Wednesday, March 11, 2015

A physicist tries to understand junk DNA: Part II

Yesterday I posted some comments on a blog post by physicist Rob Sheldon [A physicist tries to understand junk DNA ]. My comments were based on what I had seen on Uncommon Descent but it turns out that was only a summary of a longer post that appeared on Evolution News & Views (sic): More on Junk DNA and the "Onion Test".

The longer post doesn't add very much to the argument but it does have something interesting at the bottom. Here's what Rob Sheldon says about the Onion Test and junk DNA.
I don't even know why the Onion Test keeps getting mentioned anymore unless it is a red herring to impress the masses, like Carl Zimmer. The idea assumes that DNA does one job and one job only -- making protein -- with one protein per gene. So if the DNA lacks the start/stop codons needed for making protein, it obviously isn't doing its job. This was "Central Dogma" gospel thirty years ago or so.

But once the DNA was found to have moonlighting jobs doing other things -- development, differentiation, regulation, mechanical attachments, iRNA anti-virals, information compression -- then the Onion Test simply makes no sense any more.
To say that the Onion Test has something to do with assuming that the only job of DNA is to make protein is either incredibly stupid or a blatant lie. Probably both. To claim that this has something to do with the Central Dogma of Molecular Biology is also a lie.

To say that once we discovered functions for noncoding DNA, back in the 1960s, the Onion Test made no sense, is in the same category. It's a lie and furthermore it's a lie that could only be believed by someone who is very stupid about this subject, like Rob Sheldon (see photo above).

Here's what I don't understand about Intelligent Design Creationists. There are some who know full well that what Rob Sheldon says is untrue but they don't challenge him and correct the misinformation that he is spewing on the creationist websites. (I'm not talking about "journalist" Denyse O'Leary.)

You'd think that they would do this in order to maintain some level of credibility but that doesn't seem to matter. I'm reminded of Bill O'Reilly who has lied about many things in the past but this seems to be irrelevant to FOX TV. I suppose I ought to give up trying to educate the IDiots and just assume that Uncommon Decent and Evolution News & Views (sic) are not really interested in the truth.


121 comments :

  1. I'll say it again: I can't believe this moron has a Ph.D. in physics. His writing is so scrambled it is almost incomprehensible. But Denyse O'Leary always calls him "physicist", so that means there's a controversy in science, right?

    Somewhere a thesis committee deserves a boot planted in their asses. They're responsible for the embarrassment to physics that is Rob Sheldon, physicist.

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    1. As a Ph.D. in physics, I second your embarrassment. But his committee might not be to blame; I looked it up and it was 25 years ago, plenty of time for him to go from competent to crazy.

      Sheldon is truly a lunatic, as Larry Moran said above. As proof, read his most recent publication "Comets and entropy hydrodynamics: How does evolution violate the 2nd law?". For example, he thinks theory in thermodynamics labors to calculate how Boltzmann's constant in different cases, not noticing that it is actually a constant. It would be funny if it weren't so pathetic.

      Which raises the question, is it really a good idea to mock the mentally disabled?

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    2. Sheldon lives in wonderland, where all the big fancy words of science and mathematics are scrambled together to explain everything. Perhaps even a junior high school student, raised on discovery institute propaganda, might detect the craziness when it is pointed out.

      In "Comets and entropy hydrodynamics …" Sheldon has reversed the meaning of *constant* and *variable*:

      /quote…. Boltzmann’s famous equation, engraved on his gravestone:

      S = k ln W

      On the left hand side is S, a thermodynamic quantity, and on the right hand side is W, a mathematical quantity. Between the two lies k, or “Boltzmann’s Constant”, which converts one to the other, the way c^2 converts mass to energy in Einstein’s E = mc^2 equation. Boltzmann never calculated his eponymous constant, he merely asserted its existence because it is not theoretically derivable and unlike Einstein’s constant, it is not based on ratios of h, c, \pi or \alpha. It is empirically determined with some sophisticated apparatus measuring the speed of sound in a fluid. If we change the fluid, we need to change k. And if the fluid is really complex–say a protein solution, or the insides of a cell–then we really have no idea what to use for k∗. /end of quote.

      Addressing Rob Sheldon: it's called a *constant* because it does not vary! The "mathematical quantity" W is the *variable*. That is what changes when you consider different complex fluids! That quantity W, (technically the number of micro-states consistent with the macro-state of the system), is what physicists calculate to get a theoretical value for the entropy S, which can then be compared to the measured value.

      There are many more crazy statements in this paper. Moran nailed it: he is a lunatic.

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  2. Shouldn't these posts be called "A physicist doesn't try to understand junk DNA"? In part I one could just about believe that he was trying, but part II seems to make it clear that he was lying, as you say.

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  3. On the more silly side of criticism, I was struck by the ambiguity in this unclear phrase by Sheldon (the real Sheldon may be wrong, but he is rarely unclear):

    "...unless it is a red herring to impress the masses, like Carl Zimmer."

    So is Carl Zimmer "the masses" or "a red herring"? :)

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  4. Can a person who believes that evolution violates the Second Law of Thermodynamics, as Sheldon does, really be called a physicist?

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    1. He seems to think of it in terms of ideal gases and probabilistic distributions of particles. He seems only dimly aware of chemical energy.

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    2. I am working on my prototype to harness the energy that must be locked up in low ID-entropy states. I take a book - Shakespeare is favourite at the moment - and allow the words and letters to fall into their 'disordered' state, tapping into the energy released as they do so. Soon, whole libraries will become power stations. Although so far, the energy release is substantially less than simply burning 'em. Early days.

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    3. Hmm, creationists and book burning.

      Don't be giving them ideas, they're badly enough behaved as it is.

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  5. Dunno about a physicist, but I do know of a Nobel prize-winning biologist who believed that life, not just evolution, violated the 2nd Law.

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    1. At least he would be consistent in his error since it is no use talking about evolution when life itself would be a violation according to the same understanding. Hopefully he would also point out that building a house violates the 2nd law too. But I suppose, for some people, certain necessary exceptions to laws (miracles) abound in this universe.

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    2. Hopefully he would also point out that building a house violates the 2nd law too.

      Damn! I knew there had to be a reason why I can't build a house or even fix things in my existing house. My wife will be pleased to hear that. :-)

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    3. yes I'm betting that your wife is a rational person and will understand that you are no miracle worker.

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    4. Building a house requires controlled and directed energy (intelligence) to assemble bricks, cement, wood and nails to turn disorder into an order to construct a house. How is energy constructively controlled and directed in life and evolution?

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    5. Johnny, intelligence is not "controlled and directed energy." Furthermore, what is your evidence that a constructed house has more "order" (you mean less entropy) than its constituent parts? By how much? Did you compute that? No. Did you also compute the HEAT radiated to the environment by the house building process? No.

      Without those two numbers, you have not even begun a thermodynamic analysis of the house building process. Much less an evolutionary process. So how can you generalize about thermodynamic processes when you have not even one valid analysis from which to generalize?

      P.S. Houses don't have sex organs and don't make baby houses, so bad analogy to evolution KTHNX

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    6. Read my post again. I think you have a problem understanding it either deliberately or just out of pure ignorance.

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    7. Hey Johnny,

      Does building a termite mound "require[s] controlled and directed energy (intelligence) to assemble" ?

      How about an ant hill ?

      Or a wasp nest ?

      Or a coral reef ?

      Or a stalactite ?

      I suspect that all of these structure have lower entropy than the constituent materials.

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    8. Again,

      Building a house requires energy to be intelligently controlled and directed to assemble bricks, cement, wood and nails to turn disorder into an order to construct a house.

      How is energy intelligently, constructively controlled and directed in life forms and in the process of evolution?

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    9. It's not. Did you have trouble understanding what I wrote? I said intelligence is not directed energy as you clearly claimed.

      In evolution, energy is not "intelligently, constructively controlled and directed."

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    10. Building a house requires controlled and directed energy (intelligence) to assemble bricks, cement, wood and nails to turn disorder into an order to construct a house.

      Last time I checked, humans were part of nature and functioned as purely naturalistic entities. Thus, natural processes can "violate" the 2nd Law by creating a house.

      Or, are you saying that you need the help of gods to build a house?

      That would explain a lot. It really is a miracle when a house gets built. :-)

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    11. Is it me or both Larry and possibly Theobald don't get it?

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    12. I forgot to laugh. I'm sorry for not laughing earlier.

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    13. It's a miracle if the contractor shows up at the agreed upon time.

      Assuming you even find one of those critters.

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    14. Johnny: "Is it me or both Larry and possibly Theobald don't get it?"

      It's you.

      Let me guess. Do you ever comment at UD?

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    15. I don't. I'm sorry to disappoint you. But you can prove me wrong here with some experimental evidence. My guess is you will not. Let's see.

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    16. I don't hate UD. I just find it too, too confusing. There are too many people with seemingly similar ideas who often contradict each other. Hey! That's my view.

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    17. "Building a house requires energy to be intelligently controlled and directed to assemble bricks, cement, wood and nails to turn disorder into an order to construct a house."
      Intelligence isn't inherently different from any other "undirected" natural phenomenon. You may think there's some intrinsic disconnect going on that allows you to "direct" the energy, instead of the properties of the atoms in your brain simply doing what they do and behaving according to the same basic properties they had before they became part of your organism.

      Basically your argument is assuming you have some kind of "libertarian free will" that makes it possible for you to overrule the basic rules of chemistry, so that the atoms in your brain can be made to do something they would otherwise not be doing if your "intelligent will" wasn't there to "direct" them towards whatever goal you have in mind.

