The Gpuccio thread part 4

By request a further continuation of the debate with Gpuccio.  Continued from here.

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202 Responses to “The Gpuccio thread part 4”


  1. 1 Petrushka January 12, 2011 at 7:55 pm

    Just so we won’t lose a significant topic of conversation, I’ll repost the thread that GP was having trouble finding.

    http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0015364

  2. 2 Toronto January 12, 2011 at 8:06 pm

    gpuccio,

    You are going to have more sequels than “Rocky”. 🙂

  3. 3 MathGrrl January 13, 2011 at 5:13 pm

    gpuccio,

    I think this discussion has reached the point of diminishing returns, so this will be my last post, at least for a while. I’ve concluded this in large part based on your most recent posts that suggest we “agree to disagree.” Agreeing to disagree is reasonable when the topic concerns subjective matters, but we are supposed to be talking about objective, empirical science. Making that suggestion in this context is equivalent to admitting that you can’t support your position but are unwilling to retract your claims.

    As I noted here, the usual expectation in science is that the person who is making claims about a new metric is responsible for clearly defining that metric and providing enough examples of how to calculate it that others can easily replicate those calculations. You haven’t done that, but I thought that you seemed intelligent, honest, and pleasant enough that I could work with you to get to that point. I think it is clear by now that you haven’t done the necessary work to make your concept of dFSCI rigorous enough to be used as you would like. The changing definitions we’ve seen in this discussion are proof of that.

    Before you claim you haven’t changed your definitions, I suggest that you have an objective observer read through this thread. It is very clear that you have done so. dFSCI started out as an objective measurement in units of bits that could be applied to GAs like Tierra and ev. It is now a binary indicator that is defined to be the product of intelligent agency.

    That leads to my other reasons for considering this discussion to have reached the point where none of us are likely to benefit further. You recognized here that

    We must know that the variation is beyond any realistic probabilistic resources, and that no necessity mechanism is known, or even credibly imaginable, that can, alone or in association with RV, explain that output.

    yet you have refused to meet the burden of proof that you so clearly set. As I noted in that subthread, basically you want to be able to claim that dFSCI exists if no one else can prove it doesn’t. That is nothing more than a Designer of the Gaps argument (aka an argument from ignorance).

    Despite all of this discussion, you haven’t provided anything more interesting than logical fallacies wrapped in simple but unusable math. You continue to make claims like

    Functional complexity above the threshold exists only in designed artifacts, but according to empirical observations, and not by definition.

    but never show any empirical evidence. All of your claims are based on definitions and arguments from incredulity.

    It seemed to me, when we started this discussion, that your dFSCI metric was the most likely approach that I’d seen at UD to bear scientific fruit. However, until you make the effort to resolve the circular definitions, eliminate the logical fallacies, and show how to apply it to real world systems, you simply cannot make the claims you do and maintain your intellectual integrity.

    I sincerely hope you make that effort because I would be very interested to see your results. While you may think my words in this post harsh, I’m being far more circumspect than I would be in reviewing the work of a colleague or student. I have enjoyed our conversation and respect the fact that you have ventured out of a heavily moderated forum to discuss your views in a neutral venue.

  4. 5 Petrushka January 14, 2011 at 4:11 pm

    http://www.life.illinois.edu/ccheng/Deng%20et%20al%20PNAS2010_online.pdf

    The evolutionary model escape from adaptive conflict (EAC) posits that adaptive conflict between the old and an emerging new function within a single gene could drive the fixation of gene duplication, where each duplicate can freely optimize one of the functions. Although EAC has been suggested as a common process in functional evolution, definitive cases of neofunctionalization under EAC are lacking, and the molecular mechanisms leading to functional innovation are not well-understood. We report here clear experimental evidence for EAC-driven evolution of type III antifreeze protein gene from an old sialic acid synthase (SAS) gene in an Antarctic zoarcid fish. We found that an SAS gene, having both sialic acid synthase and rudimentary ice-binding activities, became duplicated. In one duplicate, the N-terminal SAS domain was deleted and replaced with a nascent signal peptide, removing pleiotropic structural conflict between SAS and ice-binding functions and allowing rapid optimization of the C-terminal domain to become a secreted protein capable of noncolligative freezingpoint depression. This study reveals how minor functionalities in an old gene can be transformed into a distinct survival protein
    and provides insights into how gene duplicates facing presumed
    identical selection and mutation pressures at birth could take divergent evolutionary paths.

