Friday, October 09, 2015

Brace yourselves, a new "Icons" is coming

Having narrowly escaped one catastrophe—the end of the world on October 7th—there's another looming on the horizon. Denyse O'Leary tells us that Jonathan Wells is preparing an "update" of his book Icons of Evolution [What’s happened since Icons of Evolution (2002)?].

You know what's going to happen next year if she is right? We are going to deluged with pre-publication publicity promoting the book that we can't see. We'll be told that it refutes evolution and builds on the outstanding success of the first book. We'll be told that Jonathan Wells addresses and refutes all of the criticisms of his first book and adds some more devastating proofs that the Rev. Sun Myung Moon is right.

None of this will be true, of course, but that's why the IDiots will get in their licks before we can prove it by reading the book. This is the standard ploy taken by the Discovery Institute over the past few years.

I know a lot about Icons of Evolution because for seven years it was required reading in my course on critical thinking. All my students had to write essays on one of the chapters. They had to analyze the arguments that Wells was making and decide whether they were valid or not.

Some of you may have forgotten about Icons of Evolution so you may have to refresh your memory by reading the short summary and reviews on the Wikipedia site [Icons of Evolution]. You can see that Wells has his work cut out for him if he's going to reply to all of the criticism.

Here's a few posts that I have done over the years to show that Icons of Evolution is seriously flawed. Some of them show that Jonathan Wells is dishonest—something that my students usually discovered on their own.1
I'm hoping to get a response in his new book but I'm not holding my breath. I spent a lot of time showing that his last book, The Myth of Junk DNA was flawed but here's how Jonathan Wells responded [see Jonathan Wells Sends His Regrets] ...
Oh, one last thing: “paulmc” referred to an online review of my book by University of Toronto professor Larry Moran—a review that “paulmc” called both extensive and thorough. Well, saturation bombing is extensive and thorough, too. Although “paulmc” admitted to not having read more than the Preface to The Myth of Junk DNA, I have read Mr. Moran’s review, which is so driven by confused thinking and malicious misrepresentations of my work—not to mention personal insults—that addressing it would be like trying to reason with a lynch mob.
Denyse O'Leary warns us that there may be more "icons" in the next book. She quotes someone named Stephen Batzer who claims that there are three new "show stoppers."
  1. That Darwin’s finches are simply races of the same bird. There has been no speciation.
  2. That the tree of life is not viable. “It’s a bush!” they respond. Well, then Darwin was wrong, and the model is wrong. If it’s a *bush* it isn’t a *tree*. The Darwinian model is common descent and gradual differentiation. That has been shown to be false, because of #3.
  3. ORFAN (Orphan) genes. Where do novel genes come from? If common genes mean common descent, then novel genes mean intervention and an innovator.
I wish I were still teaching my course. These are so easy to refute that all my students would have gotten A's on their essays. It shows you that the level of biology expected by Denyse O'Leary and the IDiots is nowhere near as elevated as second year university.


1. Every year I would have students setting up an appointment to see me in my office to discuss a problem they were having with their essay. They had discovered that some things in Icons seemed inconsistent with the truth and they wondered where they were going wrong.

141 comments :

  1. So, is Wells a scientist? Is Icons science?

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    1. Is everything that makes claims about the world science, then?

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    2. Isn't it fairly well established that science is hard to define and demarcate from non-science?

      I agree with LM that the idea of special creation is (or at least can be) science. My standard hypothetical is to describe an exoplanet on which all the evidence points towards the local biosphere having been designed 10,000 years ago; would a scientist who examines the planet be forbidden from postulating that an unknown (perhaps super-advanced alien) intelligence created that life? I hope not.

      The only problem is that any given real life creationists may be dishonest instead of mistaken. That would then make them a pseudoscientist instead of an incompetent scientist, but it doesn't change that special creation can be a scientific idea given the right evidence.

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    3. John, you've been seeing me explain my view of what science is for almost 20 years. I can't believe you haven't been paying attention all those years.

      Many of us believe that science is a way of knowing that relies on evidence and rational thinking (and healthy skepticism). As long as you attempt to adhere to that process you using the scientific way of getting at the truth. Some people do it badly and some people do it well.

      There's no restriction on what kind of knowledge you afe trying to acquire by this way of knowing. You could, for example, be looking for evidence of gods and that still counts as science using the broad definition.

      We reject the idea that science as a way if knowing is restricted by methodological naturalism. I'm told that this is now the majority view among philosophers of science. That's going to make for a very different trial the next time ID is challenged in court.

      I know you don't agree with the definition but please try harder to understand what we mean when we say that the search for an intelligent designer counts as science. It's mostly bad science but it still counts as science.

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    4. Larry said;

      "Many of us believe that science is a way of knowing that relies on evidence and rational thinking (and healthy skepticism). As long as you attempt to adhere to that process you using the scientific way of getting at the truth. Some people do it badly and some people do it well."

      I'll respond to that by posing a question as food for thought:

      Is a person relying on evidence, rational thinking, and healthy skepticism, and adhering to that process, when they perceive and judge everything through the filter of their preconceived religious beliefs?

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    5. Yes, they claim to be adhering to the process as long as they attempt to justify their position by claiming that it is supported by evidence and rationalism. We all try to do this even though we all have biases and preconceived beliefs. Nobody can be perfect at using the scientific way of knowing but almost all of us want to think that everything we belief is supported by evidence and is rational.

      Creationists have declared that they want to play by the rules of science rather than just declaring that their beliefs rely on some other way of knowing, like blind faith. It's now up to us to show that if they want to play that game they will lose. You don't just tell them that they aren't allowed on the field because we don't think they are going to play by the rules.

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    6. Larry,

      I don't subscribe to methodological naturalism, as you should know. I agree that anyone who uses the tools of evidence and rational thinking is doing science. We appear to differ on whether IDiots are using those tools. And I'll admit there are degrees of bias, i.e. abandonment of evidence and reason. That's why the demarcation problem is hard. Nevertheless, there must be a boundary, however fuzzy, and in my opinion ID as it's commonly practiced lies on the other side. There may be a few exceptions, in which an IDiot or two really does science (though I can't think of any at the moment), and there are certainly exceptions in the other direction, in which a scientist clings to a preconception in the face of all evidence to the contrary. But in the main, it seems to me that ID as practiced isn't science at all, not because it mentions god, but because it only uses evidence and reason as the proverbial cheap suit.

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    7. I brought up methodological naturalism because it was one of the main criteria used by Judge Jones to declare that ID is not science.

      I agree that there's a boundary somewhere but it's easier to apply it to individuals that to entire fields. For example, evolutionary psychology still counts as science even though a majority of its scientists are not doing good science.

      Also, you don't judge a field by its supporters. You can't conclude that evolutionary biology isn't science just because some of its supporters get it wrong. Similarly, you can't say that ID isn't science because of what Ben Carson says.

      I firmly believe there are Intelligent Design Creationists who are doing their very best to argue for intelligent design based on evidence and rational thinking. MIchael Behe and Michael Denton are two examples.

      They are doing science, even if I think they are doing it wrong. You can't dismiss all of ID as NOT-SCIENCE just because there are many others who aren't doing as good a job.

      Among those who practice bad science there are some who are pseudoscientists. I restrict that category to people who are deliberately trying to deceive by pretending to act like they are doing science when they aren't. Most astrologers fit into this category and so do some ID proponents. Jonathan Wells is one, so is Casey Luskin. They aren't doing science.

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    8. I agree that "Icons" is sufficiently sophisticated in its misrepresentations of the literature that Wells has to know that he is lying. I also agree that it is quite difficult to demarcate science from nonscience. However, when someone is lying about the data in order to reach desired conclusions (as opposed to merely being wrong), they have stopped doing science> It's no longer a question of whether or not it's 'good science' or 'acceptable science' but it has stopped being science altogether.

      I applaud your teaching about intelligent design. I used to be strongly in favor of using "creation science" to teach about the scientific method (it made a lovely counter-example, and their mistakes and lies were just sophisticated enough to be challenging and were close enough to real science that students could pick the arguments apart easily and learn some good science in the process. I stopped trying to do that with intelligent design, because so many of their arguments rely on obfuscation and nuance, which proved difficult and unrewarding for students to pick apart, leading to conclusions of "it's all so confusing - you really have to know this stuff to figure out who's correct, so who knows, maybe they've got something." Undoubtedly a better teacher willing to invest more time would have more success. I used to offer my intro class a dollar for any creation science argument they could find that I couldn't refute, but when ID came along it would take 15-20 minutes to work through some of the Dembski stuff, and many students still wouldn't really get it, so I stopped.

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    9. The judge in the Dover trial cited methodological naturalism because the plaintiff's expert in philosophy, Barbara Forrest, testified that it is the foundation of science, in her opinion. In this, Ken Miller concurred in a comment made on this very blog several years ago. I don't claim the be an expert in philosophy but it is my impression that the majority of scientists and philosophers agree with her.

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    10. I don't claim the be an expert in philosophy but it is my impression that the majority of scientists and philosophers agree with her.

      I've heard experts (philosphers) who say differently but that's not really the point. If the people testifying in the trail were being honest and truthful, they would have said that there are differing opinions within the philosophy of science community. Judge Jones would then have written, truthfully, that if one accepts that science is limited by methodological naturalism then ID is not science but a substantial number of experts in the field disagree with such a limitation.

