave an argument against this. To summarize: In order to have evidence for or against competing hypotheses, we need something like prior probabilities, and also some expectation of what we should observe under the various competing scenarios. But we are missing both of these pieces in the case of the hypothesis that God guided evolution.

      I am curious, which part(s) of this argument do you reject?

      You responded to my analogy by saying that even if God tricks us into believing evolution is unguided, nevertheless you will still be correct in asserting that we have evidence against his guidance "because I have been successfully duped, just as God intended." But this does not follow. If God dupes you into believing that evolution is unguided, that says nothing to whether we actually have evidence that evolution is unguided.

      Regards,
      Ben

      Delete
    4. Ben Wallis,

      Now, you APPEAR to insist that we really do have evidence against God's guiding Hand in evolution. (You only say this about guidance in general, but I'm talking about God's guidance in particular.)

      That's not a fair representation of what I said. I say that, using the scientific way of knowing, it looks like the history of life was not guided. In other words, there's no reason to suspect that something unusual is going on that might have caused the history of life to unfold in ways that can't be explained by natural processes.

      Now, if someone is a believer in God then they probably believe that God created life and/or humans. If they also believe in evolution then they might think that God guided evolution. That's fine, but I see no evidence that might cause ME to believe such as story or even entertain it as a hypothesis. Similarly, I see no evidence that might cause me to suspect that the Flying Spaghetti Monster guided evolution when someone suggests that possibility.

      Thus, I'm not really interested in finding evidence AGAINST the belief that God guided evolution. It's sufficient to say that science concludes that there's no evidence to suggest we even need to explain evolution by any non-naturalistic means. Is this what you think?

      But I gave an argument against this. To summarize: In order to have evidence for or against competing hypotheses, we need something like prior probabilities, and also some expectation of what we should observe under the various competing scenarios. But we are missing both of these pieces in the case of the hypothesis that God guided evolution.

      Scientific hypotheses are supposed to explain something that needs explaining. In this case, the hypothesis that God guides evolution is supposed to explain something about the history of life that can't be explained by natural processes. Since I don't see any such "something," I don't see any reason for God hypotheses. I have no need of such hypotheses and neither should anyone else if they understand the science.

      I don't even bother to look for evidence AGAINST the God hypothesis because the hypothesis isn't needed.

      I don't know if this is what you mean. is it?

      Delete
    5. Prof Moran,

      Okay, cool---I pretty much agree with all of that.

      So I guess the point I just want to stress is that even though

      (1) we have no evidence whatsoever that evolution has been guided by God,

      nevertheless, that is not the same as the notion that

      (2) we have evidence that God did not guide evolution.

      When you say things like, "all available evidence indicates that evolution is unguided," it sounds like you're endorsing (2). But (2) is false, and that's what I have been arguing. If you agree, then that's all I wanted. : )

      Regards,
      Ben

      Delete
    6. Ben Wallis says,

      When you say things like, "all available evidence indicates that evolution is unguided," it sounds like you're endorsing (2). But (2) is false, and that's what I have been arguing. If you agree, then that's all I wanted.

      Cool.

      Let's try and go (together) one more baby step.

      If a theist claims that there IS evidence that evolution is guided by God then is it okay (by you) to respond by saying, "That claim conflicts with the scientific evidence we have available to us."

      In other words, is there a conflict between science and any religious belief that includes the idea that God created life or used evolution to guide it to a certain outcome?

      Delete
    7. Prof. Moran,

      Unfortunately no, I cannot follow you there.

      If you really do agree that we don't have evidence against God's guiding Hand in evolution, then in what sense do you think it's true that the notion of God's guiding Hand conflicts with the evidence?

      There is a kind of conflict between science and religion, but it's not due to the evidence. Rather, it's due to the fact that when scientists study some part of the natural world, in order to do their science properly they must assume, almost a priori, that God isn't involved in disturbing that part of the natural world. But it's not about evidence. It's about the assumptions necessary for the methodology.

      Regards,
      Ben

      Delete
  10. It is philosophical and theological questions such as these that ultimately have driven me away from the Christian faith. I wrestled with them for years, at the same time that I was expanding my understanding of cosmology and evolutionary biology. Eventually I realized that it was simply much easier, cognitively, to assume that God was either not involved in the natural world or, if he was, his intervention was completely undetectable and therefore irrelevant to my life.

    It has been tremendously liberating, freeing me up to focus on the real and tangible, rather than the theoretical and insubstantial.

    ReplyDelete
    Replies
    1. Agreed completely. This greater cognitive ease is the point of Occam's razor, which Plantinga seems to ignore. See also my response to Joe Felsentein above.

      Delete
  11. When I said, "Natural selection plays almost no role in the construction of phylogenetic trees from sequence data. We can safely ignore it.

    Claudiu Bandea asked,

    Seriously, Larry, how can you say that:

    I think that goes against the foundation of the entire theory of evolution?


    Claudiu Bandea appears to be a microbiologist at the Center for Disease Control (CDC) in Atlanta, Georgia (USA). We can safely assume that he is a scientist. We know that he writes and comment frequently on topics such as evolution.

    It would, therefore, be reasonable to assume that he has a basic understanding of evolution.

    When phylogenetic trees are constructed from sequence data the technique involves aligning homologous sequences from numerous species. The phylogenetic distance between any two species is determined from the differences in their sequences.

    Everything we know about evolution points to the conclusion that the vast majority of those differences are due to nearly neutral substitutions, insertions, and deletions in the DNA sequences. Only a miniscule fraction could be due to positive selection at a particular locus.

    When we build the tree we notice something quite remarkable. In general, all the lineages show a similar number of changes from their common ancestor. In other words, there's an approximate molecular clock.