  5. 6 Petrushka January 15, 2011 at 3:52 pm

    http://onlinelibrary.wiley.com/doi/10.1111/j.1742-4658.2005.04653.x/pdf

    Finally, it has recently been discovered that the RRM domain, for a long time thought
    to belong exclusively to the eukaryotic world, is also
    present in bacteria, viruses and mitochondria. From
    an evolutionary point of view, it would be very
    interesting to investigate the function of this domain
    in such organisms and maybe discover their common
    ancestor. In conclusion, further structural investigations on RRM domains possibly coupled with thermodynamic and kinetic studies are still needed to
    confirm present hypotheses and possibly to reveal
    more surprises

  6. 7 gpuccio January 16, 2011 at 12:43 pm

    Guys,

    Sorry that I cannot at present contribute daily (not enough time), but if you are patient, and comply with a slower rythm, we can still go on for years 🙂 (well, just kidding, at least I hope).

  7. 8 gpuccio January 16, 2011 at 12:59 pm

    Toronto:

    I am not sure I understand your “new” points.

    Let’s see:

    “If you tried to equate human engineering to the complexity we see in biology you have to compare on a point to point basis.”

    According to which new personal interpretation of the scientific method? I have made an inference by analogy, and I have detailed all the pertinent points of that inference. I don’t understand what you mean with this “point to point” stuff.

    “For instance, when humans design, they specify first. We don’t see specs from the designer related to biology.”

    Either I am old and tired, or you are not clear again (or both). What do you mean here?

    “Humans make mistakes which we see all the time. We don’t see that in biology.”

    Really? Are you so sure of that? You should probably inform your fellow darwinists, who usually declare the contrary. A complete absence of mistakes would probably be a strong argument for design, and possibly for divine design.

    But I personally think that mistakes and imperfections are there.

    “ID accepts micro-evolution but human designs have never been able to do that”

    Eh? Here I am completely in the dark. Human designers have never been able to implement microevolution? What about protein engineering?

    “ID determines the “S” in dFSCI after the fact. From you to Dembski and all ID’ers in-between, the “S” is never considered in the design until after the design has been completed.”

    And so? The theory is a theory of design detection, not of incomplete design detection.

    “You actually have no way of determining “S” at all. You can only determine “F” after the design is complete and you actually see it “functioning”.”

    I can’t see what you mean by determining “S”. “FS” is for “functional specification”. That means that the object is specified because it is functional. They are not two separate concepts. Dembski defines specification in different ways. But I have always referred only to functional specification in the concept of dFSCI. So, I can’t see what you mean with “determining S”.

    “Show me how to determine “S” without regard to “F”.”

    There is very little to show. An object is functionally specified if we can explicitly define a function, whose presence can be objectively measured, for the object. Which is always the same concept as in my original definition.

  8. 9 gpuccio January 16, 2011 at 1:15 pm

    Petrushka:

    Thank you for the link. I am studying the paper. Some comments are obvious, but I will wait and give feedback when I have finished reading it in depth.

  9. 10 gpuccio January 16, 2011 at 1:19 pm

    Petrushka:

    “Functional complexity above the threshold exists only in designed artifacts, but according to empirical observations, and not by definition.

    What have I done? I have stated a simnple truth.

    —————————

    Where are the empirical observations of biological objects being designed?”

    The usual non sequitur. The phrase “Functional complexity above the threshold exists only in designed artifacts, but according to empirical observations, and not by definition.” is obviously referred to the detection of design in human artifacts, not in biological information.

    For human artifacts, we can detect design and obtain independent confirmation of the design from empirical observation. For biological information, we make an inference by analogy, as I have always said.