      That's not what Judge Jones said. Instead he said, "Methodological naturalism is a "ground rule" of science today which requires scientists to seek explanations in the world around us based upon what we can observe, test, replicate, and verify. (1:59-64, 2:41-43 (Miller); 5:8, 23-30 (Pennock))."

      You can read the entire paragraph at: What did Judge Jones say in 2005? (Part I). Jones relied heavily on the testimony of a religious scientist (Miller) and a religious philosopher (Haught).

      Jones says, " While supernatural explanations may be important and have merit, they are not part of science." If that's true then ID cannot be science. But today I don't think most philosophers of science would agree. They recognize that science has a long tradition of of investigating supernatural claims and finding them to be without merit. Science has disproved, for example, the claims of Young Earth Creationists even though the explanation was supernatural.

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    11. Actually, according to the judge himself, based on several presentations he has given given subsequent to the trial, he relied heavily on the testimony of Prof. Forrest, because she was the one who testified about how the authors of Of Pandas and People replaced creationism and various cognates thereof with intelligent design and various cognates thereof. In fact, the defense was deathly afraid of Prof. Forrest and moved heaven and earth try to keep her off the stand. By the way, she makes a distinction between methodological naturalism and philosophical naturalism, despite herself being an atheist, something that the defense tried to exploit; the judge was not impressed. As Prof. Miller stated in a comment on this very blog, he is a methodological naturalist and a philosophical theist.

      My own position is that methodological naturalism is a necessary condition for doing scientific investigations. That's because supernatural explanations are unbounded. Contrary to your claim, apparent non-natural events can be investigated using the tools of science. There have been numerous such investigations of PK and ESP, none of which have turned up anything more then experimental anomalies which barely pass the 5% significance level.

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    12. "Creationists have declared that they want to play by the rules of science "

      But they haven't done that - this is what they declare: http://creation.com/about-us , including "By definition, therefore, no interpretation of facts in any field, including history and chronology, can be valid if it contradicts the scriptural record."

      That is not a declaration to play by the rules of science, but rather to ignore those rules.

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    13. I firmly believe there are Intelligent Design Creationists who are doing their very best to argue for intelligent design based on evidence and rational thinking. MIchael Behe and Michael Denton are two examples.

      Since Dr. Behe has had errors in his probability calculations pointed out to him numerous times (he persists in calculating the chances of specific evolutionary changes occurring, rather than calculating the chances of evolution occurring at all, then representing the results erroneously as the unlikelihood of evolution occurring at all), yet persists in using the same tactics, do you think he is doing his "very best" to base his conclusions on evidence and rational thinking? At what point does extreme reluctance to acknowledge the correctness of a contrary position (how to do probability calculations regarding the question of whether evolution is possible at all) shade into dishonesty?

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    14. LoL! The only reason probability calculations are used is because your position doesn't have any actual evidence or model. How does one model undirected processes producing something like a bacterial flagellum?

      OTOH genetic and evolutionary algorithms are perfect models of directed evolution.

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    15. judmarc asks,

      At what point does extreme reluctance to acknowledge the correctness of a contrary position (how to do probability calculations regarding the question of whether evolution is possible at all) shade into dishonesty?

      I don't know. I can't decide whether Jim Shapiro and John Mattick, for example, are deluded or dishonest. Same for Michael Behe.

      But in some sense it doesn't matter because what we are talking about is whether they are doing science correctly or not. At no point in time have I ever considered that John Mattick is not doing science and therefore should not be allowed to publish in science journals.

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  2. How the hell is #3 an "Icon of Evolution"? More like an icon of God of the Gaps.

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  3. What about Miller-Urey experiment? Any progress there? I'm willing to bet $100 that neither Larry nor any other of Darwin's apostles will be able to add anything new to this icon. No progress since 1950-ties at all.

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    1. Hi Jojo,

      It would improve on the image you give if at least you were a bit less arrogant in your ignorance. Those two things, arrogance with ignorance, are incompatible. They make you look rather stupid, and I would think that, given that you're here representing your belief system (whether you want to or not), well, at least because you, supposedly, have respect for such belief system, you should present yourself accordingly. This is just a suggestion, of course. If you want to show off as an exemplar of stupidity for your beliefs, who am I to stop you?

      Miller-Urey demonstrated, quite successfully, that more complex organic molecules could arise from less complex chemicals in an environment devoid of life. It was quite the success, though (here exemplifying that humility I'm talking about above) I don't remember if this was the first time someone showed that complex organic molecules could be formed in the absence of life (the word "organic" is an archaism, originally casted because of the idea that these molecules could only come from life, if my memory does't fail).

      But you're asking more than that. You're asking of there's progress in experiments related to abiogenesis. Well, yes. Lots. Only today the ideas are tested at different levels, and from many different angles. You could have saved yourself some embarrassment by googling and reading.

      Is there already life sprouting out of labs? Well, I don't think so. But there's progress nonetheless. The idea of metabolism first, self-replicating chemicals, organic molecules formed in environments devoid of life under many different conditions (because of the uncertainty about what the conditions were for the successful abiogenesis that landed all the way to us), etc, etc. At other levels how primitive catalytic and genetic (as in information carrying) molecules could be one and the same (like in the RNA world hypothesis), etc.

      But you need a lot of patience to piece all of that information together. Happy reading Jojo. May that be an educational experience for you.

      P.S. Do you think that if we were unable to ever figure out ways in which life could have originated then all of the sciences would collapse, implode, and presto, the planet is 6000 years old, we are not relative to the other apes, We're Noah's offspring, and Christ died for your sins?

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    2. P: "Is there already life sprouting out of labs? Well, I don't think so. But there's progress nonetheless."

      Abiogenesis has always been one of the ID arguments. If we think we know how it occurred, why has nobody produced life in a lab? But if the day ever comes that we are capable of doing so, you can guarantee that the IDists will simply argue that it is evidence for design. After all, the experiment was designed.

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    3. You betcha William Spearshake. But then we can confidently respond that god created only evolutionists in his image, since obviously creationist intelligence is not up to par when it comes to recreating gawd's design. And of course a complete revision of the book of genesis will be required.

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  4. So we're about to discover that Sun Ayung Moon was Jesus Christ resurrected? When will he come for the third failed time?

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  5. Won't it be interesting to see how he revises his claims for the original "icons" ? In view of the withering criticisms he has received for them, he would be well-advised to at least adjust them. It may look like squirming ...

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  6. Not that it really matters but I've always wondered why you don't have a Wikipedia page Professor Moran? Are there certain criteria one must have to earn one? I see the good Mr Felsenstein and Wells have theirs but still can't find anything for you. It seems your efforts in this battle would be recognized.

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  7. why not teach this/the other Well's book in classes dealing with evolution? why a criticism class only? isn't Well's making scientific criticisms etc of a theory in biology? Are his criticisms not science ones?
    His book is still remembered and will be. he's encouraged to add to it. Not discouraged.

    On the point about the finches being species. Well are they or not? do they not have the ability to reproduce with offspring to continue a population/
    I don't think species is a actual thing in biology or relevant in keeping different populations separate and not mating.
    however the bigger point is probably the finches fail Darwins hypothesis that they are the origin for important segregation. just races like they term it in humans.
    Wells is right in saying no species were created. The creation of races from evolution is another matter.

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  8. Jojo, If you have a genuine interest in the question of the Origins of Life, I suggest Iris Fry: "The Emergence of Life on Earth" might be an interesting read. It tells me that while science doesn't claim that there is evidence that life emerged by natural means, science knows no reason why that shouldn't be the case. And science is doing its best to investigate the subject. What else can they do? To me, the scientific attitude seems to be "As long as we don't know we have to do our best to find out." Although I believe the suspicion that no divine intervention was required is widespread.

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  9. I notice that his book was subtitled "Why much of what we teach about evolution is wrong". Who is "we" in this sentence: logically it means Wells and his colleagues in the Discovery Institute. If so I don't disagree with it, except that I'd put it more strongly: "Nearly all of what we teach about evolution is wrong".

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  10. Ralf,

    We all do. Dodging the question by referring to a book full of unfounded speculations doesn't resolve the issue. No matter what you chose to believe, the fact that if unintelligent processes lead to the origin of life, intelligence should be able to replicated that process.

    Dodging the obvious and logical conclusion that a higher intelligence with the source of life energy had to have been behind the origins of life doesn't make your beliefs even remotely real. You simply chose to ignore what's obvious and believe in a delusion. The question remains why?

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    1. "No matter what you chose to believe, the fact that if unintelligent processes lead to the origin of life, intelligence should be able to replicated that process."

      By "intelligence", do you mean humans? Are you asserting that since humans haven't already replicated the origin of life, it's too late and it can't ever be done (or at least understood), so humans should stop trying and just swallow your fairy tale religious beliefs? If so, you're the one who is delusional.

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    2. "if unintelligent processes lead to the origin of life, intelligence should be able to replicated that process"

      That doesn't follow. We have a pretty good understanding of how the solar system began. Yet we cannot replicate the process (for scale reasons).

      "Dodging the obvious and logical conclusion that a higher intelligence with the source of life energy had to have been behind the origins of life doesn't make your beliefs even remotely real."

      That doesn't follow either. You're saying that if intelligence can't replicate the process, intelligence did it. Doesn't sound like a very logical conclusion.

      "You simply chose to ignore what's obvious and believe in a delusion. The question remains why?"

      You're talking to the mirror now.

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    3. I also suspect that you don't know what the wording "unfounded speculations" means.