    Why? Because these are neutral changes evolving at the mutation rate exactly as predicted by modern evolutionary theory (population genetics). That's not consistent with changes due to natural selection.

    I wish everyone knew this. It means that 99% of all long-term evolutionary change is due to fixation of nearly neutral alleles by random genetic drift.

    ReplyDelete
    Replies
    1. It is possible that Claudiu might have thought you were referring to the construction of phylogenetic trees by _nature_, rather than our reconstruction of trees from sequence data.

      BUT even for phylogeny construction from sequence data, selection is important and is taken into account, especially for coding sequences. To construct a phylogeny you must first construct an alignment; both protein sequence alignments and the phylogenies constructed from them are critically informed by amino acid exchangeabilities, as quantified in substitution matrices such as BloSum. The unequal exchangeabilities of different amino acid pairs results (mainly) from purifying selection. Using better models of selection to obtain improved substitution matrices leads to improved phylogeny reconstruction. E.g. as demonstrated here: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0028898

      Also, I'm sure you are aware that the molecular clock is only _very_ approximate. Selective pressure certainly varies from branch to branch and we have tools for quantifying this variation (http://mbe.oxfordjournals.org/content/early/2011/06/11/molbev.msr125.abstract). We also have tools for identifying sites that evolve under purifying or positive selection on a subset of branches (http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002764). All of these effects affect branch lengths.

      Sorry about the self-citations - of course there are also other studies demonstrating these points, but I can find the urls of my own publicatoins more quickly.

      Delete
    2. Larry Moran: Claudiu Bandea appears to be a microbiologist…

      Thanks for the introduction, Larry! However, it might have been better to use your energy to answer this question, which you have already dodged 2 times (see my comment above):

      “Back to the paper in discussion here, do you think it is valid? I mean, was the rate of mutation directly associated with the rate of transcription?”

      I also want to say that, unlike you, I’m firmly convinced that you do have “a basic understanding of evolution”

      I think that the readers should know the context in which you made the statement that:

      Natural selection plays almost no role in the construction of phylogenetic trees from sequence data. We can safely ignore it.

      It was in a discussion ( here) about a paper published in a highly respected science journal, Journal of Bacteriology, which presented strong experimental evidence for the hypothesis that the rate of mutation is directly associated with the rate of gene transcription (i.e. expression).

      This means that there is more genetic variation produced in the genes that are highly transcribed compared to those that are silent or transcribed at low levels, and hence they would have a differential rate of evolution.

      Although Larry dogged the questions I was asking, he made an excellent point, which could lead to a very good study (maybe a PhD dissertation, anyone?) and would farther test the hypothesis that the rate transcription impacts the rate mutation.

      The study was to compare the length of phylogenetic branches of the genes that are expressed at high level in the germ line vs those that are not. In expanding on this proposal, I made the point that the focus of the analysis should be on sequences that are not under selective pressure in order to better capture the rate of mutation. And, then is when Larry said:

      Natural selection plays almost no role in the construction of phylogenetic trees from sequence data. We can safely ignore it.

      Delete
    3. OMG, no, don't listen to Larry on this one!

      If there is a causal effect it could be in either direction or there could be a mutual cause - you seem to be suggesting that higher transcription rates lead to higher mutation rates, but how would transcription (rather than replication) errors affect mutations in DNA? Instead, my guess would be that highly expressed genes may be preferentially located in mutation hotspots because it would be easier for them to have evolved there in the first place. At any rate it is entirely believable that such a correlation might exist.

      BUT it is well established that highly expressed genes evolve more slowly - i.e. regardless of the mutation rate, the substitution rate is lower. This is not surprising, because it is reasonable that purifying selection would be stronger in highly expressed genes. So we can absolutely _not_ ignore the role of selection here: it _inverts_ the correlation.

      Instead of working with phylogenetic branch lengths, which are strongly affected by selection, you should use a model that estimates mutation rates separately. I guess the simplest would be to use the synonymous substitution rate (estimated under a codon model, e.g. using software at www.hyphy.org) as a proxy for mutation rate (the argument being that, to a rough first approximation, synonymous substitutions can be thought of as neutral - in which case their rate is proportional to the mutation rate). For an introduction to codon models and related methodology, I recommend "The phylogenetic handbook", 2nd ed 2009, edited by Lemey, Salemi and Vandamme.

      Delete
    4. Larry: "It means that 99% of all long-term evolutionary change is due to fixation of nearly neutral alleles by random genetic drift."

      This is absolutely unknown - trying to get a ballpark idea of that number is a major goal of molecular evolution. Please don't misinform your readers by claiming to know something you don't.

      Delete
    5. To clarify: we have some idea what % of _mutations_ evolve near-neutrally. The majority evolve under purifying selection, a sizeable minority are near-neutral, and perhaps around 1%(?) are adaptive.

      But we really do not know what % of _observed changes_ are fixed due to drift. Here all the mutations that don't make it (the vast majority) are thrown out and we are left with some unknown % that are fixed despite purifying selection against them (a tiny fraction of the huge number of mutations under purifying selection), some unknown % that are near-neutral (a less tiny fraction of the still large number of neutral mutations), and some unknown % that are adaptive (a relatively large fraction of the tiny number of adaptive mutations) - this last % is larger than the % of adaptive mutations, but we don't know how much larger - my rough guess would be around 10%, but it could be much higher or much lower. The rest (my rough guess is somewhere around 90%) are due to drift. Larry's figure of 99% might be right, or it might be way off.

      Delete
    6. konrad: It was in a discussion ( here) about a paper published in a highly respected science journal, Journal of Bacteriology, which presented strong experimental evidence for the hypothesis that the rate of mutation is directly associated with the rate of gene transcription (i.e. expression).