  10. 11 Toronto January 16, 2011 at 2:14 pm

    gpuccio: I can’t see what you mean by determining “S”. “FS” is for “functional specification”. That means that the object is specified because it is functional.

    What you are implying here is that if I order a red car from a car salesman and he delivers one to me that is blue, he has met my functional specification, since either paint colour performs the same function, which is to keep the car from rusting.

    I however, clearly “specified” something other than what was “designed”.

    This is one of ID’s biggest holes, that it equates ultimate function with intention.

    Human designers have “specific” functions in mind before the design is started, while ID proponents completely ignore this extremely important aspect of design.

    It is evolution that does not require a “specific” intent, ID needs it to validate it as a theory.

    Show me how the specification that is needed for ID is arrived at.

    If you can’t show me specific intent, the ‘S’ in dFSCI is not warranted.

  11. 12 gpuccio January 16, 2011 at 2:24 pm

    Zachriel:

    “Can you provide a clear reason why extrapolation doesn’t apply, but inference does?”

    No, if you mean “extrapolation” as an exact synonym of “inference”, it’s fine for me. I just wanted to be clear on the technical meaning of the word.

    “Of course you reject evolution. You say you have reasons to do so.”

    Again, “evolution” is vague. Neo-darwinian model is more precise.

    “Then, instead of providing an entailment of ID, you provided a supposed falsified entailment of evolutionary theory.”

    Again, you have a wrong concept of the method. For me, there is something to explain, and the existing models that try to explain that. Each model has different entailments, and favors particular formal patterns. The competition is between existing models. The model which explain things best, including new facts, is to be considered the best.

    At present, there are only two models which have potentially the power to explain biological information. One is the neo-darwinian model, the other is the design model. That’s why the constant discovery of new patterns which are best explained by the design model, and whose explanation is impossible under the neo darwinian model, are empirical confirmation of ID as the best model.

    “You mean even if you falsify the “neodarwinian model”, but haven’t falsified other proposed models, that it doesn’t matter?”

    Which other model? Please, explain. I am ready to falsify them all. The only reason why I concentrate on the neo darwinian model is because I am not aware of any other model for which it is worthwhile to make the effort.

    “It’s not an analogy, but an argument. We have a complex functional phenomena without an explanation. We conclude design.”

    It’s an analogy, because there is no dFSCI in the movement of planets.

  12. 13 gpuccio January 16, 2011 at 2:25 pm

    Toronto:

    “You are going to have more sequels than “Rocky”.

    Indeed, we are sharing that honor as a group! 🙂

  13. 14 gpuccio January 16, 2011 at 2:35 pm

    Mathgrrl:

    “we are supposed to be talking about objective, empirical science. ”

    Wrong. Empirical science is not objective. Please, review your philosophy of science. Scientists have always disagreed. Sometimes they agree to disagree, other times they simply disagree.

    Just for a recent example, see Einstein and Bohr.

    “Making that suggestion in this context is equivalent to admitting that you can’t support your position but are unwilling to retract your claims.”

    Really silly. And unfair.

    “As I noted here, the usual expectation in science is that the person who is making claims about a new metric is responsible for clearly defining that metric and providing enough examples of how to calculate it that others can easily replicate those calculations. You haven’t done that, but I thought that you seemed intelligent, honest, and pleasant enough that I could work with you to get to that point. I think it is clear by now that you haven’t done the necessary work to make your concept of dFSCI rigorous enough to be used as you would like. The changing definitions we’ve seen in this discussion are proof of that.”

    Well, one thing seems clear. One of us is not intelligent, honest, or pleasant enough.

    “Before you claim you haven’t changed your definitions, I suggest that you have an objective observer read through this thread. It is very clear that you have done so. dFSCI started out as an objective measurement in units of bits that could be applied to GAs like Tierra and ev. It is now a binary indicator that is defined to be the product of intelligent agency.”

    Really silly, and unfair.

    And so on, and so on.

    “While you may think my words in this post harsh,”

    Not harsh at all. But silly, and unfair.

    ” I have enjoyed our conversation”

    Me too, up to a point.

    “and respect the fact that you have ventured out of a heavily moderated forum to discuss your views in a neutral venue.”