      I'm afraid you're mistaken. The atoms that make up your brain are not under some different, "intelligent" set of laws. However unpleasant it is for you to accept, the simple fact is that what you are and how you act is due to the same basic laws of physics as those found everywhere else.

      We convert energy to produce local reductions in disorder, but the whole system still tends towards equilibrium, that's fully compatible with the 2nd law. There is not even a superficial conflict. We're basically just like verything else, just more complex.

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    18. Follow the thread. You might find it helpful. Why should you stray from the real theme? It's not beneficial to your well being. Trust me.

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    19. That's not even a response to anything I wrote. Why are you engaging in empty dismissals?

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    20. Anyway Johnny, the point wasn't a comparison between evolution and building a house, but rather how ridiculous it is to reject evolution on the belief that it violates the laws of thermodynamics when, by the same rationale, many other common phenomenon would also. But it is a frequently used creationist point because to ignorant audiences it sounds like a sophisticated scientific argument.

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    21. Rumraket wrote: "Basically your argument is assuming you have some kind of "libertarian free will" that makes it possible for you to overrule the basic rules of chemistry, so that the atoms in your brain can be made to do something they would otherwise not be doing if your "intelligent will" wasn't there to "direct" them towards whatever goal you have in mind."

      So in your opinion a house or a freeway is just the end result of random materialistic processes and not a manifestation of the intentionality of the human mind?

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    22. "So in your opinion a house or a freeway is just the end result of random materialistic processes and not a manifestation of the intentionality of the human mind?"

      The "intentionality of the human" mind is just another "random materialistic process". It's subject to the same constraints and laws of physics as everything else.

      If you disagree, kindly produce evidence from an experiment where the human brain violated the laws of physics.

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    23. Wait a second guys:

      So in your opinion a house or a freeway is just the end result of random materialistic processes and not a manifestation of the intentionality of the human mind?

      Let's start from the beginning Andy. What do you mean by materialistic? What makes you think that if it is physical (I am guessing that's what you mean by "materialistic," if I'm wrong, kindly rephrase), it therefore should be random? Make sure that you also explain what "random" means, should that also be necessary.

      Make sure that your explanations don't preclude such things as the sun, or crystallization, or chemical reactions, from doing what they do despite being "materialistic" processes.

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    24. Rumraket wrote: "The "intentionality of the human" mind is just another "random materialistic process". It's subject to the same constraints and laws of physics as everything else. If you disagree, kindly produce evidence from an experiment where the human brain violated the laws of physics."

      If the brain controls the hands (which has been demonstrated) then you either have to take the stance that all human crafts are random creations, which is ludicrous, or (as you put it) there is "some kind of "libertarian free will" that makes it possible for you to overrule the basic rules of chemistry, so that the atoms in your brain can be made to do something they would otherwise not be doing if your "intelligent will" wasn't there to "direct" them towards whatever goal you have in mind."

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    25. I guess you need to reword your question, Rumraket. Poor Andy obviously didn't understand it, and wrote about something else entirely.

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    26. SRM, "Anyway Johnny, the point wasn't a comparison between evolution and building a house, but rather how ridiculous it is to reject evolution on the belief that it violates the laws of thermodynamics when, by the same rationale, many other common phenomenon would also. But it is a frequently used creationist point because to ignorant audiences it sounds like a sophisticated scientific argument."

      We could argue all day long what evolution is or what it means. I just find naturalistic explanation of the origin of life and biochemical evolution unsatisfactory. There is absolutely no scientific proof behind it. None. If you want me to become your believer you have to persuade me with empirical evidence. That 's what science stands for the way I see it.

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    27. "If the brain controls the hands (which has been demonstrated) then you either have to take the stance that all human crafts are random creations, which is ludicrous, or (as you put it) there is "some kind of "libertarian free will" that makes it possible for you to overrule the basic rules of chemistry, so that the atoms in your brain can be made to do something they would otherwise not be doing if your "intelligent will" wasn't there to "direct" them towards whatever goal you have in mind."

      Andy, do you really think the atoms in your brain are causing the atoms in your arms to voilate the laws of physics? You know it's just simple electrochemical signals traveling through your nervecells that cause your muscles to fire, right? So following the chain of caueses back in time, when your arm moves, it's because the brain is telling it to. Not with magic, but with simple electrochemical signals being released. Your arm muscles also convert chemical energy into movement. All this is well within the laws of physics.

      So the next step is figuring out what is causing your brain to send this signal to your arm? This is where you provide evidence of a supernatural and immaterial will that is causing your brain-atoms to act in ways they would not otherwise be doing.

      By the way Andy, explain why everything that isn't due to your supernatural and immaterial will has to be random. Is gravity random? It seems to always pull down, not much "random" about it. So what do you even mean by "random" and why can't it build anything? Last I checked, gravity made planets, stars and galaxies from large clouds of gas and dust.

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    28. Rumraket, are you backing off from your original claim that the mind is fully explained by "the basic rules of chemistry"? Does that not lead to the conclusion that all the output of the mind, all human creativity, is just an illusion? It's all just the result of random processes, or even more silly by deterministic law.

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    29. @Andy Wilberforce
      You're not answering my questions Andy. Explain where the immaterial soul force sets in and starts making your brain-atoms start a causal series that results in your arm-atoms moving. With an empirical experiment preferably.

      I know you believe you have some sort of free will that isn't "just" the chemistry and physics of your brain-atoms interacting with your surroundings and your arm-atoms. So where is the evidence of the immaterial soul-force causing your actions? Do you have a soul-sensitive receiver we can set up and detect the soul-act signal? You must have detected it since you seem to think your brain-atoms are doing things differently from what they would be doing if they were "just chemistry and physics".

      Start answering questions, I'm answering all of yours.

      "Rumraket, are you backing off from your original claim that the mind is fully explained by "the basic rules of chemistry"?"

      No.

      "Does that not lead to the conclusion that all the output of the mind, all human creativity, is just an illusion?"

      No. Why the fuck would it? Whether I paint a painting or write a novel, or it's made by some other combination of natural forces, it's there and exists and is not an illusion in either case. Why would it be? Are things that are made by wind illusions? The sun is an illusion? It was made by mindless laws, so it's an illusion? Please make sense.

      "It's all just the result of random processes"
      What do you mean by random? Explain how you use that word, what does it refer to, give an example of something we know to be random.

      "or even more silly by deterministic law."
      Or a combination of both in varying degrees? Why the false dichotomy?

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    30. Rumraket, you try to hold contradictory opinions. Creativity can not be random nor driven by law. Combining the two does not change the silliness of the argument. Either creativity exists or it is an illusion. If you argue that it's all chemical reactions, then clearly you must hold that creativity is an illusion.
      I can help you out a little when it comes to you indecisiveness between random and deterministic. You have to look at how it works in quantum mechanics. It could be called "determined probabilities".

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    31. "Rumraket, you try to hold contradictory opinions."

      No I do not and you have not shown that I do. And you're still not answering my questions, you're dodging them and you know it.

      "Creativity can not be random nor driven by law."

      Yes it can, it can be both. Both stochastic (aka random) and deterministic processes have been shown to have creative power. Gravity makes planets, stars and entire galaxies. That's pretty creative. The position and momentum of all particles in a graviational field are subject to heisenberg uncertainty, so it's also stochastic (aka random).
      So there is simultaneously a degree of randomness and a lawlike determinism in this process and it has created almost everything we see in the cosmos.
      You could not be any more wrong.

      "Combining the two does not change the silliness of the argument. Either creativity exists or it is an illusion."

      Of course it exists and it is not an illusion. The problem is you think it requires a mind with what philosophers call "libertarian free will". It clearly does not as I have just explained with a perfectly sensible example.

      "If you argue that it's all chemical reactions, then clearly you must hold that creativity is an illusion."

      I clearly must not. The problem is that when you use the word creativity you mean something that by definition requires libertarian free will. I simply disagree that such a thing is required for creativity and I have given a good example.

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    32. "I can help you out a little when it comes to you indecisiveness between random and deterministic. You have to look at how it works in quantum mechanics. It could be called "determined probabilities"."

      Thank you but I already understand it well enough to know there is no indecisiveness or contradictions in anything I've said.

      And you're still dodging my questions.

      Start answering questions, I'm answering all of yours.

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    33. Rumraket,
      We have discussed this before so please feel free to take it as a rhetorical question: Can you see any difference between a pile of rock "created" by the gravitional effect leading to a landslide and the architectural master creation Taj Mahal?

      Did you ever see the movie "A fish called Wanda"? If you did you may remember the scene where Jamie Lee explains to Kevin Kline how he has misunderstood philosophy. That's how I feel when you write about Quantum Mechanics. Just a few things there is no Quantum Theory for gravity, if there were one then its effect would be at the Planck scale and the path integral decides the probability for a certain trajectory not Heisenberg's uncertainty principle.

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    34. @Andy Wilberforce
      Andy, you're still dodging my questions. What's it like to have to do this? What's it like to try to avoid answering uncomfortable questions?

      "We have discussed this before so please feel free to take it as a rhetorical question: Can you see any difference between a pile of rock "created" by the gravitional effect leading to a landslide and the architectural master creation Taj Mahal?"

      Yes, they're very different objects. They were also created in different ways. Not fundamentally different though. Both were created by the laws of physics. It's just that the process creating the one was much more complex. But it was still, at bottom, the laws of physics creating it.