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    4. "No matter what you chose to believe, the fact that if unintelligent processes lead to the origin of life, intelligence should be able to replicated that process. "

      This is the quintessential creationist god-of-the-gaps reasoning. You are aware, I hope, that at one point in history we had no idea how the sun worked, how stars formed, how birds could fly, how mountains formed, how trees could grow and so on and so forth. You could have erected your same silly argument back then too.

      Notice how once we actually figured it out, none of these phenomena turned out to be supernatural events. The origin of life isn't going to be any different and those of you who hold out faith that this problem isn't eventually going to be solved (and that the answer isn't another natural process) are deluding yourselves.

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    5. Mikkel,

      "You could have erected your same silly argument back then too."

      They did!

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    6. Liesforthedevil (who I think is Seal Cordova?) says: if unintelligent processes lead to the origin of life, intelligence should be able to replicated that process.

      Incredibly stupid, Sal. You're saying: Because intelligent beings have never been observed to create life; therefore an intelligent being created life.

      We've pointed out this very logical fallacy to you a dozen times, and you just keep repeating it. Why?

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    7. @Diogenes

      Sal is called "Liarsfordarwin". This dude is one of the many strange incarnations of Andre Gross (or his... fans?), I think. I forget the name, he's changed it so often.

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    8. So many non-sequiturs packed in a paragraph and he still has the audacity of pontificating his "obvious and logical conclusion"

      Creatards, smfh

      As usual, Salvita

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    9. Get your source of life energy that had to have been behind the origins of life, here!

      Everything Is Energy
      https://www.youtube.com/watch?v=c9qHS5IrO0I

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  11. Stephen Batzer is a mechanical engineer (Salem Hypothesis award winner) who popped up on the IDiot's blog a few years ago proving evolution was impossible because of, well, just because. Can't have engineering without an engineer, blessed be he.

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  12. liesforthedevil, if life is a product of events early in the life of our planet, involving processes we maybe never may be able to figure out, and over a length of time we have no means of estimating, it is not reasonable to expect that

    ... intelligence should be able to replicated that process.

    I don't see any reason to think that the process may be replicated by us. Your reply only shows you assume science can do 'miracles' on a scale beyond what I think it presently can, or ever may be able to do. I find it sufficient to know that for the time being, nothing is known that says such 'miracles' cannot be attributed to nature itself.

    You're free to think otherwise but anyway, the fact of evolution stands even if we never may figure out the details of how the first life may have started without divine intervention..

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  13. Hi Rolf
    When you say evolution here do you mean the Neo-Darwinian synthesis?

    "You're free to think otherwise but anyway, the fact of evolution stands even if we never may figure out the details of how the first life may have started without divine intervention"..

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  14. I mean the ToE; you are free to chose between any variations within that grand theory, as much a fact as the theories of heliocentrism, gravity and other scientific achievements.

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    1. Hi Rolf
      What is causing variations in the grand theory? The theory or gravity (General Relativity) has been repeatably tested and verified with the eclipse and other recent tests. Does the Grand Theory have an equivalent test?

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    2. What is causing variations in the grand theory? The theory or gravity (General Relativity) has been repeatably tested and verified with the eclipse and other recent tests. Does the Grand Theory have an equivalent test?

      Just as with evolution, the theory of gravitation is a subject of active research into "variations." They are both well established scientific theories with active discussions and research ongoing on the frontiers between what's considered known and what's not.

      With gravitation, some current active research areas include dark matter, dark energy, MOND, and various characteristics of edge cases like black holes/singularities, and of course the relationship between relativity and quantum physics.

      With regard to your question about an "equivalent test," the cross-confirming evidence from many different areas of science includes various forms of radiometric dating and geology showing that indeed fossil ages line up as expected from evaluation of morphology. Then genetic testing became available and provided yet another cross-confirmation of the same thing. (In other words, which species developed from which common ancestors and approximately when was first reconstructed from their comparative anatomies and the geological strata where they were found; this was confirmed when radiometric dating was developed, and re-confirmed when genetic testing came along later.)

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    3. Hi Judmarc
      The mechanism of gravity, curvature of space time has been validated through experiment. Has the mechanism(s) of any large scale evolutionary change been validated through experiment?

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    4. Wow Bill, haven't you read what Judmarc wrote? Are you just plain ignorant or acting the 'interested' creationist?

      "With regard to your question about an "equivalent test," the cross-confirming evidence from many different areas of science includes various forms of radiometric dating and geology showing that indeed fossil ages line up as expected from evaluation of morphology. Then genetic testing became available and provided yet another cross-confirmation of the same thing. (In other words, which species developed from which common ancestors and approximately when was first reconstructed from their comparative anatomies and the geological strata where they were found; this was confirmed when radiometric dating was developed, and re-confirmed when genetic testing came along later.)"

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    5. Has the mechanism(s) of any large scale evolutionary change been validated through experiment?

      Large scale evolutionary changes appear to happen after large scale extinctions. I doubt there would be funding for crashing a largish asteroid into the earth and wiping out most of the life here.

      On the other hand, no one is creating black holes here on earth either. What's happening in both fields is a tremendous amount of careful observational research (observing the universe in the case of gravitation, and past and present life here on earth in the case of evolution), and experiments on smaller than cataclysmic scales (e.g., the Large Hadron Collider in the case of quantum physics, with some implications for gravitation, such as the Higgs boson; in the case of evolution, Dr. Lenski's Long Term Evolution Experiment would be one of a huge number of examples).

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    6. Hi Ed Jumarc
      No, I am not a creationist. I think Lenski's experiment is a good example of adaption and natural selection but not validation of creating a protein de novo with a unique amino acid sequence. I agree with your point that good observational research is being done in both areas but again evolutionary theory does not yet have experimental evidence of a mechanism that can validate large scale changes.

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    7. What's that "large scale" mechanism of gravity that differs from "small scale" gravitational mechanisms? Can "large scale" gravity be explained as an aggregation of "small scale" gravitation?

      Newton's law of gravity doesn't work at very large scales. Was he wrong all along until Einstein came up with a better model?

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    8. Hi Bill,
      apologies for my hasty conclusion on your earlier post.
      But, why the emphasis on a de novo protein? Lenski's experiment shows bacteria mutating over many generations, slowly adapting to a change in environment. And some strains currently are capable of using a substrate their ancestors at the beginning of the experiment couldn't.

      So why should it be a de novo protein and only a de novo protein as proof for ToE?

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    9. Hi Dazz
      I agree that Newton's equations were not wrong all along, because they are certainly useful for (local) gravitational measurements.

      What's that "large scale" mechanism of gravity that differs from "small scale" gravitational mechanisms? Can "large scale" gravity be explained as an aggregation of "small scale" gravitation?

      The mathematical model for local gravitation and cosmological gravitation is very different. Newtons model compares masses and their distances to come up with a force. This can be done with simple algebra. Einsteins field equations are based on gravity being the curvature of space time. This mathematical model required tensor calculus and was very difficult to derive specifically because curvature creates lots of mathematical complications for calculus. The equation was a model and was not terribly useful until others like Swartzchild made simpler application specific versions like the equation that calculates the size of a black hole. The equation successfully predicted Mercury's orbit and was validated by the eclipse experiment that was repeated several times.

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    10. Hi Ed
      Thanks for the gracious apology. "But, why the emphasis on a de novo protein?" The large scale evolutionary change we observe requires new proteins with new and different functions. An example of this is the transition from prokaryotic to eukaryotic cells and two large protein complexes, the spliceosome and the nuclear pore complex. These required dramatic changes to the DNA sequences.

      Re Lenski experiment I agree that it showed natural selection leading to adaption by allowing citrate to be consumed in an aerobic environment. If the enzyme that allows citrate to be consumed had evolved de novo (a protein containing almost 500 amino acids) then we would have had experimental evidence for a large scale evolutionary change. The citrate enzyme already existed so the mutation activated it. This experiment was exceptional at showing adaptive change through mutation.

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    11. But Bill, Newton's Law is not a "local scale" theory, and Quantum Gravitation is not a "large scale" theory. Quantum theory works on both scales, and the same principles that work at the Planck scale apply at larger scales for all I know. Newton's gravity can also be applied to large scales by aggregation of smaller objects

      Why should evolution be assumed to be different?

      Also, I'm no biologist, but I think there's plenty evidence that novel proteins arise by random mutation, no exotic mechanism needs to be invoked.

      Take this paper for example, posted here a few times already:

      Experimental Rugged Fitness Landscape in Protein Sequence Space

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    12. Hi Judmarc
      The mechanism of gravity, curvature of space time has been validated through experiment.


      Ah, think carefully - validation was *not* through experiment, but through careful observation (of Mercury's orbit, the gravitational redshift of light, and Eddington's eclipse observations). Hundreds of thousands of careful observations of macroevolution have been made, which all cross-confirm from various scientific disciplines (paleoanatomic with genetic with radiometric with geological). So (macro- and micro-) evolution has been confirmed just as well as general relativity if not better, down to the genetic level.

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    13. Re judmarc

      Newton's theory of gravitation is used in most problems in celestial mechanics, with relativistic effects treated as small perturbations. For instance, in the case of the precession rate of the orbit of Mercury, the relativistic contribution is 43 seconds of arc per century. That's about 8% of the total observed rate of precession, which is mostly due to the 2 body interactions between Mercury and the other planets, which, by the way, are also treated as small perturbations which allows the separation of the many body problem, which is not solvable in closed form into a series of 2 body problems which can be solved.

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    14. Hi Judmarc

      Hundreds of thousands of careful observations of macroevolution have been made, which all cross-confirm from various scientific disciplines (paleoanatomic with genetic with radiometric with geological).