      This is the opposite of what you would expect from transcription coupled repair. This is a mechanistically very well established pathway whereby highly transcribed sequence are repaired more efficiently, that is, mutated less frequently, than non-transcribed sequences.

      Delete
    7. Claudiu,

      Please think about this very carefully.

      1. You are extrapolating very specific results into a realm where they might be irrelevant.
      2. Those experiments were about "adaptive mutagenesis." They were not about what kinds are the most frequent to fix in a population.
      3. They had a very specific experimental design aiming at showing a possible mechanism by which mutagenesis could occur that could be mistaken for "directed" mutagenesis. Namely, because the gene in question is over-exressed, it might suffer a higher rate of mutation. For this they mutated the gene (made it functionless), and followed the rate of reversion. Again. not necessarily having anything to do with which kinds of mutations normally get fixed in a population.
      4. You would have to agree then that these experiments say nothing about the kinds of mutations normally accumulating in populations, and thus, neutral and semi-neutral mutations might play a role in the construction of phylogenetic trees, which, according to the mathematical models behind neutral and semi-neutral theory, tend to be neutral and semi-neutral. Thus, naturally selected mutations might contribute little to phylogenetic trees compared to these neutral and semi-neutral mutations.

      Thus, your conclusions from one little paper are too far fetched. A non-sequitur would be the proper word. I understand how you would get confused and mistaken, but careful examination of the experiments and what they tell you should suffice for you to notice your mistake.

      Best!

      Delete
    8. Ups sorry, I forgot the caveat, but it was mentioned by Konrad. I consider purifying selection as natural selection despite many rather think of positive selection as "Darwinian" which makes the whole thing confusing. It has been demonstrated quite well that functional regions have lower mutation rates than regions where the specific sequence is not important (like such junk as pseudogenes). Thus, natural selection (purifying/negative) plays a sizeable role in phylogenetic trees when build with functional sequences.

      So, sure genetic drift. Neutral and semi-neutral mutations, but not truly purely random mutations.

      In any event. Claudiu is making a huge mistake in extrapolating from that study on "adaptive mutagenesis" into phylogenetic trees.

      Delete
    9. Konrad: construction of phylogenetic trees by _nature_, rather than our reconstruction of trees from sequence data

      That’s a keeper Konrad! Can I get permission to use it occasionally?

      Konrad: you seem to be suggesting that higher transcription rates lead to higher mutation rates, but how would transcription (rather than replication) errors affect mutations in DNA?”

      Here are 2 excerpts from the original 1990 paper, entitled “A Mechanism for Adaptive Mutagenesis”, which addresses your question (you can take a look at this very short paper here at Sandwalk: http://sandwalk.blogspot.com/2012/05/on-difference-between-evolutionary.html):

      “Cells possess several repair mechanisms for reducing the mutation rate (3). A decrease in the repair efficiency would result in an increased rate of mutations. Transcription may interfere with the repair process by obstructing the activity of repair enzymes. Transcription interference has been reported in other cases (4,5).

      During transcription, the DNA template becomes locally single stranded which makes it more susceptible to attack by some mutagenic agents. This is another way in which transcription may increase the rate of mutation


      I agree with you points, including:

      “BUT it is well established that highly expressed genes evolve more slowly - i.e. regardless of the mutation rate, the substitution rate is lower. This is not surprising, because it is reasonable that purifying selection would be stronger in highly expressed genes. So we can absolutely _not_ ignore the role of selection here: it _inverts_ the correlation.”

      However, the principal point of the discussion was whether the conclusion of the study by Pybus C. et al. http://www.ncbi.nlm.nih.gov/pubmed/20435731 that: "These experiments clearly demonstrate an influence of transcription on the adaptive mutation phenomenon" was correct, or not?

      For whatever reason, Larry doesn’t want to answer this question. What do you think Konrad?

      Delete
    10. AJP: This is the opposite of what you would expect from transcription coupled repair.

      This is good point on a very interesting and well-studied phenomenon. What happens is that during transcription, the transcription elongation complexes get stalled at various DNA lesions (e.g. nucleotide mismatch). To be able continue, the nucleotide excision repair machinery needs to fix the lesions. There are two important things here to consider: first, is that these are pre-existing lesions, and that after these lesions are fixed the resulting sequence can be the wild-type sequence, or a mutated sequence.

      Delete
    11. @Negative Entropy

      I hear you, and for that reason I tried to keep the focus on the study by Pybus C. et al. It was Larry who extrapolated my ‘little hypothesis’ to another organisms (such as those that have globin and a germ-line) and to phylogenetic trees and branches; I just followed! So, it is Larry’s ‘fault’ that we are having this interesting scientific discussion!

      As interesting as this subject on “adaptive mutagenesis” might be, the ‘junk DNA’ topic is very popular now becouse of ENCODE. And, unfortunately, Larry refuses to engage in a constructive discussion and evaluation of my model on the evolution of genome size and the protective function of junk DNA (see: http://sandwalk.blogspot.com/2012/09/athena-andreadis-writes-for-sceintific.html)

      Delete
    12. konrad says,

      Also, I'm sure you are aware that the molecular clock is only _very_ approximate.

      Yes, but it's pretty much what you expect of a stochastic clock.

      Selective pressure certainly varies from branch to branch and we have tools for quantifying this variation ...

      Using certain assumptions you can write code that will quantify almost anything you want. It doesn't PROVE that there are significant differences in the fitness of different alleles in different lineages and it doesn't prove that these effects are anything more than rare events in a huge background of evolution by random genetic drift.