      "Did you ever see the movie "A fish called Wanda"? If you did you may remember the scene where Jamie Lee explains to Kevin Kline how he has misunderstood philosophy. That's how I feel when you write about Quantum Mechanics. Just a few things there is no Quantum Theory for gravity"

      I know there is no quantum theory of gravity, I was not suggesting a quantum theory of gravity. What I was saying is that while gravity pulls, the momentum and position of every particle in a gravitational field is still subject to Heisenberg uncertainty. This is not the same as saying gravity itself is a quantum phenomenon.

      You're not answering my questions Andy.

      Explain where the immaterial soul force sets in and starts making your brain-atoms start a causal series that results in your arm-atoms moving. With an empirical experiment preferably.

      I know you believe you have some sort of free will that isn't "just" the chemistry and physics of your brain-atoms interacting with the atoms in your surroundings and your arm-atoms. So where is the evidence of the immaterial soul-force causing your actions? Do you have a soul-sensitive receiver we can set up and detect the soul-act signal? You must have detected it since you seem to think your brain-atoms are doing things differently from what they would be doing if they were "just chemistry and physics".

      Start answering questions, I'm answering all of yours.

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    35. Rumraket, could you in your own words explain the purpose of the statement "What I was saying is that while gravity pulls, the momentum and position of every particle in a gravitational field is still subject to Heisenberg uncertainty." To me it sounds like utter nonsense akin to "when the car drives down the road the power of the engine causes it accelerate but but each particle in the car is still subject to Heisenberg uncertainty."

      You say that you answer my questions, but I still have not seen you seriously engaging in the core issue of my original question: how can mindless processes have outcomes that explain the human mind. Or more specific: how does chemical processes explain craft, art and architecture. You made assertions that it does explain it, but not made a plausible explanation of how.

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    36. @Cowardly Andy Wilberforce.

      You're not answering my questions. It is obvious that you are scared to death of addressing my question, yet I continue to answer all of yours. At this stage it is manifest that you are trying your hardest to avoid answering and will pursue any tangent and digression to obfuscate the fact that you know you can't answer my question. Which shows you are holding a baseless and irrational faith in the existence of an immaterial and supernatural soul.

      " To me it sounds like utter nonsense akin to "when the car drives down the road the power of the engine causes it accelerate but but each particle in the car is still subject to Heisenberg uncertainty.""

      Yes, it's exactly like your analogy. That is actually correct, it isn't nonsense.

      "You say that you answer my questions"

      And I do, but you don't answer mine. Stop running away from my question Andy. What are you scared of?

      ", but I still have not seen you seriously engaging in the core issue of my original question: how can mindless processes have outcomes that explain the human mind. Or more specific: how does chemical processes explain craft, art and architecture. You made assertions that it does explain it, but not made a plausible explanation of how."

      That's the first time you ask that question, so that's not your "original question". Regardless it's rather easy to answer: Complexity. It is the complexity of the human organism, and the complexity of the human brain and it's interactions with it's environment that explains those things. So while they are still, at bottom, physical and chemical interactions taking place in your body and brain, which all still act according to the laws of physics, it's just that the structures are so many and so varied, there are so many different possible outcomes of those interactions that you some times get human creations, instead of just sand, rocks and mountainranges.

      So Andy, going to start providing evidence of your supernatural and immmaterial soul-force causing your brain-atoms to do something anytime soon? Explain where the immaterial soul force sets in and starts making your brain-atoms start a causal series that results in your arm-atoms moving. With an empirical experiment preferably.

      I know you believe you have some sort of free will that isn't "just" the chemistry and physics of your brain-atoms interacting with the atoms in your surroundings and your arm-atoms. So where is the evidence of the immaterial soul-force causing your actions? Do you have a soul-sensitive receiver we can set up and detect the soul-act signal? You must have detected it since you seem to think your brain-atoms are doing things differently from what they would be doing if they were "just chemistry and physics".

      Start answering questions, I'm answering all of yours.

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    37. Ok, Rumraket let me answer your question the same way that you answer mine, then maybe you will see that it’s just assertions, not explanations:

      “It's rather easy to answer: Mind. It is the mind of the human organism, and the mind of the human brain and it's interactions with its environment that explains those things. So while the mind still at bottom is non-physical and non-chemical, interactions take place in your brain. It's just because the mind is so varied that you get human creations, instead of just sand, rocks and mountain ranges.”

      Also, a nonsense statement can be true, let me try another analogy and see if you get the message: the trajectory of the ball flying through the air is explained by the laws of gravity and aerodynamics, but the text printed on the side still says “made in China”.

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    38. @Andy "Ok, Rumraket let me answer your question the same way that you answer mine, then maybe you will see that it’s just assertions, not explanations:"

      Thank you for finally getting around to that, one wonders why it took you so long.

      "“It's rather easy to answer: Mind. It is the mind of the human organism, and the mind of the human brain and it's interactions with its environment that explains those things. So while the mind still at bottom is non-physical and non-chemical, interactions take place in your brain. It's just because the mind is so varied that you get human creations, instead of just sand, rocks and mountain ranges.”"

      There is no actual explanation here. It is exactly because we know what physical and chemical interactions are, and how they work, that my answer actually constitutes an explanation. There is an actual mechanism that explains the causal chain. Atoms in environment influence atoms in brains (through the senses) through physics (electromagnetic radiation hits the eyes, vibrations in air molecules hit the ears and skin and so on), the atoms in the brain in turn are forced to interact and an output results, which is the movement of the limbs. This is an actual explanation, there is a mechanism.

      In contrast you posit non-physical and non-chemical interactions. Where do we go to see those? Can you reproduce them in a laboratory? What are the rules that govern their behavior? Are there any such rules?
      What are non-physical and non-chemical interactions even in the first place, how do they take place in brains? How do they interact with the brain's atoms without interacting with atoms in rocks and the air?

      How does the "non-physical" and "non-chemical" "mind" know it needs to interact with a carbon atom in a brain, instead of a carbon atom in a lump of coal? How does it know whether a carbon atom is even part of a larger brain structure, instead of part of the central nervous system, or your liver, or a carbon atom in the brain of a dead person? How does it know that it should only make living people act and breathe and think and move when dead people are almost identical?

      All these things are explained by chemistry and physics itself, we don't have to posit some external immaterial mind and once we do, we get all sorts of problems with explaining how this is supposed to work.

      "Also, a nonsense statement can be true, let me try another analogy and see if you get the message: the trajectory of the ball flying through the air is explained by the laws of gravity and aerodynamics, but the text printed on the side still says “made in China”."

      That's not a nonsense statement. In fact it makes total sense. The flying of the ball is explained by gravity and aerodynamics, and this has obviously not got any influence on what it says on the ball. What's nonsense about this? There is nothing analogous to what I said.

      But any way, thank you for finally getting around to trying to answer my question, however flawed your attempt was.

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    39. Rumraket, it was not an attempt to answer. As I explained I just took your reply and exchanged "complex" with "mind". But at least we agree that it does not provide an explanation.

      If you don't agree that the print "made in China" is analogous to your statement about Heisenberg uncertainty, then explain what effect it has on the gravity.

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    40. It doesn't have an effect on gravity itself, it has an effect on the position and momentum of any given particle that moves through the gravitational field. So while there is a degree of determinism in the system (things will tend towards the gravitational center), there is also stochasticity(aka "randomness"), we cannot predict exactly how each particle will move through the gravitational field at atomic resolution. We have to give answers in terms of probabilities. Basically they're biases in the probability distributions. They can be nonbiased or they can be extremely biased, with almost certain outcomes. On the one end of the spectrum most people would colloquially refer to them as "random"(little to no bias), while at the end (heavy bias) we could call it predictable and this would be what most people think is what is meant by deterministic. It comes in degrees, it doesn't have to be fully one or the other.

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  6. What's the penalty for life and evolution violating the 2nd law?

    :p

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    1. Our Prime Minister and his Conservative Party are in the process of revising Canadian law in order to put lots more people in jail. (We're way behind the USA in terms of the percentage of people we have in Canadian prisons.)

      I'm guessing the the penalty for violating the 2nd law would be a minimum of 25 years in prison with no chance of parole. If you violate the 1st law the Conservatives will demand life imprisonment with no chance of parole. (We don't have the death penalty and even the Conservatives are not stupid enough to bring it back.)

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    2. Since you brought up politics... the conservative government seems hell bent on americanizing (Republican-style) Canada in numerous ways. Note how the rapidly proliferting military recruitment ads speak of "protecting our values and freedom" around the world. Ugh, classic republican/right wing language. They know a hyper-nationalistic mindset favors conservative power.

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  7. Turning into antimatter, so that when you encounter matter ...

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  8. Since we're on the topic of Junk DNA, Ewan "80%" Birney has been appointed the head of EMBL. Urkh.

    Petition of protest? Surely there should be some accountability for that equivocating 80%, press release asshole.

    I'm serious about an anti-Birney petition. I'd write it and I'd be restrained and respectable, not at all like my actual self.

    Who would sign it? Larry? Joe?

    ReplyDelete
    Replies
    1. I would sign it. I don't know Birney but his behavior in responding to objections to his abstract and press release was disgraceful. Blah-blah-blah apparently "functional" is a complex concept blah-blah-blah. A not-pology.

      (In what looked suspiciously like a reward he was also made a member of the Royal Society).

      Delete
    2. Diogenes,

      He has been appointed half-head; EMBL will as of now be run by a duumvirate.