      Can you site an observation that validates the mechanism of non directed genetic change followed by natural selection creating a new protein structure?

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    15. Hi Dazz
      You are talking about Quantum gravity here and I am not sure why. This is a theory different then Einstein and Newtons theory.

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    16. My bad. I really don't know much about these things. I still think, someone correct me if I'm wrong, there's no distinction between the gravitational "process" at small and large scales.

      I also think that the paper I linked above is a good example of a new protein evolving under selective pressure

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    17. Re Bill Cole

      Quantum gravity is a theory that, as we sit here today, does not exist.

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    18. Can you site an observation that validates the mechanism of non directed genetic change followed by natural selection creating a new protein structure?

      Heck, I can cite multiple observations of genetic change acted upon by natural selection creating whole new *species*, let alone a single novel protein structure. Google papers on the genetic differences between us and chimps, and the particular genetic differences that show evidence of being under selective pressure (as opposed to those that are a result of random genetic drift).

      Of course the kicker is "non-directed." No, I don't have time lapse photography showing Yahweh or one of the other usual suspects wasn't there tinkering with genes and gene products in his/her/their spare time away from shoving little propellers into microbe butts. But changes in genes and gene products to something else workable, though quite rare as individual events, are nothing special in the great long history of life on earth (unless of course you are a subscriber to Dr. Behe's particular version of terribly incorrect probability math, which you can see is wrong every time there's news of another lottery winner).

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    19. "Can you site an observation that validates the mechanism of non directed genetic change . . ." You're making a basic logical error. Non-directed change is the null hypothesis -- the thing that has to be disproven. You have to provide evidence that change is directed.

      Even as far back as when I was in college the first time (we're talking decades now) we were given examples of bacteria facing a stress in the lab and producing mutations of various sorts, but not necessarily the sort they needed to deal with the stress. That result was consistent with non-directed mutation and not with directed mutation.

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    20. I think I've posted this before, but theistic or directed evolution, apart of unscientific of course, sounds like grasping at straws to me. What's the point of believing in a god like that? I mean really, if one's idea of god is one that messes with tiny strains of DNA, often causing all sort of horrible diseases, malformations, conferring viruses resistance to antibiotics so they can kill more people, and go to extreme lengths to make it look like it's all random... with all due respect, how anyone can reconcile that with anything worth worshiping is beyond me

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    21. Bill Cole asked:

      "Can you site an observation that validates the mechanism of non directed genetic change followed by natural selection creating a new protein structure?"

      Non-directed by whom or what? Validates according to whom? Why only "genetic change followed by natural selection"?

      Can you cite an observation that validates the mechanism of directed genetic change (by whichever so-called 'God' you believe in) creating a new protein structure?

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    22. Hi Dazz
      Thanks for clarifying about quantum gravity. I do not believe just because the theory has challenges means that the supernatural needs to be discussed. Once we invoke the supernatural the science stops. I honestly believe that the theory of evolution is very cool but it is not without challenges. The origin of the ordered sequences in DNA that produce proteins is very difficult to validate. Despite this I think there are many observable mechanisms that can be identified in biochemistry that can support this great theory. I hope this conversation can move forward identifying causes that we can validate through observation and experiment.

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    23. Hi Colnago80
      Thanks your insights on gravitational theory.

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    24. Bill. According yo your Blogger profile...

      I became interested in Evolution when I became aware of the sequencing challenge that the structure of DNA created for the Neo-Darwinian synthesis. I was astounded that a theory that I believed in for 59 years of my life could have so many difficulties

      Is it rude on my part to ask if your realizing that "evolution has so many difficulties" happened when you had some sort of religious epiphany?

      I take it from that you don't "believe" in evolution anymore, after 59 years, is that correct?

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    25. Can you site an observation that validates the mechanism of non directed genetic change followed by natural selection creating a new protein structure?

      I think this question is framed using a misunderstanding of protein evolution. I would suggest reading;

      http://www.ncbi.nlm.nih.gov/pubmed/?term=12938173

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    26. @Bill Cole - what's the fundamental difficulty with protein evolution occurring? You presumably think that proteins are 'islanded' in some way, such that it is not possible to reach a novel structure (however defined?) from a current one. But without investigating protein space, how do you know you need an extra mechanism? Certainly many experiments demonstrate that functional proteins (and RNAs) exist at a significant frequency in random space, and that NS can tune these for function. That is not, of course, evolution 'in the wild', but the evolutionary experiment runs to trillions of organisms over millions of years, rendering it impractical.

      The converse question can be asked of the mechanism you import to bridge the assumed gaps. How does 'directed' evolution come up with new viable and beneficial structures? How does it get them into multiple genomes? To what extent has this alternative been verified with the same rigour you appear to demand of evolution?

      As to Lenski, I think you are asking a lot from a dozen flasks of culture in a highly constricted and bottlenecked environment, even over 20 years. I eagerly await the 'Million-Whale-Million-Year' experiment!

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    27. That is not, of course, evolution 'in the wild', but the evolutionary experiment runs to trillions of organisms over millions of years, rendering it impractical.

      It is, however, worth pointing out that no observations about the biochemistry of life on earth (evolution "in the wild") have shown a need for any novel mechanism for the evolution of proteins.

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  15. I wonder if he will apologize for editing a quote from Jain, Lake and Rivera's paper on the symbiosis theory of eukaryote origins to make it seem like they were bashing the entire field of molecular phylogenetics. I doubt it.

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  16. @Bill Cole,

    The ToE is a complex theory, with data from many diverse fields of science. I don't see comparison with gravity as relevant. The subject of natural selection (at least to people like me) looks like an obvious factor to be reckoned with, and not easily overturned. I don't see the demise of NS looming on the horizon.

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  17. Hi Rolf
    I completely agree that natural selection is a great theory and is here to stay. The only question is it the whole show and I don't think the evidence supports that it is. The challenge with the Grand Theory is finding a mechanism(s) that can explain the cause of the changes over time. Saying the theory is as solid as the theory of gravity would imply that it is as testable and unfortunately it is not. Is there a paradigm change that can make it testable?

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  18. Bill Cole, the best you can do is to spend a lot of time studying all (no, that's to tall an order,) but a lot more of the available science. Then you may perhaps come up with some new arguments. The old ones have not done too well in the marketplace.

    Mechanism? The most striking features are all the various methods nature employs to cause changes in the genome. Some, maybe most of them harmful, but once in a while, something productive happens. Nature have lots of time, and plenty of stuff to work with. So things do happen sometimes, and over time we can observe the results.

    Just look at a lazy river, it looks so peaceful but anyway, given time it may meander through many different paths.

    You probably realize on your own that there couldn't possibly be a simple method that would make evolution testable. That applies to much of the universe as well, and yet we already know and understand much more than anyone would have thought possible. And there still is much, very much left that we don't know, so the end of science is nowhere in sight. There are miracles yet to be unveiled.

    Science has an impressive track record and at least to me, there doesn't seem to be any good reasons to believe that science should be dead wrong wrt how it attempts to answer the basic questions about the history of this planet and its biology.

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  19. Hi Allan Rolf
    I agree with most of your points. Allan, I agree that the Lenski experiment was a great accomplishment and met expectations for what it was set out to do. I see that you guys both agree that large scale evolutionary change is hard to test for. I have been tasked to come up with an observable testable version of the theory. While I do not think that I will come of with a version that can answer a final testable cause of diversity, I do think there is opportunity to find some intermediate drivers. My hypothesis is that these drivers will be important for cancer research. The architecture of the protein manufacturing mechanism is made up of ordered sequences that are difficult to form with a random process but allow the opportunity for tremendous diversity (broad range of functioning proteins). My hypothesis is that this ordered sequence architecture and all its subunits like repair, splicing (alternative splicing also creates ordered sequences), gene transposition etc is an observable driver of evolution that can move the science forward with further study. I know this is a big paradigm change but I would appreciate your feedback.

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  20. Hi Dazz Judmarc
    I am just blogging to better understand the theory for an assignment I have. As we explore the facts I am ok however the chips fall. If I challenge you guys it is just to test the information you are giving me until I think it is factual. judmarc what do mean by the following?It is, however, worth pointing out that no observations about the biochemistry of life on earth (evolution "in the wild") have shown a need for any novel mechanism for the evolution of proteins.

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    1. I mean that the normal mutation rates are adequate to explain the number and speed of changes we see between species, including changes in proteins consequent to those mutations.

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    2. It just seems strange to me to doubt the fact of evolutionary change, for which there are innumerable actual examples, until someone can disprove a conjecture - "directed" evolution - for which no evidence exists. To me, it's something like looking past all the archaeological evidence about the pyramids at Giza and choosing to believe they were built by space aliens until someone can prove to you on a purely theoretical basis that Egyptians 5000 years ago could have had the necessary technology.

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    3. I haven't found an article I was looking for with more recent work on the topic, but here's a web page to the same general effect, showing the number of known protein folds/domains is in the 1300-1400 range, with nothing new having been discovered in quite a long while: http://www.proteinstructures.com/Structure/Structure/protein-fold.html

      So changes in folds/domains have a limited structural space to explore, and it isn't at all improbable the new structure might have some biological activity. Of course that could mean something bad, like cancer. Or it could mean nothing much happens. But it's not impossible some of these changes might very occasionally and under the right circumstances prove useful enough for selection to "see" them.