      Delete
    13. Cladiu Bandea says,

      Thanks for the introduction, Larry!

      You're welcome. Always glad to help. Please try and remember the lesson.

      However, it might have been better to use your energy to answer this question, which you have already dodged 2 times (see my comment above):

      I'm not interested in discussing that paper.

      Delete
    14. konrad says,

      BUT it is well established that highly expressed genes evolve more slowly - i.e. regardless of the mutation rate, the substitution rate is lower. This is not surprising, because it is reasonable that purifying selection would be stronger in highly expressed genes. So we can absolutely _not_ ignore the role of selection here: it _inverts_ the correlation.

      Here's a better way of saying that.

      Genes have a particular adaptive function that depends on the sequence. Natural selection, in the form of purifying selection, prevents evolution in those parts of the genes that are essential (i.e. conserved). So, we don't see any evolution (defined as a CHANGE in the frequency of alleles) in those parts of the gene.

      Almost all of the evolution we see (CHANGE) is due to fixation of nearly neutral alleles by random genetic drift.

      Instead of working with phylogenetic branch lengths, which are strongly affected by selection ...

      No they aren't, unless you are being EXTREMELY selective in your choices.

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    15. konrad,

      Larry: "It means that 99% of all long-term evolutionary change is due to fixation of nearly neutral alleles by random genetic drift."

      This is absolutely unknown - trying to get a ballpark idea of that number is a major goal of molecular evolution. Please don't misinform your readers by claiming to know something you don't.


      We can easily construct phylogenetic trees using orthologous regions of junk DNA. Do you honestly think that there might be some underlying selection going on in such a tree?

      We frequently construct phylogenetic trees using the amino acid sequences of orthologous proteins. In some cases—like all the ones I've worked with—we know the structure of the protein. We observe that most of the changes we see cluster in parts of the sequence and these parts usually map to parts of the protein that do not come in contact with other proteins and are not near the active site.

      Often those parts of the protein are on external loops and often they are associated with insertions and deletions. Sometimes we see all sorts of radical substitutions like lysine for proline and sometimes we only see similar substitutions like valine for leucine.

      Everything we know about biochemistry and about the individual protein suggests that almost all of these substitutions have no effect on the function of the protein.

      This is not something that is "unknown" and mysterious. It's something that is totally consistent with what we know and, in some cases, it's something that has been experimentally verified. You would have to be completely ignorant of all of this to maintain that any significant fraction of those substitutions are due to selection in different lineages. Not only would that be inconsistent with biochemistry, it would be inconsistent with our understanding of population genetics.

      Delete
    16. Claudiu: Interesting, thanks for the excerpts. Re the Pybus paper, I only read the abstract so can't give an informed opinion. But by "acquisition of mutations", don't they really mean substitutions? I.e. the acquisition process is affected by selection? In that case, the claim is consistent with stronger selection acting on highly transcribed genes, the difference being that usually the stronger selection is purifying, but here it seems to be artificially induced positive selection.

      Delete
    17. Larry: "it doesn't prove that these effects are anything more than rare events in a huge background of evolution by random genetic drift"

      Actually these analyses are based on rigorous models of the type that you have stated more than once on this blog that you do not understand. That doesn't leave you very well placed for argument by assertion. In fact the evidence that events detected by these methods are not just random drift is pretty robust.

      Selection analysis is essentially based on the idea of having a null expectation for how often we expect to see substitutions under drift and then looking (in a statistically rigorous way) for cases where we see substitutions way more often. The only explanations for this are:

      1) the baseline rate may be too low - this is a real concern because we normally use the synonymous rate as a proxy for the neutral rate, and we know that synonymous changes are under slight purifying selection, and that the strength of this selection varies from site to site. But it is still a good approximation and will only affect the cases where the inferred positive selection is very weak.

      or

      2) the mutation rate might be varying wildly all over the place. We ignore this possibility because it is not consistent with observations.

      or

      3) you could try to argue that some of the model assumptions are incorrect in a way that has led them to artificially inflate the number of inferred substitutions to the point of false statistical significance - this is a very constructive thing to do if you can do so successfully, and typically leads to the problem being patched with improved estimates - at present I am not aware of hugely problematic assumptions that invalidate the state-of-the-art, rather most of the assumptions bias us towards _conservative_ inference

      or

      4) the sites with the excess substitutions are experiencing positive selection.

      This is a pretty simple argument. If you can demonstrate a problem with it, it would be a significant advance and the molecular evolution community would appreciate it if you published your critique (which obviously should address the more rigorous version of the argument as found in the literature, not my hastily typed summary above).

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    18. Larry:

      You claim that we don't see changes in the presence of purifying selection. This is false - selective strength varies gradually between strong purifying selection and near neutrality, with accompanying variation in how much change is seen.

      "We can easily construct phylogenetic trees using orthologous regions of junk DNA. Do you honestly think that there might be some underlying selection going on in such a tree?" - Sorry, I should have made it clearer that I am discussing protein coding regions - I assume the transcribed regions in the comment that sparked this of are coding.

      I don't have numbers to hand, so the guesses I gave above are very rough. We don't normally quantify it as a % of substitutions, partly because most substitutions are not even observed. I do not think there are currently any trustable estimates of that quantity. As I said, my guesses are very rough and could be completely wrong.

      Delete
    19. konrad says,

      Larry: "it doesn't prove that these effects are anything more than rare events in a huge background of evolution by random genetic drift"

      Actually these analyses are based on rigorous models of the type that you have stated more than once on this blog that you do not understand.


      Point taken. I do not understand the kinds of mathematical analyses that you and others do and I have no desire to invest the time and effort that it would take to learn them.