      Delete
    3. Diogenes,

      Regarding your anti-Birney petition, be aware that he and the other ENCODE leaders are highly sophisticated scientists, who knew well what they were doing.

      For reasons I elaborated elsewhere (http://www.ncbi.nlm.nih.gov/pubmed/23479647), the ENCODE authors went out of their way not to address the functionality of the human genome and the fundamental knowledge in the field of genome biology in their scientific publications.

      Instead, the ENCODE leaders convinced a few science writers and editors to spread their propagandist message about the functionality of the human genome and dismissal of the ‘junk DNA’ paradigm. This is why the scientists who criticized the ENCODE message (see, for example, Ford Doolittle’s PNAS paper) had no choice but to quote from these secondary sources, rather than from the ENCODE articles. Whereas the Editors of PNAS were apparently OK with these sources, I don’t think they will resonate with the EMBL crowd.

      In any case, I would suggest you post your petition draft here at Sandwalk and get input from readers.

      Delete
    4. I’m copying Athel’s reply here, in order to link the discussion.

      “Athel Cornish-Bowden Friday, March 13, 2015 8:36:00 AM

      Claudiu, I’m not at all convinced by your efforts to defend the indefensible. Above, you say Instead, the ENCODE leaders convinced a few science writers and editors to spread their propagandist message about the functionality of the human genome and dismissal of the ‘junk DNA’ paradigm. If that was really their strategy it was thoroughly dishonest.

      In your NIH comment, you say David Comings writes: “These considerations suggest that up to 20% of the genome is actively used and the remaining 80+% is junk. But being junk doesn’t mean it is entirely useless. Common sense suggests that anything that is completely useless would be discarded.”

      That’s the sort of argument we expect from the Discovery Institute: I can’t believe it is really junk, so it isn’t junk; common sense tells me. It may have been legitimate to think in 1972 that useless DNA would be discarded, but it certainly wasn’t legitimate in 2014, when you quoted it.”

      Delete
    5. Athel: “Claudiu, I’m not at all convinced by your efforts to defend the indefensible”“If that was really their strategy it was thoroughly dishonest.”

      My intend was not to defend them, but to report what I think represents a more realistic evaluation of the events associated with the ENCODE fiasco.

      For example, as I pointed out in my PubMed notes, I think it is unrealistic (and, therefore, questionable) to accuse the ENCODE scientists, which represent the finest academic institutions in the world, of scientific incompetence, as suggested by Dan Graur and others.

      I agree with you that the ENCODE fiasco was the result of a dishonest sideshow. However, our entire ‘science system’, particularly as it orbits around funding, is plagued with various degree of dishonesty (for example, without hype and distorted reports, few grant applications or research programs would become competitive).

      So, in a system in which ‘curing cancer’ is the name of the game (and yes, this was, literarily, part of ENCODE’s scientific objectives), the ENCODE leaders probably felt that it was acceptable to hype their findings, with the hope of reaching the public and political opinion and lure them into increasing the funding for NIH and genomic research, which ultimately might be considered a noble act (never mind, that in the due course, they might highly benefit personally, as evidenced by Birney’s honors and promotions).

      In line with this rationale, and with the realization that the ENCODE fiasco was not associated with research findings as reported in the scientific literature, but with the ‘lobbing effort’ carried out by a few science writers and editors ‘hired’ by ENCODE, it is not an easy task to ‘attack’ the scientific competency and leadership skills of Birney and the other ENCODE leaders. And, after all, EMBL might be in better position with somebody like Birney at the top, as he has proven skills of effective lobbing.

      Delete
    6. Athel wrote: “In your NIH comment, you say David Comings writes: “These considerations suggest that up to 20% of the genome is actively used and the remaining 80+% is junk. But being junk doesn’t mean it is entirely useless. Common sense suggests that anything that is completely useless would be discarded.”

      Comings’s quote from his 1972 paper was one of a series of historical examples on poor use of words in communicating scientific observations, which has led to significant misrepresentations and confusion in the field of genome biology for many decades. Indeed, what does “being junk doesn't mean it is entirely useless” mean?

      First of all, anything that “is not entirely useless” is by definition useful (is that correct Piotr?). Also, did Comings refer to the entire 80% of the human genome (which he labeled “junk DNA”) as not being “entirely useless,” or he intended to say that some specific sequences (let’s say a few thousands of DNA fragments) located within this bulk “junk DNA” might not be “entirely useless”.

      As you know, hundreds of scientific publications debunking the concept of “junk DNA” were based simply on the findings that some sequences were indeed functional. The relevant question is not if a few hundred or a few thousands of these sequences are functional, but if most of this genomic DNA it is functional, or not. This widespread error has inspired Michael Eisen to entitle his blog “It is not junk”

      For a more recent example of this widespread confusion, I quoted from a recent paper (2012) on ‘junk DNA’ and ENCODE by Sean Eddy who wrote: “These data support a view that eukaryotic genomes contain a substantial fraction of DNA that serves little useful purpose for the organism….” What does “little useful purpose” means? Again, if this DNA has “little useful purpose”, then by definition it is functional; whether a piece of DNA has a little, or a big function, that piece of DNA is functional.

      This confusion in the field of genome biology is almost as bad as the ‘near neutral’ terminology used in support of Neutral Evolution, which apparently has nothing to do with adaptation and, therefore, is of little (sic!) relevance.

      Delete
    7. Claudiu Bandea says,

      I think it is unrealistic (and, therefore, questionable) to accuse the ENCODE scientists, which represent the finest academic institutions in the world, of scientific incompetence, as suggested by Dan Graur and others.

      I am one of those "others" and I stand by my accusation.

      ... the ENCODE leaders probably felt that it was acceptable to hype their findings, with the hope of reaching the public and political opinion and lure them into increasing the funding for NIH and genomic research, ...

      It is unacceptable. You have just demonstrated a clear example of scientific incompetence by ENCODE leaders at the "finest academic institutions."

      QED

      Delete
    8. Claudiu writes: "the ENCODE authors went out of their way not to address the functionality of the human genome and the fundamental knowledge in the field of genome biology in their scientific publications.

      Instead, the ENCODE leaders convinced a few science writers and editors to spread their propagandist message about the functionality of the human genome and dismissal of the ‘junk DNA’ paradigm. This is why the scientists who criticized the ENCODE message (see, for example, Ford Doolittle’s PNAS paper) had no choice but to quote from these secondary sources, rather than from the ENCODE articles."


      Yes Claudiu, I get that. That is the gravamen of my accusation, that there was a large discrepancy between what was written in the peer-reviewed papers and what appeared in the press release, Nature hype, and the animated cartoon where the ENCODE giant robot slays cancer. I even coined the term "press release sociopath" or "pressiopath" to describe those who tolerate huge disjunctions between the claims in their peer-reviewed articles and what the university's press office releases on their behalf.

      I know I cannot accuse ENCODE leaders of scientific fraud, but dishonesty takes more than one form, and press release sociopathy is one of them. My argument will be that press release sociopathy, while it is NOT scientific fraud, is academic misconduct.

      If anyone has a better wording than "academic misconduct" or "malpractice", I would like to know what it is.

      I would accuse some ENCODE leaders of the follwing:

      1. Equivocation. Ewan Birney chose to redefine "Function" so as to yield a large % of functional DNA, but the new definition was not relevant to the Junk DNA hypothesis. He admitted he did this to get publicity.

      2. A large disjunction between what the peer-reviewed papers said and what was claimed in the press releases, Nature hype, and animated cartoon where the giant ENCODE robot slays cancer.

      3. Straw-man misrepresentation of the Junk DNA hypothesis which they claimed they had disproven. Junk DNA was replaced by a stupider hypothesis, "If we don't know its function, it must have no function", which the opponents of jDNA invented, and which was NOT the Junk DNA hypothesis. In fact that hypothesis was not based on ignorance, but on positive evidence that most human DNA cannot suffer deleterious mutations. In particular, Comings in 1972 already knew that most of the mouse genome was transcribed into RNA, but was still mostly junk, yet the ENCODE leaders repeatedly claimed that widespread RNA transcription by itself disproved the junk DNA hypothesis. In fact they were arguing against a stupider hypothesis of their own invention.

      4. Not addressing the positive evidence for Junk DNA. This is worse than the usual case of ignoring evidence contrary to one's own position; here it is especially egregious because it dovetailed with ENCODE's straw-man misrepresentation of the jDNA hypothesis, "If we don't know its function, it must have no function", to make previous generations of scientists look incredibly arrogant and stupid in the eyes of the general public. For example, when Ewan Birney was asked what was his answer to the onion test he tweeted "Polyploidy" because he did not know that onions were chosen for the Test because they are not polyploid, and that in the C value paradox, C is divided by the number of copies of chromosomes. He did not familiarize himself with the content of the hypothesis, or the evidence for it, before he replaced it with a stupider hypothesis that he could disprove.

      I have to write it in a way so that it also appeals to people who don't believe in the Junk DNA hypothesis. Even if you don't buy the hypothesis, you have to admit that some ENCODE leaders engaged in academic misconduct, malpractice, unethical behavior, and/or intellectual dishonesty.... what wording do you all think is best?

      Delete
    9. ENCODE published preliminary results back in 2007(?) where they analyzed 1% of the genome. They made some of the same claims they made in 2012; namely that most of the genome was transcribed and there was a plethora of regulatory sites. The conclusion was that most of the genome was functional.