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    4. Hi judmac
      Thanks for the article. There is no doubt that change is factual its just difficult to test for its cause when change to DNA structure is involved. We know that DNA change is likely because of all the genome data we have now. We also believe that change to DNA can cause nasty diseases. We also believe that this change can affect how proteins interact and can cause run away mitosis which is what cancer essentially is. The non coding areas of DNA are also an area of study. Natural selection is a concept that is currently used in cancer research.

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    5. Hi judmarc
      mean that the normal mutation rates are adequate to explain the number and speed of changes we see between species, including changes in proteins consequent to those mutations.
      Do you have calculations that shows how this can work?

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    6. I think you may be in danger of mixing up two areas because they both involve DNA, and changes therein. 'Runaway mitosis' is a problem for multicellular organisms. But in obligate sexual organisms, it isn't a problem for the germ line - it can't be. Cancerous cell lines are a dead end; evolution is about something somewhat different, although there is overlap, with mutational factors held in common.

      I don't see why evolutionary proteins are considered 'difficult to form with a random process', even if the random processes of somatic lineage often lead to disaster. They contain common motifs which can be shuffled around, particularly during meiosis, in a manner that is indistinguishable from 'random'. Disasters in the germline are filtered with greater efficiency, via their effect on viability, and the impact of multiple rounds of selection (LLN).

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    7. its just difficult to test for its cause when change to DNA structure is involved

      Very few of these changes are advantageous. Yep, sure sounds intentional and designed to me! ;-)

      I don't get it, what about this process would lead you to want to test for a cause other than non-directed mutation?

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    8. Do you have calculations that shows how this can work?

      https://en.wikipedia.org/wiki/Molecular_clock

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    9. Hi Allan
      Sorry for the delayed response...had a bad travel day yesterday. The commonality I see between cancer and evolution is the common mechanism that creates proteins from DNA or the non coding sections that lead to enabling a pathway such as the hedgehog pathway that can create un wanted stem cells and eventually metastasis. The challenge I see to diversity being created by random change is the large space ordered sequences create and that occurrence of real protein folds that have to be charge and shape compatible. Here is a paper that discusses protein sequential space vs protein folds that I originally read on this blog2. Author Hunt (2007) : http://www.pandasthumb.org/archives/2007/01/92-second-st-fa.html

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    10. Hi judmarc
      Thanks for the article on molecular clocks. Here is a quote from the article.
      The notion of the existence of a so-called "molecular clock" was first attributed to Emile Zuckerkandl and Linus Pauling who, in 1962, noticed that the number of amino acid differences in hemoglobin between different lineages changes roughly linearly with time, as estimated from fossil evidence.

      The original study came from the change in hemoglobin. The evolution of hemoglobin is a bigger challenge. This is a by 4 multi protein complex that contains about 580 amino acids all together. If you look at Authur Hunts paper and use it as a reference can you come up with any explanation how hemoglobin genetic DNA sequences formed with a process involving random change? This is why I am skeptical that we have a reasonable final cause explanation for diversity.Author Hunt (2007) : http://www.pandasthumb.org/archives/2007/01/92-second-st-fa.html

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    11. @Bill Cole

      Ah, good old Douglas Axe. His work manages to "prove" only 1 out of 10^77 protein folds are functional, when actual observational work carried out by real scientists shows there are only 1200 or so protein folds in existence. So he's only off by 74 orders of magnitude. :-)

      Guess maybe he ought to check his probability calculations, eh?

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    12. Come on guys,. the cure of cancer is at stake here!, if you can't provide a step by step mutational pathway for human hemoglobin from the Pre-Cambrian, there's no hope for people with leukemia!

      Mr. Cole, your agenda is far too obvious.

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    13. @Bill Cole,

      I think you may have an incomplete view of mechanisms of generating protein sequences. You (like Hoyle before you) think that it is a question of random trials for each position, with all 20 acids bumping up the probabilities. It isn't. For example a simple short sequence of 14 residues with a binary pattern of polar and nonpolar will generate a turn or two of a helix - a fold. The probability of such a sequence given equal chances for polar and nonpolar residues from a 20-acid library is 2^14 or 1 in 16,384, not 20^14 as some ID-ers think. End-join two copies of such a module together and you might be fooled into thinking you had a peptide with a probability of 2^28, or even 20^28. You'd be wrong.

      Bitwise probability calculations are not realistic, given the mechanisms in play.

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    14. Hi Allan
      Do you think that Author Hunts probability estimates are credible? If I use your example and say we can get minimal enzyme activity with a 14 chain poly peptide how do we get from here to a working protein sub unit? Then how do we get to hemoglobin?

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    15. Then how do we get to hemoglobin?

      Wrong question. The probability of arriving at exactly the same result is always microscopic, because there are so, so many branch points along the way. Similarly, you can show the probability you don't exist is prohibitively huge. What are the chances your parents, of all the people alive on earth, would meet each other, fall in love, decide to get married, make love on one particular night, that one particular sperm would fertilize one particular egg...multiplied by all the generations of humanity leading to yours. So if you do things that way, evolution doesn't happen and you don't exist, and oh, no one ever wins the Powerball lottery, because you know the odds against any particular person winning it are ~175 million to one.

      OK, let's go back to the real world where you do exist and someone wins the lottery every month or so if not every couple of weeks. In that real world where we all actually do live, the question is not how you get to hemoglobin, but how you get to some functional metabolism. There are at least chlorophyll and hemoglobin and whatever runs the metabolisms of the life around hydrothermal vents. (Note that the basic shared structure of hemoglobin and chlorophyll is likely enough that it happened twice, once around magnesium and once around iron.) Given billions of years, cobbling a couple of molecules together turns out not to be so very unlikely.

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    16. Hi Jumarc
      A very thoughtful response, thanks. The required protein to aid in metabolic activity to multicellular animals had to carry oxygen because that is whats available. So the configuration could not be any configuration but one that can carry oxygen and also carbon dioxide because of the atmosphere on earth was fixed at that point of evolution. Also once you get the first side chain to evolve the next one ( approximate 140 amino acids) must fit by charge and shape with the first and have compatible function. Not much sequence flexibility here so now you are dealing with 20^140 of sequential space with very limited folds working. This is why I think final cause is so tough to get a solid handle on. I think your argument is a good one until you get to multi protein complexes where protein one needs to be compatible with protein 2 and 3 and 4 etc.

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    17. Bill,

      Aren't you, maybe unconsciously, just trying to get evolution to look impossible for your own satisfaction, while, maybe, holding to the fantasies about gods with a much lower standard of inquiry?

      Anyway, to your "point." Same answer. You're doing things backwards. The very fact that something that binds iron, even different versions of the hemoglobin that "won the race" so to speak, are so abundant, helps see that your point is moot. There's tons of different proteins that bind iron and are descendants of some unknown original hemoglobin. So, thinking of a precise 140 aa long protein does not help your case because most positions (most of the aa that you see) could have been (actually were) different to the one we have. That means that even for an hemoglobin you have tons of possible proteins that would work. Not just the one you see.

      But, as judmarc said, the fact is that there's a hemoglobin, and that calculating probabilities after-the-fact is meaningless. A meaningful question would be what kind of functional space might exist in sequence space. I would bet that it's a hell of a lot. Not only that, if you take a course in something like biochemistry, you will learn that functions, and bindings, etc, are not as black and white as we imagine before we take such kinds of courses. Proteins can vary in how strongly they bind iron, how much they bind to each other, etc, so much that sometimes it's hard to put a line and decide to call something an iron-binding protein or not. Such continuums easily show how the evolution of proteins that "bind" one thing or another, or one protein or another, could evolve. What matters in real life is for protein to get sufficient of one of the many sorts of things they might end up doing to get somewhere. This can happen in a primitive life with smallish peptides, and a bunch of smallish, functional, peptides is all it might take to start an evolutionary cascade. An evolutionary chain reaction.

      I hope that was clear enough. The main point is: it's not black and white. Proteins have lots of sub and unspecific interactions. Those easily serve as pinpoints for evolving more precise ones. After-the-fact "Probabilities" are just games. They are helpful only to make us notice if we might be asking the wrong question. What those should help you understand is that, obviously, hemoglobin is but one of many many possible answers to binding and transporting iron. That, obviously, even that one hemoglobin, did not appear from a random assemblage of amino-acids, but was rather built from an evolutionary process. It should also help you realize that maybe, just maybe, you've been thinking about evolution the wrong way.

      I hope that helps a bit. If unclear, apologies. I'm too familiar with these ideas, and might jump details here and there. Also, hell, this is just a comment in a blog, not a dissertation or treatise.

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    18. Hi photosynthesis
      I currently do believe that the current evolutionary mechanism(s) are not well enough developed to claim final cause. I think the enormous sequential space of the genome creates a formable challenge to the theory. I am open to become convinced otherwise and thats why I am on this blog trying to get my thoughts challenged and I appreciate you doing that. My outcome in not religious it is simply to determine if the theory has adequate evidence to claim final cause of diversity and if not can a testable theory be developed that identifies intermediate cause. I want to read your response carefully and will generate some questions hopefully by tomorrow.

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    19. Hi photosynthesis
      Thanks for you thoughtful response. I agree with most your points. There is one in particular that I disagree with and hopefully I can make my point clear enough.

      "But, as judmarc said, the fact is that there's a hemoglobin, and that calculating probabilities after-the-fact is meaningless."