    Thank you. That, at least, is more than Maya has ever tried.

  14. 15 Alan Fox January 16, 2011 at 3:34 pm

    Sorry that I cannot at present contribute daily (not enough time), but if you are patient, and comply with a slower rythm, we can still go on for years.

    I am sure everyone appreciates that a working MD has limited time for internet exchanges.

    “and respect the fact that you have ventured out of a heavily moderated forum to discuss your views in a neutral venue.”

    Thank you. That, at least, is more than Maya has ever tried.

    I don’t think that’s true.

    Maya tries hard to argue her case but gets banninated.

    Though “If she begins to make positive contributions to UD I may even lift her ban.” says the assistant banninator.

  15. 16 Alan Fox January 16, 2011 at 3:40 pm

    BTW gpuccio, if you do find time to address the point that there is mounting evidence that there is reason to suspect functionality is far from rare in random protein sequences and there is no contra-evidence for the contra-claim that

    islands of functionality are extremely small in relation to the search space

    as you put it here

  16. 17 Alan Fox January 16, 2011 at 3:43 pm

    Oops, double negative.

    “no evidence for the contra-claim”

    Hi Mark. I am sure it is easy to select a preview or edit option on the dashboard which would assist the keyboardally challenged!

  17. 18 Zachriel January 16, 2011 at 3:50 pm

    gppucio: No, if you mean “extrapolation” as an exact synonym of “inference”, it’s fine for me. I just wanted to be clear on the technical meaning of the word.

    That’s what you were asked, to explain the difference in how you are using the terms.

    gppucio: Neo-darwinian model is more precise.

    As the term is a century old, and as the modern Theory of Evolution has substantially changed, it isn’t particularly precise. Presumably, you mean to draw a distinction between telic evolution and non-telic evolution. The former isn’t well-defined, while the latter is usually called simply “evolution”.

    gppucio: Again, “evolution” is vague.

    Generally, when people say “evolution” during a discussion of biology, they mean evolution via the mechanisms of the Theory of Evolution, fecundity, variation, selection, divergence. Instead of redefining the usual term, in order to avoid confusion, you should develop a different term to describe your own position.

    Zachriel: Then, instead of providing an entailment of ID, you provided a supposed falsified entailment of evolutionary theory.

    gppucio: Again, you have a wrong concept of the method. For me, there is something to explain, and the existing models that try to explain that. Each model has different entailments, and favors particular formal patterns. The competition is between existing models. The model which explain things best, including new facts, is to be considered the best.

    That’s fine. Except ID doesn’t propose a testable model. It has no entailments to compare to other models.

    gppucio: At present, there are only two models which have potentially the power to explain biological information. One is the neo-darwinian model, the other is the design model. That’s why the constant discovery of new patterns which are best explained by the design model, and whose explanation is impossible under the neo darwinian model, are empirical confirmation of ID as the best model.

    There’s only one model (and its variants) that constitutes a testable, scientific model. Without independent entailments, then ID is just a Gap argument.

    gppucio: It’s an analogy, because there is no dFSCI in the movement of planets.

    But there is FSCI. Please explain why a design argument concerning the movements of the classical planets is not valid.

  18. 20 Zachriel January 16, 2011 at 4:13 pm

    gpuccio: Wrong. Empirical science is not objective.

    Though objectivity is never perfect, that doesn’t mean it doesn’t have merit. For instance, people may watch the moonrise together. They might even write down what they see so that others may verify their observations.

    Bright star, would I were steadfast as thou art
    Not in lone splendour hung aloft the night,
    And watching, with eternal lids apart,
    Like nature’s patient sleepless eremite,

    Mathgrrl: we are supposed to be talking about objective, empirical science.

    gpuccio: Wrong. Empirical science is not objective.

    All science relies upon independent verification of empirical observations, in particular, that we can propose a hypothesis, make empirical predictions, and then you or anyone else can verify those predictions. If you reject that we can share empirical observation, which is what we mean by scientific objectivity, then it is doubtful any constructive scientific discussion is possible.