      Those conclusions were widely challenged on blogs AND in the scientific literature. There were, for example, a number of papers pointing out that most of the transcripts were spurious and that it was important to report the amount of an RNA species that was detected in order to judge whether it might be functional. (That recommendation was ignored.)

      As far as I know. none of those criticisms were addressed in any of the recent papers and none of criticism in the scientific literature was included in the list of references. There may be a few exceptions, but you would be hard-pressed to find any serious discussion of spurious transcripts and spurious binding sites in the Nature papers.

      Anyone reading those papers will come away with the idea that all of the transcripts and all of the binding sites are biologically significant. That's because this is what most of the authors believe in spite of all the criticisms from five yesrs earlier.

      It is scientifically incompetent to ignore challenges to the interpretation of your own data that have been published in the scientific literature and pretend that your interpretation of the data is the only possibility. This is not how competent scientists should behave.

      Delete
    10. Diogenes: “I have to write it in a way so that it also appeals to people who don't believe in the Junk DNA hypothesis.”

      I think that’s an essential point.

      Diogenes: “Even if you don't buy the hypothesis, you have to admit that some ENCODE leaders engaged in academic misconduct, malpractice, unethical behavior, and/or intellectual dishonesty.... what wording do you all think is best?”

      I think all these terms have merit and should be used.

      Diogenes: I know I cannot accuse ENCODE leaders of scientific fraud, but dishonesty takes more than one form, and press release sociopathy is one of them. My argument will be that press release sociopathy, while it is NOT scientific fraud, is academic misconduct.

      You might want to reconsider that. Here is an excerpt from a recent paper discussing this matter (Gupta A. Fraud and misconduct in clinical research: A concern, Perspect Clin Res. 2013; (http://www.picronline.org/temp/PerspectClinRes42144-358344_095714.pdf).

      “Fraud and misconduct are the two terminologies often used interchangeably. However, there is a gross distinction between the two. Scientific misconduct/fraud is a violation of the standard codes of scholarly conduct and ethical behavior in scientific research. Definition of fraud as defined in court is “the knowing breach of the standard of good faith and fair dealing as understood in the community, involving deception or breach of trust, for money.”[1] Fraud is an intentional deception made for personal gain or to damage another individual, for instance, intentionally falsifying and/or fabricating research data, and misleading reporting of the results. Misconduct may not be an intentional action, rather an act of poor management. It also includes failure to follow established protocols if this failure results in unreasonable risk or harm to humans.[3] Fraud should have an element of deliberate action, which is not the case with misconduct.

      Just to make my position clear, I’m not defending the ENCODE leaders from wrong-doing (see Athel’s comment above). The point I’m trying to make is that the ENCODE leaders are not ‘stupid’ (i.e. scientifically incompetent), but highly competent and versed individuals in the ‘business of science’, who knew well what they were doing, but who, given the chance, would play the ‘stupid card’ to ‘get out of jail’.

      Another point I was trying to make, here and elsewhere (https://liorpachter.wordpress.com/2014/02/12/why-i-read-the-network-nonsense-papers/), which is somewhat in the defense of the ENCODE leaders and other reckless scientists, is that, ultimately, the big problem is with the current corrupt scientific culture; we know that people have the potential of doing wonderful or despicable things, depending of the system in which they operate, just look at history.

      In this highly competitive and corrupt scientific culture, particularly associated with funding and academic promotions, which encourages dishonesty, the scientists have little choice but to adapt (there is a good reason for the well know dictum: *be dishonest, or perish*).

      Delete
    11. Diogenes,

      Here are 2 additional inspirational articles, supported by some highly regarded scientists, but there are plenty more on the web:

      “It's time to criminalise serious scientific misconduct. Research misconduct degrades trust in science and causes real-world harm. As such, it should be a crime akin to fraud, argues Richard Smith” (http://www.newscientist.com/article/mg22329864.100-its-time-to-criminalise-serious-scientific-misconduct.html#.VCAs_XYpDq5)

      “Journals like 'Nature', 'Science' or 'Cell' prey on people's vanity” (http://metode.cat/en/Issues/Interview/Randy-Schekman)

      Delete
    12. Laurence A. Moran: “Those conclusions were widely challenged on blogs AND in the scientific literature. There were, for example, a number of papers pointing out that most of the transcripts were spurious and that it was important to report the amount of an RNA species that was detected in order to judge whether it might be functional. (That recommendation was ignored.)”

      It is difficult to get a man to understand something, when his salary depends upon his not understanding it! (Upton Sinclair)

      Delete
    13. Claudiu, thanks for your thoughtful responses; I will look at your links.

      Delete
    14. I don't remember if this has already been pointed out and I don't want to go back through every comment in two threads to find out:

      Onion Exposé : Carl Zimmer on Why Junk DNA Had Better Be Real

      http://creationrevolution.com/onion-expose-carl-zimmer-on-why-junk-dna-had-better-be-real/

      Delete
  9. http://www.evolutionnews.org/2015/03/finally_a_detai094271.html

    "The big problem for ID advocates in pointing out the extreme difficulties of putting together complex biological systems such as the flagellum or clotting cascade by unintelligent processes is that the other side sees it simply as a challenge to invent a facile story. That's one reason I wrote The Edge of Evolution -- to say that we no longer have to rely on our imaginations, that we have good evidence to show what Darwinian processes are capable of doing. When we look to see what they do when we are watching, we never see the sorts of progressive building of coherent systems that Darwinists imagine. Rather, we see tinkering around the edges with preexisting systems or degradation of complex systems to gain short-term advantage."

    Professor Moran, is M. Behe right in when he says there is no evidence for "progressive building of coherent systems that Darwinists imagine"? Can you provide some evidence that he is wrong?

    I am no scientist but I make an attempt to predict 3 things.
    1. Every scientist on this blog is going to say Behe is wrong
    2. None will provide any evidence that he is wrong
    3. None will write an open letter to M. Behe to show how wrong he is.

    ReplyDelete
    Replies
    1. Professor Moran, is M. Behe right in when he says there is no evidence for "progressive building of coherent systems that Darwinists imagine"?

      Hmmmm ... let me think about that for a second .....

      No.

      Can you provide some evidence that he is wrong?

      There are tons of examples. One of the best ones that I used in the introductory biochemistry course is the gradual evolution of the complex photosynthesis complexes in plants from much simpler molecules whose representatives still exists in some bacteria. You can read all about it in my textbook.

      Behe admits that there's good evidence for the evolution of the citric acid cycle, which is clearly an irreducibly complex system.

      I am no scientist but I make an attempt to predict 3 things.
      1. Every scientist on this blog is going to say Behe is wrong
      2. None will provide any evidence that he is wrong
      3. None will write an open letter to M. Behe to show how wrong he is.


      I have blogged about this in the past and Behe has responded in the comments. I have corresponded by email with Michael Behe, and I have discussed this with him in person.

      Delete
    2. Unknown,

      Regarding number 1: Yeah, that's likely.

      Regarding number 2: I have a feeling that some will provide some evidence but I don't think it's necessary for them to do so since all of Behe's claims have already been responded to a gazillion times.

      Regarding number 3: An "open" letter? What does that even mean?

      Tell you what, instead of posting a comment where you bring up some vague statements from Behe, why don't you write an "open" letter to Behe and ask him to come here and make some specific claims that can then be responded to? After all, you do notice, don't you, that ENV is NOT open to responses? If Behe is confident that his claims are valid, he shouldn't have any fear of responses from scientists here, right? He should welcome open discussion/debate of his claims, right? In fact, he should be anxious to put forth and defend his claims here, right? So, get your "open" letter to Behe right away.

      Delete
    3. I would be far more interested in creationists/IDists actually presenting some positive evidence FOR their claims rather than them demanding that either we prove them wrong or present even more detailed evidence for evolution. Tell us all Unknown and TWT - why are there exactly zero papers from creationists detailing the mechanisms or providing any actual evidence for any of their claims? And please - the whole 'expelled' thing won't work, since they cannot even seem to muster enough research to put in their own "journals" (PSCID? Bio-Complexity? CRSQ?).

      Delete
    4. I believe Unknown here is abortion ambulance chaser, and current moderator of Uncommon Descent, Barry Arrington.

      Barry, you know very well that I have many times responded to your repeated demands for an open letter to Prof. Behe. I will not write Behe an open letter because he is not my equal, because Behe has proven he is dishonest enough to twist our words and strawman our arguments. Then you IDiots will claim victory because he shat some words on the internet, never mind if they are true.

      However, I have repeatedly offered to go you one better and debate Behe face to face in his home state of Pennsylvania. If I had him face to face, I would not let him get away with strawmanning my arguments as he did last time when he misrepresented my calculations. Is that why you never respond to my offers to debate Prof. Behe, Barry?

      Barry, why do you always disappear from threads whenever I offer to debate your only ID authority who has even a modicum of scientific respectability? Now since you, as moderator of UD, must have some pull at the Duplicity Institute, why don't YOU write an open letter to Prof. Behe encouraging him to debate me face to face, or explaining why he should not. YOU write the open letter to Behe, Barry. YOU write it.

      Delete
    5. N. Manning, it looks as though you have misinterpreted my position. I am not defending ID-creationists.

      Delete
    6. P.S. On the evolution of Irreducibly Complex systems, the PCP degradation pathway, and citrate digestion in Lenski's E. coli are examples of recently evolved IC systems.

      Behe has made numerous idiotic claims that were easily falsified, such as idiotically claiming that disulfide bridges (! two cystines) are IC and can never evolve, that protein binding sites can never evolve etc. All obviously falsified-- hell, every time you recover from a cold, your immune system evolved a new protein binding site. Behe is very ignorant of molecular biology, to claim such things can't evolve!