      Calculating probabilities and other use of statistics after the fact is a valid way used in the scientific method to narrow down and identify cause of a historic event. This can be used to determine the cause of death in a potential crime scene or the root cause of a high failure rate of an integrated circuit that is causing havoc for a cell phone manufacturer. Jumarc is correct that when you look at an exact historic set of events and calculate that exact probability of the event happening it is always 100% but, as you would say, that is not the right question. The question is, given the probabilities we are observing what is the cause. If for instance we looked at a video of a night of poker and looked at all the hands, the chance that they all occurred is 100%. Lets instead look at the chance that everyone played by the rules. If we look at hands from player number 1 we see a distribution of no pairs to a straight. If we look at a distribution and spread (standard deviation) of this hand it would fall into an expected category. If we looked at player number 2 and saw his hand ranged from a full house to a straight flush we would not consider the probability of this result normal and would suspect he was not playing by the proper rules. The outcome is not what we would expect so we would then try to narrow down the cause which is out of the realm of standard poker rules.

      When I imagine you as a person who can walk, do work, taste, hear, see, smell, make persuasive arguments etc, I then think about the 20000 different proteins that allow you to do all these things. The question is could the ordered sequences inside DNA that allow all these proteins to be manufactured with the correct timing through RNA translation have formed by the current identified mechanism. Given the current probabilities of what we are observing do we think the identified evolutionary mechanisms are the likely cause of photosynthesis evolving? Is there another scientific answer, like, we have not yet identified a viable final cause. If so is there another intermediate cause we can identify. These are questions I would ask myself when I was solving problems with the scientific method during my career. If I think finding final cause is temporarily out of reach, can I identify an intermediate cause that get me closer. In this case the spliceosome may be a viable intermediate cause. If you are interested I can send you the papers I have collected on this subject.

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    20. Bill, you fail see the obvious problem: evolution is not teleological. In all your examples there's a "goal". You assume there's a goal in evolution, so you assume it's teleological (guided evolution). You are assuming your conclusion.

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    21. Hi Dazz
      Below is the scientific method. I think if you review it and look how I applied it to the above analysis you will see that i have not made any premature assumptions.

      Ask a Question
      Do Background Research
      Construct a Hypothesis
      Test Your Hypothesis by Doing an Experiment
      Analyze Your Data and Draw a Conclusion
      Communicate Your Results

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    22. You didn't do any of that. You claimed that it was valid to "calculate" the probability of hemoglobin evolving after the fact and you said that it's ok to do that based on a bunch of examples.

      In your own words:

      The outcome is not what we would expect so we would then try to narrow down the cause which is out of the realm of standard poker rules.

      Nothing in evolution dictates that we should necessarily expect hemoglobin or any other particular protein for that matter.
      Why should we "expect" hemoglobin if it's not because it's part of some target?

      There are many organisms that thrive without hemoglobin, including this fish:

      Chionodraco rastrospinosus

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    23. Ok...lets ask a question...step one of the scientific method. Did hemoglobin form through random mutation and natural selection. Do you want to take it from here?

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    24. It's your hypothesis, so you shouldn't need to ask me. Fill me in on how you go about all those phases in the scientific method

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    25. Hi Dazz
      Sorry for being a bit of a dick here but you have to admit I owed you one. The challenge to the proposed mechanism is that you cannot test it so it will not pass the scientific method. Also it assumes that you can mutate through ordered sequences which are the largest mathematical spaces in the universe. I think we need to look at intermediate cause which we have many potential candidates...I actually found 2 more today. We can test these because they can be observed through biochemical experiments. This is not final cause but it puts us on the way to a theory the creationists cannot touch and on very solid scientific grounds.

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    26. Of course we can test it. It's your persevering that hemoglobin in particular must be explained to unfathomable detail or else didn't happen what makes no sense as a challenge to evolution.

      Why not apply your required level of detail to other disciplines of science?

      What about the Moon? Can you explain how it came to be by accretion? I mean the "mathematical space" of possible particles, rocks, asteroids, etc.. to produce the particular end result in the current Moon must be humongous. There surely must be something else to gravity, right? What is the "intermediate cause" for the moon?

      Take your pick

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    27. Ok Dazz here is a theory that will pass.
      Ask a question: Does mass/energy bend space time
      Background research: Einsteins elevator thought experiment
      Construct a hypothesis: Since gravity is equivalent to acceleration and shining a light through an elevator accelerating will cause the light to bend and light has no mass spacetime must be curving.
      Test the hypothesis: Several versions of this were done over the years with using the sun as the mass bending starlight during and eclipse.
      OK the rest is history...Einstein becomes a rockstar
      Dude: great theories are testable this is why string theory is not mainstream

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    28. That doesn't explain the Moon though.

      Just because you're not willing to accept all the available positive evidence for evolution doesn't mean it doesn't exist:

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

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    29. I am trying to bring more evidence to the party!! Change over time is real and this will pass the scientific method. Just because we don't have a testable final cause mechanism does not make the theory bad it just means it needs work the same way many other theories do. Dazz: I am willing to accept all the available testable/observable evidence...bring it on!!!

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    30. By the way...

      "Ask a question: Does mass/energy bend space time"

      That's not the question that kicked off Einstein's inquiries, that was his discovery! Talk about having science backwards

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    31. Dazz:
      Good point....I agree. I think it started with trying to predict planetary orbits that Newtons law had errors with.
      I read the article you gave me and I think it is solid. You will see below that it does not claim a macroevolutionary mechanism.

      Therefore, the evidence for common descent discussed here is independent of specific gradualistic explanatory mechanisms. None of the dozens of predictions directly address how macroevolution has occurred, how fins were able to develop into limbs, how the leopard got its spots, or how the vertebrate eye evolved. None of the evidence recounted here assumes that natural selection is valid. None of the evidence assumes that natural selection is sufficient for generating adaptations or the differences between species and other taxa. Because of this evidentiary independence, the validity of the macroevolutionary conclusion does not depend on whether natural selection, or the inheritance of acquired characaters, or a force vitale, or something else is the true mechanism of adaptive evolutionary change. The scientific case for common descent stands, regardless.

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    32. Natural selection is not the only evolutionary mechanism. They are only clarifying that for those who keep babbling about "Darwinian" evolution not being sufficient to explain evolutionary events.

      That doesn't mean that natural selection, genetic drift, etc, have no supporting evidence. We have tons of that.

      Once again, if you claim that the known mechanisms are not enough for "large scale" events, what other mechanism(s) do you propose? Molecular clock calculations are consistent with random mutation accounting for the differences in genomes, for example, between human and chimps, and can be used to estimate when both lineages diverged, without assuming some esoteric, unknown mechanism.

      I want to make it very clear that I'm no biologist and not even too knowledgeable for a layman probably, but for all I know, all of the above is true. Somebody correct me if I'm wrong

      But please explain why do you assume gravity is enough to explain the formation of the Moon or the Earth by accretion? Do you need to see every single step in the process or else the theory is challenged?

      Also, do you understand now why calculating the probability of a single random, unguided event a posteriori doesn't tell you much about anything?
      You moved the goalpost and this needs clarifying

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    33. Also, do you understand now why calculating the probability of a single random, unguided event a posteriori doesn't tell you much about anything?

      Yes I understand this. Do you understand how using probability theory and the scientific method along with multiple historic events can tell you a lot about the cause of that event?
      But please explain why do you assume gravity is enough to explain the formation of the Moon or the Earth by accretion? Not sure why this is relevant.

      "I want to make it very clear that I'm no biologist and not even too knowledgeable for a layman probably, but for all I know, all of the above is true." Not relevant to me as long as you work hard to understand this issues.

      Once again, if you claim that the known mechanisms are not enough for "large scale" events, what other mechanism(s) do you propose?

      I propose we take a step back and look for testable mechanisms. They may not be final cause but they can start us making real progress. Ultimate cause is often difficult for science in any area so where we are with this theory is no surprise. I think the probability challenges we see to the genome is really an opportunity to advance the theory. The probability challenges are caused by the ordered sequences of DNA (ordered sequences are the largest mathematical space in the universe) they are the core architecture of modern language telephone numbers etc. When I observe how proteins are manufactured with the information we have at this point I see the formation of both ordered and structured sequences(an example of a structured sequence is a computer pc board or a folded protein). This architecture is what is enabling evolution. As we learn more about how this architecture works we will learn about how evolution is occurring. An example mechanism is the spliceosome which like DNA can create ordered sequences. I think the spliceosome could be the key mechanism that enabled the Cambrian explosion. This is just a question at this point...step one of the scientific method, but one that could be explored and tested. I know this is a lot to digest at this point but we can keep talking about it.

      That doesn't mean that natural selection, genetic drift, etc, have no supporting evidence. We have tons of that.

      I understand all the different proposed mechanisms. The problem is the extreme difficulty in testing these to validate final cause and all propose that ordered sequences are created through unguided change. Most everyone I have discussed this with that have a reasonable grasp of probability theory believe this is a very unlikely explanation and it is core the creationist argument. Irreducible complexity is a buzz word created by Michael Behe but the strength of the argument is that the proteins of the flagellar motor need to be created by DNA sequencing and have enough sequencing integrity to fit together. You are trying to explain 50 low probability events occurring together to create a very precise micro machine . This is like observing the poker room and seeing one guy get 50 straight flushes in a row. I honestly don't think Larry should try to take this on. I hope this helps a little getting us to a common understanding.

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    34. the probability challenges we see to the genome

      What probability challenges? Are you going to cite Axe's debunked probabilities again? Or another version of the tornado-in-a-junkyard strawman?

      Irreducible complexity is a buzz word created by Michael Behe but the strength of the argument is...