      It's the same situation we see with the ENCODE results. I can't objectively critique the computational part of the methodology because it's all pretty much a black box to me.

      What I can do is discuss the conclusions and how they fit with my own areas of expertise. The idea that most of our genome is functional, for example, would require me to reject a pile of data that says otherwise.

      Similarly, the methods you use to reach the conclusion that most substitutions are adaptive are mysterious to me. But your conclusion doesn't fit with what I know about biochemistry, evolution, and population genetics.

      I'm not prepared to declare that you must be right and all that other stuff must be wrong just because you are using a technique I don't understand.

      I'll try and be more careful with my wording in the future. Meanwhile, you could try harder to explain why your conclusions seem so at odds with what we conclude by looking at the actual substitutions from a biochemical and evolutionary perspective. (I assume you understand those fields?)

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    20. Larry,

      Similarly, the methods you use to reach the conclusion that most substitutions are adaptive are mysterious to me. But your conclusion doesn't fit with what I know about biochemistry, evolution, and population genetics.

      I don't think that Konrad means that most substitutions are adaptive, but rather that most are not maladaptive. So you are right, most of what we see is from nearly-neutral to neutral, then perhaps adaptive. But, at the same time, we can't say that most of what we see is random because we don;t see the maladaptive ones (or perhaps rarely, as long as the organisms can still survive).

      After all, regions with no functions (pseudogenes, regions between genes other than the regulatory signals, et cetera), have a higher rate of mutations fixed than, say, coding ones, thus indicating that not any mutations gets fixed within functional parts. I think that's the confusing part. If we say that natural selection plays almost no role in phylogenetic trees build with coding genes, we are claiming that any mutations can make it into the sequence. Genetic drift might be neutral to semi-neutral, but it is not that random.

      I know, seems, and is, a problem with semantics. But these seem pretty important semantics.

      Best.

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    21. Laurence A. Moran says: Cladiu Bandea says

      Here you go Larry, misspelling my name, again! In an earlier comment (see above), I was “Claudi Bandewa ”! This seems to be an intentional act, which is a sign of relief; for a moment there, I thought that my questions/issues are putting Larry under too much stress!

      Larry says : I'm not interested in discussing that paper

      That paper (see above) is about a study showing that, at least in some organisms under certain conditions, a high rate of transcription can increase the mutation rate in some gene. This paper supports a hypothetical mechanism for adaptive mutagenesis that I proposed more than two decades ago.

      In another, parallel thread( http://sandwalk.blogspot.com/2012/09/athena-andreadis-writes-for-sceintific.html), I tried to convince Larry and other readers to take a look at an old model on the evolution of genome size and the protective function of the so called ‘junk DNA’ (jDNA) that might resolve these long standing and enigmatic issues.

      I was rather surprised that Larry has been hesitant to engage in an open and thorough evaluation of either of these 2 ideas, but I’m sure that he has good reasons. So, in respect for him, I’ll not be challenging him on these problems, unless he asks me.

      Instead, I’m going to focus on issues that should have untainted scientific implications. One of these issues happens to be at the heart of biochemistry, which is Larry’s profession and passion, as reflected by the subtitle of his blog: Strolling with a skeptical biochemist.

      I’m talking about protein biochemistry; specifically, protein folding. Protein folding is central to understanding the structure and functions of the proteins, the workhorses of molecular processes in all organisms on Earth, as far as we know.

      Interestingly, protein folding, more precisely protein misfolding, has been fundamental in defining one of the most remarkable biological phenomenon in the last few decades, the prion phenomenon, as well as in studying and understanding one of the most devastating group of diseases, including Alzheimer’s disease, Parkinson’s disease, ALS, CJD, Huntington’s disease and other devastating neurodegenerative diseases, which have been defined and labeled as protein misfolding diseases.

      As I stated in two previous comments on this blog ( http://sandwalk.blogspot.com/2012/09/how-do-intelligent-design-creationists.html#more; http://sandwalk.blogspot.com/2012/09/the-story-of-you-encode-and-human.html), I think that both of these working hypotheses, the protein misfolding concept and the prion hypothesis, which have directed most of the work in these fields for decades, are flawed.

      Many readers might think they don’t have the expertise to evaluate these working hypotheses, but that’s not true. In fact, it might be huge advantage to have a fresh, unbiased approach. And, as I pointed out:

      “What it’s lacking in the field is an open and comprehensive evaluation of the prion hypothesis and protein misfolding theory based on biological and evolutionary principles, common sense reasoning and resilient inquiry. The field needs your skepticism and inconvenient questions, and your front-line energy of searching for the truth

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    22. konrad: But by "acquisition of mutations", don't they really mean substitutions? I.e. the acquisition process is affected by selection?

      They placed a defective Leu C allele, carrying a missense mutation, under the control of an IPTG-inducible promoter and compared the accumulations of Leu C revertants under conditions of transcriptional induction and repression. Leu C reversions increased significantly in parallel with the induced increase in transcription levels.

      In order to detect them phenotypically, the Leu C revertants were indeed positively selected in this experiment, but the presumption is that all possible nucleotides changes at the missense position, as well as at the other nucleotide positions in this gene, were generated more or less randomly and at similar rates.

      Delete
    23. I did not claim that most substitutions are adaptive - the reason I gave some rough guesses was to make it clear that I do _not_ think that. We do not know whether the % of adaptive substitutions is closer to 1% (i.e. more or less negligible, as Larry claims) or closer to 10% (a non-negligible minority) or even higher. What we do have is a large number of characterised instances of adaptive substitutions and these do tend (when this information is available) to correspond to functional sites in proteins.