      It is obvious that natural processes can create Irreducibly Complex systems. Natural bridges and arches are IC and are made by natural processes. They are often crossed by roads and have the same function as "intelligently designed" bridges. But Behe says disulfide bridges, consisting of two cystines (!), are IC so they can never evolve! Ignorant.

      Delete
    7. Dionogenes,

      I believe you are Douglas Theobald

      Delete
    8. Ooh busted. I am so totally Theobald.

      Delete
    9. This is going to be very easy to confirm soon when you sign the petition.
      If you back out, we will know why, unless you want to sign it "Diogenes" ;-P

      Delete
    10. Ooh busted. I am so totally Theobald.

      I know Douglas Theobald, Douglas Theobald is a friend of mine. You're no Douglas Theobald. [Bentson vs. Quayle]

      Delete
    11. I think Diogenes was implying that he aspires to be Doug Theobald, and that he appreciate's Pest's compliment. But of course who doesn't aspire to be Doug Theobald?

      Delete
    12. This confusion may very well be my fault. I think Peer referred to Diogenes in such a way as if he'd insinuated that Diogenes was Douglas Theobald.

      Delete
    13. John: "I think Diogenes was implying that he aspires to be Doug Theobald, and that he appreciate's Pest's compliment."

      No I meant that I actually am Douglas Theobald, at least on Tuesdays and Thursdays. In my laboratory I have concocted a bubbling potion which, when drunk, transforms me into Douglas Theobald. I then terrorize the innocent citizens of London by assaulting them with phylogenetic trees.

      Delete
    14. Diogenes,

      "On the evolution of Irreducibly Complex systems, the PCP degradation pathway, and citrate digestion in Lenski's E. coli are examples of recently evolved IC systems."

      Here is a quote from Behe reg. your claim:

      "In short, improvements had been made by breaking existing genes, or fiddling with them in minor ways, but not by making new genes or regulatory elements. From this information I formulated "The First Rule of Adaptive Evolution": Break or blunt any functional coded element whose loss would yield a net fitness gain. To say the least, the First Rule is not what you would expect from a process, such as Darwinian evolution, which is touted as being able to build amazingly sophisticated molecular machinery."

      Behe's response to Lenski's E. coli experiments results


      The analogy could be illustrated this way: Darwinian evolution collapsed a bridge. The remaining parts of the bridge formed a gangway, so that instead of trains and cars, now people and some animals can pass over the body of water.

      Delete
    15. No Pest, Behe's quote does not address my point: the PCP degradation pathway involves the evolution of an enzyme with a new function and its integration into an IC system. So Behe's wrong; your quote only demonstrates his dishonesty or ignorance.

      Second, as for the E. coli experiment, Behe was proven dead wrong: he predicted that no new functional encoded elements would appear in the E. coli; in fact, it had a new gene AND new non-coding regulatory elements. So Behe was handed his ass on that, as he has been handed his ass on ever prediction he has ever made and every topic he has ever substantively addressed, except when he agreed with evolutionists.

      Delete
    16. I'm confused. Does it address your point or doesn't it? If it doesn't, how could Behe be lying about something he didn't address? Make up your mind or don't drink and drive... your point nowhere.

      Delete
    17. There is nothing in the Lenski long-term evolution experiment with E coli that lends support to Behe's propagandist interpretation. There is nothing analogous to bridges being collapsed.

      Rather genes were duplicated in the right places which allowed transport that weren't there before. If you wish to draw an analogy to traffic, another highway was built, crossing over a previously untraversable swamp.

      Behe (and by extension the people who mindlessly quote him all the time and gobble up every turd he leaves on the ID blogs) is spewing manifest falsehoods.

      Delete
  10. In case anyone is interested in more about (and from) Sheldon, go here:

    http://recursed.blogspot.com/2010/11/creationist-mathematics.html

    Jeffrey's "reprint it" link will take you here:

    http://www.uncommondescent.com/intelligent-design/infinitely-wrong/

    Don't miss comment number 12 from Sheldon.

    You'll find that the links at Jeffrey's site and at UD no longer take you to Sheldon's complete article. Fortunately, the wayback machine has the page archived and it's here:

    https://web.archive.org/web/20110825033208/http://procrustes.blogtownhall.com/2010/11/05/infinitely_wrong.thtml

    ReplyDelete
  11. "I have blogged about this in the past and Behe has responded in the comments. I have corresponded by email with Michael Behe, and I have discussed this with him in person."

    And what did he say about your "evidence"? M. Behe every month writes an article in which he concludes

    "When we look to see what they do when we are watching, we never see the sorts of progressive building of coherent systems that Darwinists imagine. Rather, we see tinkering around the edges with preexisting systems or degradation of complex systems to gain short-term advantage.""

    I can't understand why don't you show once and for all that he is wrong and or he is lying by showing your tons of evidence? Is it because you know he is actually right?

    ReplyDelete
    Replies
    1. If Unknown ever reads ANYTHING on this blog or Panda's Thumb, then he is lying outright when he writes: "I can't understand why don't you show once and for all that he is wrong and or he is lying by showing your tons of evidence? "

      Virtually every substantive claim made by Behe has been refuted many times over both here and at Panda's Thumb and elsewhere.

      Then after we repeat the refutations 20 times, some IDiot always shows up and says, "Why don't you refute Michael Behe?" Question based on false premise so to heck with you.

      Now I have to copy what I wrote above, which you will note, directly refutes Unknown's false claims about how we don't squash Behe like a little bug.

      Again: On the evolution of Irreducibly Complex systems, the PCP degradation pathway, and citrate digestion in Lenski's E. coli are examples of recently evolved IC systems.

      Behe has made numerous idiotic claims that were easily falsified, such as idiotically claiming that disulfide bridges (! two cystines) are IC and can never evolve, that protein binding sites can never evolve etc. All obviously falsified-- hell, every time you recover from a cold, your immune system evolved a new protein binding site. Behe is very ignorant of molecular biology, to claim such things can't evolve!

      It is obvious that natural processes can create Irreducibly Complex systems. Natural bridges and arches are IC and are made by natural processes. They are often crossed by roads and have the same function as "intelligently designed" bridges. But Behe says disulfide bridges, consisting of two cystines (!), are IC so they can never evolve! Ignorant.

      Delete
    2. "I can't understand why don't you show once and for all that he is wrong and or he is lying by showing your tons of evidence?"

      This has been done to destruction. It's just that Behe simply reverts to fallacious probability arguments to baffle you with every time and you uncritically gobble it up because you fail to think any deeper about it.

      Delete
  12. Claudiu, I’m not at all convinced by your efforts to defend the indefensible. Above, you say Instead, the ENCODE leaders convinced a few science writers and editors to spread their propagandist message about the functionality of the human genome and dismissal of the ‘junk DNA’ paradigm. If that was really their strategy it was thoroughly dishonest.

    In your NIH comment, you say David Comings writes: “These considerations suggest that up to 20% of the genome is actively used and the remaining 80+% is junk. But being junk doesn’t mean it is entirely useless. Common sense suggests that anything that is completely useless would be discarded.”

    That’s the sort of argument we expect from the Discovery Institute: I can’t believe it is really junk, so it isn’t junk; common sense tells me. It may have been legitimate to think in 1972 that useless DNA would be discarded, but it certainly wasn’t legitimate in 2014, when you quoted it.

    ReplyDelete
  13. I don't understand why Liar has to intervene every time I ask something professor Moran. I am going to prove him liar once again because he is not going to be able to provide a quote from Behe where he says binding sites can't evolve.
    The only thing I am interested from Liar is an open letter which would prove to me he is not chicken and he is not bluffing with his examples.

    As I told many times I am not scientist, the only way I can give credit to a "scientist" is if he is not afraid to address the challenges in public. (Commenting on a blog doesn't count because real scientists don't stay all day long following, answering comments). So open letter or a blog post please.

    So far every "scientist" on this blog is very shy about addressing Behe's challenge even though everybody knows M. Behe never lets a response to him unanswered.

    Take prof Moran for example, he never lets an opportunity go by without attacking Luskin on the issue of darwinism, but he never, never attacks M. Behe on the exact same matter even though he has the opportunity to address Behe's challenge

    M. Behe: "When we look to see what they do when we are watching, we never see the sorts of progressive building of coherent systems that Darwinists imagine. Rather, we see tinkering around the edges with preexisting systems or degradation of complex systems to gain short-term advantage.""

    and show him look professor Behe we've got tons of evidence that neutral theory can do all these things you claim darwinian processes can't do.

    But of course prof Moran knows very well that prof Behe wouldn't let him get away with his unsupported claims.

    ReplyDelete
    Replies
    1. To pick a recent example Behe was already handed his ass on the whole chloroquine resistance fiasco of his. Go read the posts.

      Delete
    2. Ouch. It seems that Unknown's numerous lies (or ignorant blurts, if you prefer) are so easily rebutted simply with a list of links or quotes directly refuting his ridiculous claims.

      Both Prof. Moran and Rumraket have left their bootprints deep in Unknown's ass, and that's just today!

      Now it's my turn, ha ha.

      Delete
    3. Unknown,

      I'm not qualified to tell you how to be an IDiot, but I would suggest that you first check a bit around before making claims. That could save you a bit of embarrassment. Not that anybody here knows who you are, but still, if not for you, personally, perhaps for your beliefs. Think a bit. Searching is not that hard. Reading is not that hard. Thinking, well, you might not be used to it, but give it a try. What can you lose?