      Are you seriously arguing that IC has any merit after being disproved time and again?

      Honestly, you just sound as the run of the mill creationist and I think I've had enough of this.

      If you really had an alternative, testable mechanism you should propose it, but we both know what that "mechanism" is. Magic

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    35. Bill,

      Would you please the explanations? It's quite frustrating if you don't actually read them, and makes me think that you really are trying to avoid understanding.

      "Calculating probabilities and other use of statistics after the fact is a valid way used in the scientific method to narrow down and identify cause of a historic event."

      Sure. But the most you can say from your probabilities calculation is that if hemoglobin was required to have the exact sequence that it has in humans, then a random assemblage of amino-acids would never get there. That's it. It tells you nothing about whether hemoglobin was produced by a natural process or not. It tells you that you're approaching this problem the wrong way. Before dismissing evolutionary and/or natural explanations (I would never consider a god, since those are mere fantasies, but let's play a bit), you have to understand those probabilities in a very different way. You have to learn whether hemoglobin is but one of many potential proteins that could bind and carry iron. Maybe that single sequence is but one of many possible such proteins (it is). You have to understand how evolution actually works. It's not a continuously running random assemblage of amino-acids. It is more of a historical buildup on top of prior successful molecules. I explained this a more above, which you ignored. Should I explain the whole thing again? Are you unable to read for understanding?

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    36. Bill,

      "and all propose that ordered sequences are created through unguided change"

      Depends on what you call unguided. The example of the moon and earth and accretion models shows that the solar system was not built "randomly," gravitation, a natural phenomenon, explain how it happened. You might as well call that "guided," as long as you remember that gravitation is a natural phenomenon, not a conscious being nor a god.

      Same for evolution. That the phenomenon is not guided by a conscious being, it is "guided" by natural processes. Randomness plays a role, but there's no such real dichotomy between it's either random or god-did-it. Accretion is an excellent example, without some randomness there would be no accretion, since no part would have a bit more of matter where to start the reaction. But randomness is not enough, gravitation plays a role too.

      So, in brief, natural phenomena does not mean abject randomness. A dichotomy between randomness and gods is but creationist rhetorical bullshit.

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    37. Interestingly, legumes have a form of hemoglobin, "leghemoglobin". Fairly different amino acid sequences than ours, but it has a heme group and binds oxygen. Legumes produce it in the root nodules. I think its function there is interesting because it's almost the opposite of hemoglobin in us. Leghemoblogin has a higher affinity for oxygen than ours does, and its useful function (or one of them) is to keep oxygen out of the root nodule.

      From the legume's point of view, the function of the bacteria in the root nodule is to fix nitrogen -- to break down nitrogen gas and make it available to the plant. But the enzyme that breaks down nitrogen gas also breaks down oxygen gas, producing oxygen that has to be dealt with. The whole process is more efficient at making fertilizer if the oxygen is kept out.

      The protein part of leghemoglobin is made by the plant, though there seems to be some disagreement about whether the heme component is made by the plant or the bacteria.

      Looks like hemoglobins are ancient molecules, or easy to evolve.

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    38. Dazz...did you read this?

      I propose we take a step back and look for testable mechanisms. They may not be final cause but they can start us making real progress. Ultimate cause is often difficult for science in any area so where we are with this theory is no surprise. I think the probability challenges we see to the genome is really an opportunity to advance the theory. The probability challenges are caused by the ordered sequences of DNA (ordered sequences are the largest mathematical space in the universe) they are the core architecture of modern language telephone numbers etc. When I observe how proteins are manufactured with the information we have at this point I see the formation of both ordered and structured sequences(an example of a structured sequence is a computer pc board or a folded protein). This architecture is what is enabling evolution. As we learn more about how this architecture works we will learn about how evolution is occurring. An example mechanism is the spliceosome which like DNA can create ordered sequences. I think the spliceosome could be the key mechanism that enabled the Cambrian explosion. This is just a question at this point...step one of the scientific method, but one that could be explored and tested. I know this is a lot to digest at this point but we can keep talking about it.

      Delete
    39. Bill, I think you're overthinking scientific explanation. An analogy.

      My brother who lives in Seattle writes that he visited Washington D.C. He sends photos of himself at the Washington Monument, so I see evidence that he got there, but I don't know how. Did he fly? Did he drive?

      Next e-mail brings a photo of him at Carhenge near Arlington, Nebraska, a site not near a major airport, or a major anything at all, though just a few miles off the interstate highway.

      Now I conclude that he drove. Reasonable. Scientific inference.

      Do I need a photo of my brother standing at every mile post on every road before I come to that conclusion? No.

      Someday I might gain evidence that he helicoptered, but right now that alternative is so expensive, noisy, and unlikely that the reasonable conclusion is that he drove. (Scientific knowledge is always tentative.)

      This is how we really do science.

      We don't know every detail of the evolution of hemoglobin. I don't expect we ever will. But we know something about how amino acids form, how they combine into short peptides, and how natural selection will refine their function if the process ever gets started. We want to learn more about the process! But we don't need each detail.

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    40. I think the enormous sequential space of the genome creates a formable challenge to the theory.

      And this is where it can become so very simply clear, should you decide to be amenable to learning, that this is exactly the wrong mathematical approach.

      Simple question #1: Does the likelihood you will finally succeed at least once go up or down as you make more attempts?

      Let's look at the lottery for our answer. With one attempt, the odds are around 175 million to 1, and with a lottery twice a week (~100 times per year) you would expect a win about once every 1,750,000 years. But with millions of attempts each week, what happens? *Someone* wins at least every few weeks if not more often. More attempts = greater chance of success.

      This of course is why your poker analogy is exactly wrong. Every time someone wins the lottery it's 175 million to 1 against, so according to your analogy, we ought to take from this that what happens every few weeks is that someone cheats. But that's not it, no intentional agency involved; it's just pure probability math. Let's say it again: More attempts, greater chance of success.

      So how should we look at that "enormous sequential space"? You look at it with your flawed poker analogy, as more attempts (enormous sequential space) *reducing* the chances of success, which is provably incorrect as a matter of mathematics, as we just saw from the lottery example. Certainly with more players the chance of any particular one winning the game go down mathematically. But the chance of *some* player winning the game - whether the game is a lottery or the eventual formation of a molecules that can support a primitive metabolism - **rises**, as the lottery example shows.

      That is why it is always incorrect as a matter of probability math to look at the chances of one individual player winning the game. For each individual, the odds of winning the lottery are 175 million to 1. For any *specific* path to a molecule supporting metabolism, and from there eventually to hemoglobin, the chances are always microscopic. But to go from there to saying it was impossible for evolution to result in hemoglobin is to make exactly the same mathematical error as you do when you assume that it must be cheating that results in people winning the lottery every few weeks. One more time - it's the difference between the microscopic chances that an outcome will occur in a particular way (a specific individual winning the lottery, or a specific evolutionary path leading to a specific molecule, hemoglobin), and the non-microscopic chances of the outcome occurring *at all* (*someone* winning the lottery, or *some* molecule supporting metabolism at the end of *some* evolutionary path).

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    41. Hi bwilson295
      Thanks for the insight. It seems that hemoglobin does more then bind iron. How much do you think we know about the functional capabilities of human hemoglobin at this point?

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    42. We don't know every detail of the evolution of hemoglobin. I don't expect we ever will. But we know something about how amino acids form, how they combine into short peptides, and how natural selection will refine their function if the process ever gets started. We want to learn more about the process! But we don't need each detail.
      I agree...the question is how much do we need to claim we have an identified mechanism that can really tell us how the ordered sequences that make these very precise micro machines in production occurred?

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    43. Judmarc
      Your argument is the right one for trying to solve the problem, however the resources that exist on earth are limited and sequential space is essentially unlimited. You simply cannot get enough resources to go through all the possibilities that sequential space creates.

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    44. Hi Photosynthesis
      "So, in brief, natural phenomena does not mean abject randomness. A dichotomy between randomness and gods is but creationist rhetorical bullshit."

      I agree that natural phenomena does not mean randomness and understand the laws of physics and chemistry can create order.

      The simple question is can we identify a mechanism that generates order that is generated from molecule type A (nucleic acids) and creates and order in a separate molecule type B (amino acids)?

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    45. I already posted this

      Experimental Rugged Fitness Landscape in Protein Sequence Space

      Abstract

      The fitness landscape in sequence space determines the process of biomolecular evolution. To plot the fitness landscape of protein function, we carried out in vitro molecular evolution beginning with a defective fd phage carrying a random polypeptide of 139 amino acids in place of the g3p minor coat protein D2 domain, which is essential for phage infection. After 20 cycles of random substitution at sites 12–130 of the initial random polypeptide and selection for infectivity, the selected phage showed a 1.7×10^4-fold increase in infectivity, defined as the number of infected cells per ml of phage suspension. Fitness was defined as the logarithm of infectivity, and we analyzed (1) the dependence of stationary fitness on library size, which increased gradually, and (2) the time course of changes in fitness in transitional phases, based on an original theory regarding the evolutionary dynamics in Kauffman's n-k fitness landscape model. In the landscape model, single mutations at single sites among n sites affect the contribution of k other sites to fitness. Based on the results of these analyses, k was estimated to be 18–24. According to the estimated parameters, the landscape was plotted as a smooth surface up to a relative fitness of 0.4 of the global peak, whereas the landscape had a highly rugged surface with many local peaks above this relative fitness value. Based on the landscapes of these two different surfaces, it appears possible for adaptive walks with only random substitutions to climb with relative ease up to the middle region of the fitness landscape from any primordial or random sequence, whereas an enormous range of sequence diversity is required to climb further up the rugged surface above the middle region.