  19. 21 Maya January 16, 2011 at 4:22 pm

    gpuccio,

    “and respect the fact that you have ventured out of a heavily moderated forum to discuss your views in a neutral venue.”

    Thank you. That, at least, is more than Maya has ever tried.

    That’s an out and out lie. I challenged anyone at UD to debate in a neutral forum. No one took me up on it, including you.

    So, where’s this scientific theory of ID I keep hearing about and what testable predictions does it make?

  20. 22 Zachriel January 16, 2011 at 4:23 pm

    gpuccio: It’s an analogy, because there is no dFSCI in the movement of planets.

    They still form a complex system that has profound effects on the Earth and its inhabitants. Or, we could easily make discrete records of the movements of the classical planets.

  21. 23 Zachriel January 16, 2011 at 4:27 pm

    Hmm. Try this link instead.

  22. 24 Toronto January 16, 2011 at 5:40 pm

    gpuccio,

    It is extremely unfair of you to claim we on the Evo side don’t have the courage to debate the ID side.

    I have watched many on our side get banned and that includes me.

    Disagreeing with an ID proponent gets you in moderation and then banned.

    Clive volunteered that he himself put me in moderation for being uncivil but when I called him on it, he couldn’t come up with a reason.

    My last three comments at UD were removed by Clive so while he never claimed I was banned, he stopped me from commenting.

    I think I can safely say that Maya and the rest of us, would love the chance to properly debate your side on UD or anywhere, but it is your side doing the censoring.

    Could you remind Clive that I told him once, “If you don’t have the stomach for this debate, step aside”.

  23. 25 Petrushka January 17, 2011 at 12:46 am

    BTW gpuccio, if you do find time to address the point that there is mounting evidence that there is reason to suspect functionality is far from rare in random protein sequences

    I think there are several things needing addressing.

    The claim that random coding sequences cannot function in living cells.

    The claim that useful engineered proteins have never been created.

    The claim that proteins created from random coding sequences cannot be visible to natural selection.

    Those, plus the rather obvious problem that functional proteins having nothing in common with sequences found in nature make the sparseness claim questionable.

  24. 26 Maya January 17, 2011 at 10:58 am

    gpuccio,

    Toronto has an important point:

    I think I can safely say that Maya and the rest of us, would love the chance to properly debate your side on UD or anywhere, but it is your side doing the censoring.

    You need to ask yourself why it is that the same people whining about being “Expelled” are so ready to censor anyone who disagrees with them in the slightest. That’s the reaction you’d expect from people who are clinging to a failed hypothesis because they are desperate to cover their religious beliefs with a veneer of scientific respectability, not that of scientists searching for the truth.

    • 27 Pachyaena March 4, 2011 at 9:14 am

      Well said Maya. I was recently involved in discussions at the Uncommon Descent site and suddenly found that a post of mine was in moderation and then deleted a short time later. The ID advocates have no room to complain about being ‘expelled’.

  25. 28 Petrushka January 17, 2011 at 3:41 pm

    This post seems to have been ignored on the previous thread. It’s in regard to the recent paper on synthetic proteins:

    A simple question: if the natural search space of proteins is so rich in functiona as you and Zachriel seem to believe, how is it that intelligent protein engineering, in many years, has not yet found one single new protein fold which may be said really useful to something?

    https://mfinmoderation.wordpress.com/2010/11/15/why-no-intermediaries/#comment-59

    And anyway, even more in general, the darwinian hypothesis is that minimal function must be selectable by NS (IOWs, must be able to confer a positive differential reproduction) to be optimized by evolution. The Szostac protein does not meet this requirement, by far it does not meet it, not even in its “refined” form, least of all in its original form.

    And the refinement itself was accomplished through artificial intelligent selection in the lab. It could never have happened in a natural biological system. The ability to bind loosely ATP is barely enough to select the molecules in a very sensitive experimental device. That has nothing to do with conferring positive differential reproduction to a living being.