      Delete
    4. Addressing issues and providing empirical evidence for are two different things. I find that when DLs really tries to address the issue but has no evidence to support it., he/she will just write it out; wherever as long as it satisfies the inquiring mind.

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    5. I've always been wondered why evolutions were so aggressive. It must be the proof they have been withholding against the poor...

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    6. Well, repeating the same points for 156 years to people who just stick their fingers in their ears and scream "I don't hear you" does eventually make one think that something other than rational debate is what those with waxy fingers are after.

      Delete
    7. The fact that Unknown calls me "Liar" is what makes me think that he is Barry Arrington, the ethically challenged CPA who committed ethical violations while working for Michelle Bachmann's campaign, opponent of free speech (other people’s anyway), abortion ambulance chaser, and expert on bestiality “obsessed with ‘women and dogs’”. This is the kind of childish ad hominem typical of ambulance chasin' Arrington.

      So far, just today Barry (for so I shall call him) has told a variety of lies which were not difficult nor subtle, but have been so trivially easy for us to refute that one must wonder what goes on in his head when he provokes us.

      To recap:

      1. Unknown accuses Whole Truth of lying, and says no ID proponent ever claimed there are no beneficial mutations: "You [TWT] are lying. show me one quote from any IDst Meyer, Behe, Welsh, Luskin... saying beneficial mutations cannot happen." Rumraket instantly responds with a list of four quotes from prominent IDiots saying exactly that!

      Unknown's response: crickets.

      2. Unknown repeatedly claims that neither Prof. Moran nor any scientist on this blog has ever presented evidence refuting Behe's assertions: "every "scientist" on this blog is very shy about addressing Behe's challenge... Take prof Moran for example... he never, never attacks M. Behe on the exact same matter even though he has the opportunity to address Behe's challenge." Prof. Moran instantly responds with list of almost two dozen blog posts he has written against Behe, not merely "addressing his challenge" but obliterating every claim he has made!

      Unknown's response: crickets.

      3. And now it's my turn to leave a third bootprint in Unknown's ass!

      Barry says: "I am going to prove him [me] liar once again"

      Uh, "Once again"!? Have I ever NOT humiliated you in any exchange we've ever had? Link to even ONE exchange we've had where I did NOT humiliate you totally, and back up everything I said with references. Sheesh.

      But I like the thing where Barry says "I will prove him liar" right after he tried that "You are lying" shit on TWT, and Rumraket instantly put a boot in his ass. Now Barry comes back for more! Talk about a glutton for punishment.

      "because he [me] is not going to be able to provide a quote from Behe where he says binding sites can't evolve."

      Oh dear, that's so hard!

      Behe, 2005: "There are none [papers by Behe] that use that phrase ["Irreducible Complexity"], but as I indicated in my direct testimony, that I regard my paper with Professor David Snoke [2004] as to be arguing for the irreducible complexity of things such as complex protein binding sites." [Behe, Dover Trial testimony, 2005]

      Binding sites are Irreducibly Complex, says Behe. And Behe says IC systems can't evolve.

      Unknown, can Irreducibly Complex things evolve?

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    8. I'm not done planting a boot in Unknown Barry's ass.

      I'm debunking Barry's claim: "I am going to prove him [me] liar once again because he [me] is not going to be able to provide a quote from Behe where he says binding sites can't evolve."

      I provided a quote from Behe saying that, from his cross-examination in the Dover v. Kitzmiller trial. There Behe says protein binding sites are IC, and IC things can never evolve, and he says he said the same thing in his "direct testimony."

      Indeed he did. Going back a little to his direct testimony, Behe had said then as well that protein binding sites can never evolve:

      Behe direct testimony, Dover, 2005: "Here again is a little simplified cartoon version of how proteins might interact... How do we get those to bind into a conglomerate molecular machine?

      In order to get them [proteins] to bind to each other... that is a large and long, tall evolutionary order. As a matter of fact, it's so tall that one can reasonably conclude that something like this [protein binding sites] would not be expected to occur. ...[E]ven if one was to have parts in the cell which if they could develop binding sites to bind to each other, and if that binding together would produce a new selectable property, that still does not help in Darwinian processes, because you still have the problem of adjusting many, many different things before you get the final result.

      ...I make this point exactly in my article in that book "Debating Design." ...It's says, "Thus, the problem of irreducibility remains even if the separate parts originally had individual functions."


      -- [Behe, Dover Trial direct examination, Day 10, Oct. 17, 2005.]

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    9. You can actually hear Behe himself saying protein binding sites are IC in an MP3 file at the NCSE website.

      Behe from 2002: "The problem of irreducibility, irreducibility in proteins is a general one. Whenever a protein interacts with another molecule as all proteins do, it does so through a binding site whose shape and chemical properties closely match the other molecule. Binding sites however, are composed of perhaps a dozen amino acid residues, and binding is generally lost if any of the positions are changed."

      I have to pause for a moment to laugh my ass off at Behe's basic ignorance of molecular biology! This IDiot just said "binding is generally lost if any of the [amino acids] are changed"! It was 2002, and Behe had never heard of the scanning mutagenesis experiments of Clackson and Wells in the mid-90's! There's no excuse for being that ignorant.

      Continuing:

      "One can then ask the question, how long would it take for two proteins that originally interact to evolve the ability to bind each other by random mutation and natural selection, if binding only occurs when all positions have the correct residue in place... the process can be simulated on a computer. Here is just a sample of the data I have generated over the past year or so... [T]he log of the expected time to generate what I call irreducible complex, irreducibly complex protein features, is shown as the function of the log of the population size and the log of the probability of the feature. The yellow dot is the time expected to generate a new disulfide bond in a protein that did not have one if the population size is 100,000,000 organisms. The expected time is roughly a million generations.

      The red dot shows that the expected time needed to generate a new protein binding site would be 100 million generations."


      Now stop right there. First, Behe again says that protein binding sites are IC, and IC things can never evolve. By "never" in this case he says it would take 100 million generations for a population size of 100 million organisms, and longer for smaller population sizes. That's effectively never.

      "Using data from these simulations, as well as Bill Dembski's concept of probabilistic resources, we can come to several broad, tentative conclusions. First, that undirected, irreducibly complex mutations cannot have been regularly involved in the evolution of large animals; the time frame would just be too long."
      -- [Blind Evolution or Intelligent Design? Address to the American Museum of Natural History. Michael J. Behe. April 23, 2002. Discovery Institute transcript. MP3 and Transcript at NCSE.]

      The IDiot just said that IC systems can never evolve in large animals, and protein binding sties are IC systems. Uh, duh! Every time you recover from a cold, the flu, or any other virus or bacteria, your immune system has just evolved a new protein binding site. And this IDiot says that would never happen in large animals!

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    10. For at least 13 years Behe has been claiming that protein binding sites are IC and can never evolve! Even though we keep observing examples of protein binding sites evolving, and fairly quickly, like e.g., Vpu viroporin in HIV. Even though every time you recover from a virus or bacteria, your immune system evolved a novel binding site.

      Behe continues to spew this shit. Here he is saying it just last year, in an argument with Larry Moran, which Behe lost badly:

      Behe, 2014: "The third obstacle [to evolution] is irreducible complexity, or the need to take multiple steps to reach a selected state."

      He just redefined "Irreducible Complexity" again; this is definition #35-J, "the need to take multiple steps to reach a selected state." Totally different from his definition in "Darwin's Black Box."

      Continuing:

      "...This type of barrier is ubiquitous at the molecular level because new protein-protein interactions in general will require multiple mutational steps to attain (as I discussed at length in "Edge [of Evolution]"...), many of which will be unselected." [Michael Behe, The Edge of Evolution: Why Darwin's Mechanism Is Self-Limiting. ENV. July 18, 2014.]

      Behe just said protein binding sites are IC, and IC things can't evolve.

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    11. Now let's note Unknown Barry's idiotic double standard for what counts as a "valid" argument.

      Unknown Barry: "As I told many times I am not scientist, the only way I can give credit to a "scientist" is if he is not afraid to address the challenges in public. (Commenting on a blog doesn't count because real scientists don't stay all day long following, answering comments)."

      Aha. So if we refute all of Behe's claims on a blog, it doesn't count as "addressing the challenges in public" because WE did it that way.

      But Unknown Barry gives credit to Behe as a scientist, because of what Behe writes at a blog... Evolution News and Views... which does not permit comments.

      Unknown Barry: "So far every "scientist" on this blog is very shy about addressing Behe's challenge even though everybody knows M. Behe never lets a response to him unanswered."

      AT A BLOG THAT DOES NOT PERMIT COMMENTS. BEHE RESPONDS ONLY AT A BLOG THAT DOES NOT PERMIT COMMENTS. You credit him as a "scientist" because of what he writes AT A BLOG THAT DOES NOT PERMIT COMMENTS, but you dismiss what we write at blogs that DO PERMIT COMMENTS.

      According to Unknown Barry, what we write at blogs that DO permit comments is not "addressing the challenges in public", but what Behe writes at a blog that DOES NOT permit comments is "addressing the challenges in public."

      This is the kind of un-self-aware, mind-melting hypocrisy that only Ambulance Chasin' Arrington is capable of.

      Delete
    12. Unknown Barry: "The only thing I am interested from Liar [me] is an open letter which would prove to me he is not chicken and he is not bluffing with his examples."