      The other important point (particularly for Claudiu's proposed study) is that we cannot ignore substitutions that are fixed despite weak to moderate _negative_ selection. Of course the numbers depend on where you put the boundary between nearly neutral and negatively selected substitutions.

      Finally, we don't know how many undetected substitution-reversion pairs there are where a deleterious substitution is followed by an adaptive reversion.

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    24. Claudiu: unfortunately this is just not a good venue for the technical discussion you are after. And while you're probably right that readers here _could_ go and read up on that particular field with relative ease, I suspect most of us are just too busy with already existing projects...

      Also, I really don't think Larry is misspelling your name on purpose - e.g. there is still a mistake in the spelling of Maarten Boudry's name in the main post _after_ it was pointed out and he went back to correct it. So it's clearly not just you.

      Delete
    25. @konrad

      My ‘rant’ on Larry’s misspelling my name was intended to be a rather humorous take; sorry if it didn’t came that way!

      About the other point, I like the fact that here at Sandwalk and other blogs which address very broad issues, such as junk DNA, adaptive mutagenesis and central dogma. Unfortunately, these issues are usually only tangentially addressed, from a broad significance, in the conventional scientific literature, and it shows! Take, for example, ENCODE’s conclusion; I think no reasonable scientist, member of the Sandwalk readership, would have put forward such an unsupported paradigm and misleading conclusion. BTW, on the paper by Pybus C. et al., I indeed went a little more technical because it was central to our discussion on adaptive mutagenesis phenomenon.

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  12. That review was written with a scalpel. It was enormously satisfying to see Plantinga's sophistries get demolished so systematically.

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  13. Boudry: Plantinga’s core argument is that evolution by natural selection cares about survival and reproduction only, not about truth. The naturalist, who believes his own cognitive faculties to be the product of evolution, has no reason to put trust in his own beliefs, including his belief in evolution itself. Naturalism is thus self-defeating.

    Strange then, that Boudry didn't address Plantinga's core argument philosophically, because that is exactly where the difficulty lies. To give us just-so stories about how natural selection wired our brains to discern truth is to assume the conclusion!

    You *cannot* (C.S. Lewis made this clear) prove reason, any argumentation assumes the validity of thought and reason.

    And therein lies the difficulty for the philosophical naturalist.

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    Replies
    1. And I'm not quite sure what this has to do with the dialog between the naturalist and the supernaturalist. It seems it stops it--and stops it completely.

      "Your arguing is unreasonable!" (naturalist)

      "And your reasoning is unreasonable!" (supernaturalist)

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    2. lee_merrill Saturday, September 22, 2012 9:20:00 PM

      [...]

      Strange then, that Boudry didn't address Plantinga's core argument philosophically, because that is exactly where the difficulty lies. To give us just-so stories about how natural selection wired our brains to discern truth is to assume the conclusion!


      "Creatures inveterately wrong in their inductions have a pathetic but praiseworthy tendency to die before reproducing their kind."

      -- W V O Quine

      You *cannot* (C.S. Lewis made this clear) prove reason, any argumentation assumes the validity of thought and reason.

      Who cares? When I get on a plane, I'm not worried about whether the reasoning used in its design can be well-grounded philosophically. The only ground I'm concerned about is the one I don't want the plane to hit when it's not supposed to.

      Besides, Lewis was wrong. The word 'proof' has a number of meanings, including this (from Merriam-Webster):

      7: a test applied to articles or substances to determine whether they are of standard or satisfactory quality

      In fact most of the definitions embody the principle of testing something to determine whether it meets a preset standard or target.

      By this principle our science - and our reasoning - are regularly and often successfully proven by testing against observable reality. And what is that but the correspondence theory of truth?

      And therein lies the difficulty for the philosophical naturalist.

      Not just philosophical naturalists, anyone who relies on reasoning to support a particular position, including Lewis and Plantinga.

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    3. Survival ought to be correlated with ability to reason. But of course our brains are fallible, and we don't need Plantinga to tell us that.

      If different people with fallible brains argue with each other and the result is transmitted to others, they will tend to correct each other's fallacies. So the corpus of thought is much less fallible than the thought of any one person.

      Where does this happen? Here, for example.

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    4. > Ian Spedding: Who cares?

      Evidently Boudry cares, for he tries to do this, to prove that reasoning is valid.

      > Joe Felsenstein: Survival ought to be correlated with ability to reason.

      And here we have another example! The essential problem is that you have to assume that reason is valid, before you argue for the validity of reason. This involves assuming your conclusion.

      > Ian: Not just philosophical naturalists, anyone who relies on reasoning to support a particular position, including Lewis and Plantinga.

      Let's take it as an axiom, and not try and prove it! But then if philosophical naturalism is true, then again we have no reason to believe in our reason.

      This starts to get into Lewis' argument, reason cannot derive from non-reason, we never in life admit any exceptions to this rule.

      The theists may however claim that reason derives from an intelligent self-existent creator, which avoids the difficulty.

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    5. lee_merrill reasons thusly:

      And here we have another example! The essential problem is that you have to assume that reason is valid, before you argue for the validity of reason. This involves assuming your conclusion.

      Reason is imperfect, but gets better when people argue and point out holes in each others' arguments. Yes, I am assuming that reason (properly applied) works. I am not arguing in favor of reason. That would be ridiculous as it would have to be accomplished by rational arguments. Yes, I am assuming it works.

      I am rather arguing that evolution will (in reasonably intelligent beasts) tend to create the capability of reason. You have missed entirely what I was arguing.

      You're assuming that reason works too, because you're making what you hope is a rational argument. So there.