      The fitness landscape is not the vast desert you or Axe make it out to be. And how is that not protein evolution?

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    46. Hi Dazz
      The problem here is not that it needs to be as vast as Doug Axe says it only has to be as vast as Author Hunt says to be a serious problem for current evolutionary thinking. Try to build a bacterial flagellum with Hunt,s numbers.

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    47. The "serious problem for current evolutionary thinking" is only in your creationist mind.

      Functional proteins from a random-sequence library

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    48. Your argument is the right one for trying to solve the problem, however the resources that exist on earth are limited and sequential space is essentially unlimited. You simply cannot get enough resources to go through all the possibilities that sequential space creates.

      And no lottery has every single possible number combination selected. No problem, instead of a winner for every single lottery, we get a winner every few weeks.

      So not every possible combination has to be tested every single time; all that has to happen, evolution-wise, is that we have enough combinations being tested often enough to account for the changes we see. And that is what *has* happened, as the references I gave you back a ways on mutation rates and the molecular clock show.

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    49. Hi Judmarc

      So not every possible combination has to be tested every single time; all that has to happen, evolution-wise, is that we have enough combinations being tested often enough to account for the changes we see.

      I agree with this. How complex of a protein can you build given Author Hunts numbers that Dazz sighted?

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    50. How complex of a protein can you build given Author Hunts numbers that Dazz sighted?

      Wrong question again, sorry. We don't have to reach arbitrary "complexity" levels, whatever that word is supposed to mean in this context. All we have to do is have sufficient genetic and protein mutation/change rates to account for the observations (the differences in genomes and proteins between species). In other words, we need sufficient "lottery tickets" that "winning the lottery" as often as it is observed to happen has a reasonably probability of occurrence. And that, as I will now repeat from a portion of my last message you did not quote, has been demonstrated to be so by the references I gave you on mutation and protein change rates and the molecular clock.

      So yes, Bill, if you do the probability math correctly, it turns out there is a reasonable probability the general types of evolutionary changes we see can happen over the time scales during which they've historically occurred. Not a problem.

      Do be alert to the fact that every time someone asks you to concentrate on the probabilities associated with one particular evolutionary change, they are in effect inviting you to make the mathematical error of concentrating on one player's chances of winning the lottery, when the proper question is, is there a reasonable probability *someone* will win the lottery? It's like those 3-card Monte guys on the street - they're inviting you to play a game they've got rigged from the start. Remember - every single time you read about a lottery being won, that's mathematical proof these folks are wrong.

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    51. Hi Jumarc

      So yes, Bill, if you do the probability math correctly, it turns out there is a reasonable probability the general types of evolutionary changes we see can happen over the time scales during which they've historically occurred. Not a problem.

      Can you back this up with numbers?

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    52. Hi Bwilson295
      I think your analogy of your brothers trip is quite interesting. Let me think about it and hopefully respond by tomorrow. I completely agree science is tentative and we make the best conclusions we can. I also know by experience if we make hasty conclusions while following the scientific method we can make big mistakes.

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    53. Can you back this up with numbers?

      Bill, did you miss Judmarc's reference to the molecular clock somehow?

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    54. Dazz
      I am not sure how the molecular clock backs up his statement but lets just agree to disagree at this point.

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    55. Bill,

      You seem to be making an effort not to understand. You insist on forgetting everything explained and go back to thinking that each molecule comes randomly out of nowhere but a soup of randomly assemble amino-acids. That, say, we can get a function in 1e-13 in a random soup of nucleotides of amino-acids doesn't mean that every function has to start with random assemblages of nucleotides and/or amino-acids. Our molecules have a history, and that history plays a huge role. Our hemoglobin is a mutant version of previous hemoglobins that could bind iron exactly as well. There's millions of versions that work. therefore hemoglobin is but one of many possible hemoglobins. And all the hemoglobins are but one of many possibilities for proteins to bind and carry iron. And none of them started as a hemoglobin formed out of a soup of randomly assembled amino-acids. They come from a lineage of successful proteins at one thing or another.

      Shit, I'm tired of repeating. There's a lot of explanations that you just leave without even trying to understand. So I'll leave it here.

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    56. Hi Photosynthesis
      I sorry you don't think I understand your position. From your first response you wrote.

      "A meaningful question would be what kind of functional space might exist in sequence space."

      I believe this is the core of your argument. If it is not let me know what is. BTW I think this is a very astute statement and shows you understand the issues. If we can get agreement on the principle issues I think the communication will become easier. I truly appreciate you patients in trying to work through this.

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    57. Hi Bwilson
      In your analogy you wrote. "Next e-mail brings a photo of him at Carhenge near Arlington, Nebraska, a site not near a major airport, or a major anything at all, though just a few miles off the interstate highway.

      Now I conclude that he drove. Reasonable. Scientific inference."

      Yes I agree that this is a very reasonable inference and I had reached the same exact inference for the first 59 years of my life about the current evolutionary hypothesis.

      Lets say you find out that there is no direct route from Washington DC to Nebraska by any transportation type. If the route would add 2 hours to a drive then it would not change your hypothesis. If it added 2 months or more it might. If it added 2 years it certainly would change it. This is essentially what our discussion is about. Does the observation of ordered sequences in DNA that leads to the ordered sequences in proteins create a trip that puts the current evolutionary hypothesis in doubt. Dazz, Judmarc and Photosynthesis all understand that the ordered sequences create a challenge. They do, however, believe that it is manageable given the current evolutionary paradigm. I am skeptical of their conclusion because I think they are underestimating the size of the sequential space of proteins relative to the availability of functional protein space. I also believe the available protein space gets smaller as proteins need to work together to get different functions done. Thanks again for sharing you analogy I think it was an outstanding way to bridge understanding of this very challenging subject.

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    58. Please Bill, don't put words in my mouth. I don't think that "ordered sequences create a challenge". I presented two papers and Judmarc mentioned the molecular clock, which I think, demonstrate that there's positive evidence that evolution and it's mechanisms provide a solid explanation for both proteins and "large scale" evolutionary changes. For some reason, you're just ignoring the evidence

      I had reached the same exact inference for the first 59 years of my life about the current evolutionary hypothesis

      Let me try an inference here. Did your change of mind happen at the same time you had some sort of religious experience or conversion?

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    59. Bill,

      You quoted:
      "A meaningful question would be what kind of functional space might exist in sequence space."

      That's but part of the answer. It's not about being astute. It's about getting to an answer in a reasonable way. Again, you're right that after-the-fact stats are used in science, but they're never used to say "god-did-it," they are used to set and test a null hypothesis: the null hypothesis is: this is just random shit, not signal. So, again, the most you can learn from your exercise is that hemoglobin was not produced by the random assemblage of amino-acids, let alone in one go. You reject quite a ridiculous null hypothesis. I agree with that conclusion. What else can you say from that? Nothing. Just that it's not the product of a random assemblage of amino-acids. So how then? Look for data. Look for something that might answer the then how?

      When you search for data you discover many things. For one, that the particular human hemoglobin you were looking at is the descendant of prior hemoglobins that had from few to quite a lot of differences in the sequence compared to what we have in human hemoglobin(s) (there's bout to be a few variants within our human population too). So then you discover that our hemoglobin has a history. That it did not come to be out of a random assemblage of amino-acids, but rather has changed through time from an ancestral protein.

      The variety of hemoglobins you can find across life forms also attest to the fact that the particular sequence of human hemoglobin(s) is but one of many possibilities.

      Do you see that? You can learn a lot by looking for the data, rather than assuming that if your null hypothesis is so obviously wrong, it must be the gods. That far fetched null hypothesis is far from being what evolutionary theory proposes. Do you understand this now?

      I could continue, but I hope you get the idea. The model where [a particular] hemoglobin is randomly assembled from a soup of amino acids is ridiculously far from realistic. It is as much of a problem for evolutionary theory, as a model where I were randomly assembled from a bunch of cells is for reproduction.

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    60. "... Photosynthesis all understand that the ordered sequences create a challenge."

      Nope. I understand that ordered sequences mean that they are not randomly assembled sequences. It "creates" a "challenge" to a proposal that doesn't exist. As I said, you're not paying much attention. I never said or implied that ordered sequences were a challenge for evolution. Not once. It is a challenge to the idea that they come each time from a random assemblage of amino-acids. To the idea that the sequence of human hemoglobin is the only possible hemoglobin that would do the job, to the idea that evolution is all about "random chance" as creationist idiots think. It creates a challenge to creationism, because it reveals that they either don't understand evolution, or they just refuse to understand it. It presents a challenge to creationism because it means that they rather paint a model for evolution as far from what the science is about as they possibly can. It presents a challenge to creationism because it reveals that they have no idea what they're talking about.

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    61. Hi Photosynthesis
      Thank you for your explanation. I think I understand your thoughts and agree with most of them. My fall back position if the current mechanism is found to be improbable is to say we don't know and try to find another mechanism of which I have several ideas. My experience with the scientific method is if you reach a conclusion that turns out to be wrong it stalls the science until you back track and find a path that works. Testability helps keep you on track. Thanks again for your thoughtful response.

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    Replies
    1. Mkay, so you come here to a science blog, to gather information about evolution, a theory "you believed in for 59 years", appointed by someone else because you were chosen to find the cure for cancer?

      I love the smell of crackpot in the morning

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