      No Barry, I'm the one demanding an open letter from YOU.

      I demand you piss off right now, leave this blog right now, and write an open letter to Michael Fripping Behe, and tell him to drive over to the University of Pennsylvania for a face-to-face debate with me, Diogenes.

      Unknown: "the only way I can give credit to a "scientist" is if he is not afraid to address the challenges in public. (Commenting on a blog doesn't count...)"

      Hey, you know what would be public? A face to face debate in front of an audience of scientists would be public. Behe's responses, written always on the blog Evolution News and Views, "don't count" according to you. But a face to face debate would be "addressing the challenges" in public, so Unknown, you write that open letter to Behe telling him to finally "address the challenges in public" and be sure to tell Behe that what he writes on a blog doesn't count! Tell him to address the challenges in public!

      If you think it would be a bad idea for Michael Fripping Behe to debate me, Diogenes, face to face, then I demand you write an open letter Michael Fripping Behe telling him why not to do it and why it would be bad for his career and preshus reputation to have his own words projected on a screen.

      As for "proving that I am not chicken", oh I tell you what, I'll debate Fripping Behe face to face and compare his words to facts and let the audience decide for themselves if he is insane or a pathological liar. Let the audience decide if I'm chicken when I'm crushing Behe in front of them.

      Whatsa matter, Barry? Chicken? The idea of your hero Behe debating me face to face scares you? Bock bock! You chicken shit little porn-obsessed commenter-banning free-speech-suppressing accountant-books-fixing failed politican ambulance-chasing queer-hating shyster coward!

      Write that open letter NOW, chicken shit!

      Delete
  14. First I am not B Arrington although mistaken me for an american lawyer is flattering for me not the same can be told about Liar's judging capabilities.

    Unbelievable everybody noticed Liar quoting prof Behe saying binding sites can evolve. Liar can't read and he wants to debate prof Behe he would loose big time. Imagine him with a real job as an engineer where he had to build something by a written specification.

    I started to read a few of the articles posted by prof Moran and nowhere have seen the tons of evidence that prove "progressive building of coherent systems that Darwinists imagine"

    Let's quote again:
    M. Behe: "When we look to see what they do when we are watching, we never see the sorts of progressive building of coherent systems that Darwinists imagine. Rather, we see tinkering around the edges with preexisting systems or degradation of complex systems to gain short-term advantage.""

    By the way noticed Behe addressing Miller's accusations

    http://www.evolutionnews.org/2015/01/kenneth_miller_1092771.html

    "Miller's incongruous response essentially is to say: "No, I have decided to change your own model. I will switch the premise to one in which each protein binding site will necessarily be beneficial by itself." Much worse, he doesn't tell his readers that's what he's doing. His writing leads them to believe he is describing the same situation as I did. Let me be clear, if Miller had simply said that he thought there would be no actual situations in nature like I modeled -- that the subset was empty; that never in reality would two new protein binding sites be needed before any new selectable property resulted -- then that would have been fine. We could have argued amicably about whether that was true. But he didn't. Instead he conjured an entirely separate scenario, and then claimed it was I -- not he -- who was "fabricating," trying to deceive readers with a "statistical trick"!"

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    1. Could you even be any more up inside Behe's ass? I'm hard pressed to see you advancing even a single original thought or point, it's all mindless Behe quotes.

      I have a serious request for you:Please give some sort of hint that you are capable of considering a point without having to scour through your library of infallible Behe scriptures to look for a divine refutation.

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  15. "Aha. So if we refute all of Behe's claims on a blog, it doesn't count as "addressing the challenges in public" because WE did it that way."

    All I am asking is a blog post that addresses with evidence :

    M. Behe: "When we look to see what they do when we are watching, we never see the sorts of progressive building of coherent systems that Darwinists imagine. Rather, we see tinkering around the edges with preexisting systems or degradation of complex systems to gain short-term advantage."

    I said comments doesn't count because usually people don't read hundreds of comments on a blog post. Diogenes can you do a blog post with your tons of evidence?

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    1. Has Behe ever given a specific example of what he fantasizes "the sorts of progressive building of coherent systems that Darwinists imagine" would look like? I'm sure it would be very amusing.

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    2. Yeah, in court in the dover trial. He imagined the kind of answer he wants to see is mutation-by-mutation, all the way from no flagellum, to a flagellum.

      So to satisfy Behe, we have to be able to show him how the ancestor of bacteria with none of the constituents that make up the flagellum looked, before any of them evolved. Then he wants to be shown what evolved first, every single mutation one by one. How they were added together and worked, dusins upon dusins of proteins. Substitution by substitution, duplication by duplication and so on. With all the various selective pressures and periods of neutral evolution along the way.

      And of course, if you give him that, he also wants proof that all those things are how it really happened.

      So basically Behe, in order to be convinced that a man can walk across the american continent, demands to be shown how each and every step was placed, where it was placed, what kind of soil was tread on and what sound it made, then demand evidence to justify every single step of the way and if you can't do that, then to Behe you're not justified in thinking a man can walk across the american continent.

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    3. I'd be more than happy to take note of Behe if he gave an account, in equivalent detail to that he demands of 'Darwinists', of how the flagellum was actually assembled By Design.

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    4. we see tinkering around the edges with preexisting systems or degradation of complex systems

      Something Behe says I can agree with. Not a bad description of how some of the mechanisms of evolution can work.

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    5. Punkknown, did you write that open letter to Behe that I demanded? This doesn't look like an open letter to me. I told you to piss off and write an open letter to Behe telling him to meet me for a face to face debate in front of an audience of scientists-- or if you think that's a bad idea for him, then you write him an open letter explaining why he should not do it.

      So far:

      PunkKnown has been caught lying when he said 1. that no ID proponent ever claimed there were no beneficial mutations, 2. that neither Prof. Moran nor any scientist on this blog has ever presented evidence refuting Behe's assertions, and 3. that I could not produce quotes from Behe proving that he said protein binding sites could not evolve. In each case, his bizarre assertions were instantly buried under a mountain of easily accessible evidence disproving them.

      Let's focus on his third claim: that I could never produce quotes where Behe says that protein binding sites could never evolve.

      PunkKnown: "I am going to prove him [me] liar once again because he is not going to be able to provide a quote from Behe where he says binding sites can't evolve."

      That one was easy to disprove-- Behe said as much under oath on the witness stand at Dover, under both direct and cross-examination.

      I instantly presented a list of quotes from Behe saying that protein binding sites can't evolve, starting here.

      Oops. Does PunkKnown start to question his own expertise on ID "theory"? Uhhh nope.

      Punkknown's response: "Unbelievable everybody noticed Liar quoting prof Behe saying binding sites can evolve. Liar can't read...Imagine him with a real job as an engineer..."

      Uh, the claim that Behe said it's possible for protein binding sites to evolve is not true nor would it be relevant if it were true. First it wouldn't be relevant because Punkknown's claim was that I could not produce quotes where Behe says protein binding sites can't evolve-- yet I did just that-- so Punkknown was wrong once again. I gave several quotes where Behe says protein binding sites can't evolve, and Dembski has said the same. Hypothetically, if in 2002 Behe has said it was possible for protein binding sites to evolve, then that would simply constitute him contradicting his other clear statements that binding sites can't ever evolve. Behe's self-contradictions undermine his perceived expertise and authority.

      But Punkknown and I were not arguing over whether Behe ever said it was possible for binding sites to evolve; we were arguing over whether Behe ever said it was IMpossible for binding sites to evolve. Punkknown said I could never produce quotes proving Behe said it was impossible, but I produced quotes of him saying just that. If somewhere else Behe had said the evolution of binding sites was possible, that's just an IDiot contradicting himself for the 1,000th time. We were not arguing about whether Behe is self-consistent or intelligent; he isn't.

      I never said Behe was consistent about anything; my charge against him has always been that he equivocates, flips definitions to evade falsification of IC, and contradicts himself endlessly.

      Next, in the quote from the 2002 AMNH debate, Behe never says it's possible for protein binding sites to evolve. He said that for a population of 100 million organisms it would take 100 million years for a binding site to evolve, and Behe and all the other IDiots consider that to be effectively impossible, certainly for all land vertebrates and many if not all marine vertebrates, which is why Behe said it.

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    6. Our story so far:

      1. Unknown accuses Whole Truth of lying, and says no ID proponent ever claimed there are no beneficial mutations: "You [TWT] are lying. show me one quote from any IDst Meyer, Behe, Welsh, Luskin... saying beneficial mutations cannot happen." Rumraket instantly responds with a list of four quotes from prominent IDiots saying exactly that!

      Unknown's response: crickets.

      2. Unknown repeatedly claims that neither Prof. Moran nor any scientist on this blog has ever presented evidence refuting Behe's assertions: "every "scientist" on this blog is very shy about addressing Behe's challenge... Take prof Moran for example... he never, never attacks M. Behe on the exact same matter even though he has the opportunity to address Behe's challenge." Prof. Moran instantly responds with list of almost two dozen blog posts he has written against Behe, not merely "addressing his challenge" but obliterating every claim he has made!

      Unknown's response: crickets.

      3. Punkknown says I'll never be able to produce a quote from Michael Behe saying it's impossible for binding sites to evolve. Punkknown says: "I am going to prove him [me] liar once again because he [me] is not going to be able to provide a quote from Behe where he says binding sites can't evolve." I instantly presented a list of quotes from Behe saying that protein binding sites can't evolve, starting here.

      Unknown's response: Gish gallop to new, different false statements.

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