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    6. Lee,

      Plantinga is far from defending the stupidity of the TAG argument, which has been shown to be fundamentally flawed (I have no time nor desire to go through it because it is a nauseatingly rhetorical piece of crap, and I rather not vomit in public). What he is claiming, if you read carefully, is that because evolution is about survival, and survival does not necessarily mean knowing "the truth," then we cannot consider that evolution thus will produce something like valid intelligence. Then, we cannot trust the validity of evolution because the idea of evolution would have come from thinking, which we should not be able to trust because the process of evolution does not necessarily lead to truth (wow, even there I already see how deeply stupid his argument is). Now, don't get me wrong, I know that Plantinga is far from engaging in an already well-known-to-be-crap argument such as the TAG (like Lewis did). However, he is making several just-as-crappy mistakes in order to get his sophism going. To make the case for poor reasoning produced by evolution, he assumes such things as that each and every response towards survival requires a separate event in evolution (if you don't believe me, look for his arguments online, they are quite available). For example, that running from a tiger is a very specific response. So would be running from a lion, and so on. That's quite imbecilic to begin with. He continues making quite the idiot of himself when discussing biological processes that are so far from reality that the only explanation would be utter ignorance (or dishonesty, and I do consider that). Ironically, ignorance about biological processes perpetrated by the very same ass-hole who criticized Dawkins for not being a philosopher yet engage in philosophical problems. That's just the biology. Plantinga goes on to make basic mistakes in philosophy: for example, that regardless of his claims about what evolution can and cannot provide, he cannot conclude in such an absolutist forms as he does.

      OK, too much written already. I bet you won't get it. Care to try and disappoint and actually get it?

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    7. > Joe Felsenstein: I am not arguing in favor of reason.

      Are we having fun yet? Well, telling how reasoning came to be, and why it is valid, would seem to be just that.

      > You're assuming that reason works too, because you're making what you hope is a rational argument.

      Yup. It's the only way to fly. But we also must insist that reason (now that we can reason) must not come from non-reason.

      > Negative Entropy: Plantinga is far from defending the stupidity of the TAG argument, which has been shown to be fundamentally flawed...

      But Lewis' argument is not the TAG argument--see "C.S. Lewis' Dangerous Idea: In Defense of the Argument from Reason" for a relatively recent review.

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    8. Lee,

      (For your TAG rephrasing, in order to claim that reason is circular you are using reason. Thus, your claim is self-refuting because it depends on what it is trying to challenge. Your only way out would be to try and challenge reason without using it. Good luck with that.)

      Now, Lewis did defend the TAG. Yet now you now present me with another piece of crap by Lewis that I had not seen before: this misnamed "argument from reason." We could visit it carefully, but for starters, it looks a lot like an argument from incredulity mixed with some layers of equivocation fallacies (and a non-sequitur as phrased in the original). Just like most arguments for "God." Example, you wrote that reason cannot come from no-reason. Well, for starters, this is not Plantinga's crap, and I hope you understand that. Now, that cleared, your phrase is a non-sequitur. Care to try and explain how and why so?

      (This might not be a good place for this exchange, so I hope we can finish it quickly and painlessly. So try and be concise and clear. Avoid fallacies like the plague and we might be in pretty good shape.)

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    9. This might not be a good place for this exchange, so I hope we can finish it quickly and painlessly.

      This is quite unlikely. Having witnessed Lee debate before (for literally months defending one specific point by Michael Behe) he won't let this go. He'll continue endlessly with his own particular brand of opaque, incoherently written, smugly supercilious verbiage. It's not worth the effort.

      Delete
    10. Thanks anonymous. From my experience with any "apologist" using this kind of argumentation, I shall expect what you warn me about. If Lee answers, he will concentrate as many fallacies as possible within one sentence. If so I will say so, and just quit the exchange.

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  14. "This is the philosophical equivalent of doing brain surgery with an axe."
    This is great! My favourite line from the review.

    One thing I am curious with Plantinga's EAAN is if any biological implications follow. One could, as a layman it seems plausible to me at least, make certain predictions about humans from a biological standpoint. If naturalism is to be defeated by this argument, would that translate into parts of our DNA that would show a divine hand? Or, perhaps, would it have neurological or developmental implications where the sensus divinitatis is either something in addition to our regular brain processes, or that it's something that's shaped into our brain processes?

    It seems odd to me that this rests entirely on a priori argument. We have, after all, good reason to think evolution works, so an immediate objection to the EAAN is that we have good evidence that we evolved, no evidence of an outside hand, and human cognition is what it is. The mere logical possibility of an undetected hand is irrelevant. The argument, it seems to me, isn't so much right or wrong but irrelevant. If it cannot lead to any meaningful predictions about the human organism, then what can it really show? To me, the argument would have far more weight once it has experimental applications and empirical support. Until then, it's just a convenient way of shirking that scientific responsibility to say something meaningful about human evolution.

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    1. Kel, Paul Griffiths and I address this very point in our book chapters forthcoming:

      When do evolutionary explanations of belief debunk belief? http://philpapers.org/rec/GRIWDE

      and

      Evolutionary debunking arguments in three domains: Fact, value, and religion http://philpapers.org/rec/WILEDA-3

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    2. > John Wilkins: "The simplest reply to evolutionary scepticism is that the truth of beliefs in a certain domain is, in fact, connected to evolutionary success, so that evolution can be expected to design systems that produce true beliefs in that domain."

      But how does this not involve assuming that reason is valid, to make your argument?

      P.S. I can't seem to download your paper there.

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    3. It does not matter Lee. What matters is that what he is saying follows. Deviating attention from the argument to whether he assumes reason or not is inconsequential. A red-herring. Useless rhetorical bullshit.

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    4. lee_merrill: But how does this not involve assuming that reason is valid, to make your argument?