    But I am afraid you will again deny even these elementary things.

    https://mfinmoderation.wordpress.com/2010/11/15/why-no-intermediaries/#comment-192

  26. 29 Petrushka January 17, 2011 at 3:51 pm

    The totality of the evidence reveals that, although duplication can and does facilitate important adaptations by tinkering with existing compounds, molecular evolution is nonetheless constrained in each and every case.

    https://mfinmoderation.wordpress.com/2011/01/01/the-gpuccio-thread-cont/#comment-810

    I would appreciate a response to this post:

    https://mfinmoderation.wordpress.com/2011/01/12/the-gpuccio-thread-part-4/#comment-935

    regarding tis recent paper:

    http://www.life.illinois.edu/ccheng/Deng%20et%20al%20PNAS2010_online.pdf

  27. 30 Petrushka January 17, 2011 at 6:14 pm

    It’s an analogy, because there is no dFSCI in the movement of planets.

    There’s certainly functionality in the behavior of shepherd moons.

    Besides, the actual expression of genes is more probabilistic than digital. Actual biology is far too noisy to be compared to a computer program.

    As many people at UD like to point out, an instruction error in a computer program is likely to be fatal, but in biology, errors can have many different kinds of outcome.

    That’s why we speak of differential reproductive success and not binary life or death.

    One of many reasons why the analogy is limited.

  28. 31 Zachriel January 17, 2011 at 6:25 pm

    Petrushka: There’s certainly functionality in the behavior of shepherd moons.

    The classical planets include the sun, moon, mercury, venus, mars, jupiter and saturn. The sun is important to the change of seasons, the moon for tides and to light the night, the others were thought to control aspects of human destiny.

    The movements are complex, and lacking a simplifying explanation, they were attributed to design. Indeed, they analogize nicely with the astrolabe, the most complex piece of human engineering in its age, only on a cosmic scale.

  29. 32 Petrushka January 17, 2011 at 6:50 pm

    they were attributed to design

    The history of the design inference is a history of false positives. Even Newton fell for it.

    The history of the failure of the design inference is why the default hypothesis is always natural causes. It’s why Randi can bet a million dollar, claim unseen, against any hypothesis involving a violation of mainstream physics.

    It’s why the ratchet of research will always tighten against the god of gaps.

    It’s why Behe has been wrong about blood clotting and wrong about the flagellum.

    It’s why molecular biology reveals a nested hierarchy when research indicates that protein domains could have begun with any of many arbitrary sequences.

    It’s why Douglass should stop using his Axe as a wedge and start doing research that sheds light on the actual origin of protein domains.

  30. 34 gpuccio January 26, 2011 at 4:05 pm

    Alan Fox:
    log (not UD)
    “I don’t think that’s true.”

    Well, I was referring to my personal interaction with Maya here, and in another blog (not UD). No problems of banning, therefore.

    • 35 Pachyaena March 4, 2011 at 9:40 am

      Your “personal interaction” with MathGrrl (and others) is an excellent indicator of your hypocrisy. MathGrrl has asked you very reasonable questions and made very reasonable statements about your assertions, but you have avoided her questions and insulted her.

      I have to say that you’re one of the best word twisters I’ve ever come across, and your skill at ignoring, avoiding, and goal post moving is impressive, but not in a good way. You should be a politician.

      I’ll freely admit that science doesn’t have all the answers, and likely never will, but if you ever have any desire to actually verify ID, in the way you assert it, you’re going to need a lot more than inferences based on your ‘beliefs’ and current gaps in scientific knowledge. Even if all of the ToE is shown to be false someday, it doesn’t automatically mean that your ID assertions have any validity. You need to show positive evidence of ID and that evidence has to be scientifically verifiable, if you want ID to be accepted as a scientific theory.

      You seem to be in love with the word “empirical” but you don’t seem to know what it means. If you want to be taken seriously, I suggest that your beliefs are not empirical and that you should stop avoiding pertinent, reasonable questions and comments.

  31. 36 gpuccio January 26, 2011 at 4:08 pm

    Alan Fox:

    “if you do find time to address the point that there is mounting evidence that there is reason to suspect functionality is far from rare in random protein sequences ”

    I have no reason to change my mind. If you want, we could leave that oint as still undecided (it truly is).