      We all assume (you and the rest of us) that reason is valid. And if one of us assumes that their reasoning is infallible, well then they are being silly.

      And so what is the difference between us? I agree with Negative Entropy that this issue is a red herring, a nonissue.

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    5. Lee:
      "But how does this not involve assuming that reason is valid, to make your argument?"
      You don't go into a debate over which system best describes the motion of the planets by complaining that the argument presupposes an external world.

      John:
      Thanks for the papers, I'm halfway through the first paper now.

      My biggest concern when it's come to philosophical arguments is that I completely miss the mark when understanding what they're about. It's nice to know that I asked a question that is at least worth asking.

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    6. > Joe Felsenstein: We all assume (you and the rest of us) that reason is valid.

      Yes, unless the claim is then made that reason comes from unreason. Then the foundation totters.

      > And if one of us assumes that their reasoning is infallible, well then they are being silly.

      So let's not be silly!

      > And so what is the difference between us?

      Because I'm not about to try and prove our reasoning is valid, with an argument. Which I believe was attempted by Boudry and others here. That's well, being silly...

      Regards,
      Lee

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    7. Lee,

      I tried several times to show you that Boudry did not try and prove that reasoning was valid. I repeat, that was not Plantinga's bullshit, and thus that was not in Boudry's answer. Plantinga's bullshit is different to that. How many times before you read both Boudry and Plantinga carefully and notice that your argument is not the one made in the discussion?

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  15. Why aren't there more philosophers who are willing to declare openly that the Emperor has no clothes?

    Here we have a great example of base rate neglect. Ever since I started philosophy I have encountered almost no philosophers who didn't call this sort of teleological question begging bullshit, usually in those terms. It informs the whole philosophy of biology. Cherry picking some theist philosophers (and a great many philosophers I know who are theists also call bullshit here) to indicate some sort of willful ignorance or blindness on the part of my profession is, well, Larry it's just not scientific.

    To repeat: The default view in philosophy of science is that final causes and design are, as Bacon called them, barren virgins. But we give an audience to those who say things we do not agree with on the off chance they might make a good argument, for one thing every philosopher should love over being right is a good argument. In that respect we differ from scientists. I have made this point once or twice on my blog, as you may know.

    Plantinga is clearly special pleading in favour of his preferred metaphysical preconceptions. I don't mind that. Have at it. But don't think this is in any way regarded with great favour by philosophers in general.

    The thing is, book reviews are not items of work that get you much kudos, so we tend to allow the few people who do review them to say what we are all thinking (Tom Nagel represents a tradition in philosophy of mind that is open to Cartesian dualism, and so find comfort in traditional theism; we can reasonably treat him as an outlier I think). Basically Plantinga is thought by philosophers I have spoken to of as someone who is very clever when he does strict epistemology, and weird as all hell when he does philosophical theology. And if you read every little thing I publish, you'll know I have argued against him too... as a philosopher.

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  16. I would like to make it clear that the term “adaptive mutagenesis” as used in my hypothesis and in the discussion above is a misnomer.

    However, it appears that, in certain environmental or experimental conditions, the rate of generating mutations, which are random or arbitrary in nature, in the genes that are highly transcribed (i.e. expressed) is higher than in the genes that are silent or have a low rate of transcription.

    An increase in the number of random mutations in a highly transcribed gene leads to an increase in genetic variation at that locus, both at the individual and population levels, which can lead to a differential rate of evolution.

    Theoretically, testing for this hypothesis is relatively straightforward; count the number of mutations in DNA sequences that are highly transcribed versus those that are not. However, because the number of mutations is relatively low, detecting them directly, such as by DNA sequencing, is a rather difficult task, although possible. For that reason, previous studies used indirect approaches, such as counting the number of organisms in a population that undergo a phenotypic change indicative of specific nucleotide substitution. The underlying presumption is that this selected nucleotide substitution reflexes the rate of mutation.

    As discussed in the previous comments, an alternative approach would be to investigate the number of nucleotide substitutions (or other types of mutations) over many generations, in DNA sequences that are differentially transcribed and have not been under purifying or positive selection; in these cases, genetic drift notwithstanding, the rate of fixation will represent more or less the rate of mutation.

    The advantage of this approach is that it is a relatively direct account of the rate of mutation, and that it can be used in complex organisms, such as humans. In humans, for example, the study would involve a comparison between DNA sequences that are transcribed at different rates in the germ line and are not under strong positive or purifying constrains. And, the best part about this study is that the raw data is already there, in the GenBank, ready to be plugged in an analysis program. Anyone?

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  17. Everyone here will enjoy this: Boudry wrote a deliberately nonsensical spoof of Plantinga-like theological drivel, full of meaningless strings of big important-sounding words, and submitted it to two theological conferences, which both accepted it. Posted at Jerry Coyne's website today:
    http://whyevolutionistrue.wordpress.com/2012/09/25/a-sokal-style-hoax-by-an-anti-religious-philosopher-2/

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    1. It happens. Joseph Smith, Jr., wrote a spoof of King James' Bible and millions of people have accepted it as their sacred writ.

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  18. "My problem was that I found the whole book quite ridiculous and it seemed to me that Plantina's idea of logic and rationality was much closer to kindergarten philosophy than to something one might expect from a distinguished scholar."

    See mainstream philosophy, until very recently (around the 1970's).

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  19. If a natural explanation can adequately explain something like gravity or evolution then it is unnecesssary to add a supernatural explanation.

    To say that a God has guided evolution in a undetectable way is simply an hoc hypothesis. It is like believing in undetectable superbly advanced extraterrestrials guiding evolution, but when there is known to be no positive evidence For this idea The person says these aliens are invisible.

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