    I hope I can give a brief answer to Petrushka and you about that paper you referred, if I find the time.

  32. 37 gpuccio January 26, 2011 at 4:14 pm

    Zachriel:

    ” in order to avoid confusion, you should develop a different term to describe your own position.”

    That’s why I use “neo-darwinian model, referring to the so called “modern synthesis”, and to its molecular models.

    “That’s fine. Except ID doesn’t propose a testable model. It has no entailments to compare to other models.”

    I don’t agree. But we have already discussed that, and I have nothing new to add.

    “There’s only one model (and its variants) that constitutes a testable, scientific model. Without independent entailments, then ID is just a Gap argument.”

    I don’t agree. But we have already discussed that, and I have nothing new to add.

    “But there is FSCI. Please explain why a design argument concerning the movements of the classical planets is not valid.”

    I can’t see how such a design argument can be built. You do that, calculating the FSCI you are affirming, and then i will comment on that.

  33. 38 gpuccio January 26, 2011 at 4:18 pm

    Zachriel:

    “Though objectivity is never perfect, that doesn’t mean it doesn’t have merit. For instance, people may watch the moonrise together. They might even write down what they see so that others may verify their observations.”

    Again, you confound observable facts (which are in some way objective, although not in a perfect way), with explanatory theories (which are not objective, and are the true staff of empirical science). I am amazed at the phylosophy of science, and epistemology, of darwinists. Calling it confused is really a compliment.

    “All science relies upon independent verification of empirical observations, in particular, that we can propose a hypothesis, make empirical predictions, and then you or anyone else can verify those predictions. If you reject that we can share empirical observation, which is what we mean by scientific objectivity, then it is doubtful any constructive scientific discussion is possible.”

    I have never rejected that we can share empirical observation. I am not a fool.

  34. 39 gpuccio January 26, 2011 at 4:20 pm

    Maya:

    As I said before, I will not answer you. I don’t think your behaviour allows me to do that.

  35. 40 gpuccio January 26, 2011 at 4:22 pm

    Zachriel:

    As you should know, complexity is not enough. You have to compute the functional complexity, as I have done for proteins.

  36. 41 gpuccio January 26, 2011 at 4:30 pm

    Toronto:

    “It is extremely unfair of you to claim we on the Evo side don’t have the courage to debate the ID side.”

    Have i said that? Could you please provide the quote? I don’t remember saying that, and I have not the time to check.

    I don’t think that those on the Evo side necessarily lack courage. Common sense certainly, correct epistemology almost always, intellectual sincerety sometimes. But courage? Some of you are certainly normally endowed with that.

    “I have watched many on our side get banned and that includes me.”

    I am sorry for you. I appreciate your courage.

    I will not comment Clive’s behaviour. He has a difficult task, and I will not judge him. But in general, I don’t like bannings, unless extremely necessary.

    As I said before, my position about Maya has nothing to do with UD: it is only motivated by her behaviour here, and in another non ID blog, and with me personally.

    As it is a choice of not answering her, and not a ban, I suppose I am allowed that.

  37. 42 gpuccio January 26, 2011 at 4:43 pm

    Petrushka and Alan Fox:

    I owe you a comment on the famous paper (you know, I suppose, which). I have not much time now, so, if you allow, I will just give a few simple comments by memory. we can expand the discussion better another time. So, here they are:

    1) The first, and obvious point, is that the sequence in the paper are not random, but enogineered. So, at best, the paper is a good example of protein engineering.

    2) The paper correctly uses natural selection as a revealing procedure. But I have to emphasize that the procedure is based on recovering a pre-existing function, and not on expressing a completely new one. That’s important, because it is likely that the global function recovered (which is measured by the survival of the colonies) could be dependent on many other componentes, and not only on the sequence added.

    3) Even if the recovery were due only to the added sequence, the recovered funtion is extremely low level, and requires a very selective environment to be observed.

    4) While the authors have done a very good work to try to understand the molecular basis of the functionality connected to the added sequences, they have not really succeeded. Details about the real behaviour of those sequences are still lacking.

    5) According to another favourite of yours, the rugged landscape paper, low level island of finctionality are not a step to high level functionality. Indeed, just the contrary.

    So, at best, the paper shows that some basic intelligent engineering can give us a library of sequences where we can find, with a rate of about 1 in 10^6, some sequence capable of rescue in certain knock-out situations, at an extremely low level scenario, such that even in the lab no biochemical function is really measurable. That is no explanation of how higher optimized function could be found, even starting from such an intelligently designed repertoire.

  38. 43 gpuccio January 26, 2011 at 4:45 pm

    Petrushka:

    The antifreeze will have to wait, for now.

  39. 44 gpuccio January 26, 2011 at 4:51 pm

    Zachriel:

    “The classical planets include the sun, moon, mercury, venus, mars, jupiter and saturn. The sun is important to the change of seasons, the moon for tides and to light the night, the others were thought to control aspects of human destiny.”

    I think you are conflating two different things here.

    One thing is to explain the planetary movements according to known necessity laws. That is not simple, but I understand that it can be done.

    The other point is deciding if the general configuration of the splar system can be tailored to allow life, and if that possible result is a good argument for cosmological dsign. that is a specific application of the cosmological argument, a field of speculation which I deeply respect, but which I have never personally engaged in.

    The biological ID argument is completely different, as I have explained many times.

    • 45 Pachyaena March 4, 2011 at 10:49 am

      gpuccio said:

      “The other point is deciding if the general configuration of the splar system can be tailored to allow life, and if that possible result is a good argument for cosmological dsign.”

      With that statement, it seems to me you’re assuming that the solar system was (or at least may have been) designed for life on this planet. What if life adapted to the solar system? In other words, where does it say that solar systems are (or have to be) designed to “allow” life? And what if life were found in a solar system that is very different from ours?

      Even here on the Earth, life occurs in extremely different conditions. What would kill humans is an oasis for some organisms. Were all those conditions designed for all those organisms, or were the organisms designed to live in those conditions, or did those organisms adapt (evolve) to live in those conditions? And which came first, the conditions or the organisms?

  40. 46 gpuccio January 26, 2011 at 4:53 pm

    Petrushka:

    “The history of the design inference is a history of false positives. Even Newton fell for it.”

    With all that follows.

    Again, ome of your masterpieces of unfairness, bad reasoning, non sequitur.

    My compliments. You have not lost your touch.

  41. 47 Petrushka January 26, 2011 at 5:03 pm

    So, at best, the paper shows that some basic intelligent engineering can give us a library of sequences where we can find, with a rate of about 1 in 10^6

    So after two weeks you refuse to respond to the question about whether synthetic genes have proved useful in a live organism.

    You were wrong about this. Yes or no?

  42. 48 Petrushka January 26, 2011 at 5:11 pm

    Again, ome of your masterpieces of unfairness, bad reasoning, non sequitur.

    It is neither. Scientific practice is based on a long history of assumptions that have proved useful and fruitful.

    The assumption of angels (whether divine or merely alien) has never produced any useful results. It doesn’t even produce any useful questions.

    What it does is produce expectations that are continually disconfirmed. Such as the expectation that engineered gene sequences cannot be useful, or that functionality is too rare to be improved incrementally

  43. 49 gpuccio January 26, 2011 at 5:16 pm

    Alan Fox, Toronto, Maya and others,

    having felt a little bit estranged in trying to answer cryptic comments about courage of darwinists, I was rethinking the whole thing, and I had a sudden intuition.

    Is it possible that all of you misinterpreted my statement in the following exchange (with Mathgrrl, I believe)?

    “and respect the fact that you have ventured out of a heavily moderated forum to discuss your views in a neutral venue.”

    Thank you. That, at least, is more than Maya has ever tried.

    Well, I would like to say that what I meant is simply that Maya has never tried (at least IMO) to respect that fact. As I had in a precious post compared some attitudes of Mathgrrl to similar ones of Maya, I though I owed her (Mathgrrl) a recognition of that difference.

    I never intended, or even would think, that Maya never had the courage to venture anywhere. Maya’s courage is not my concern, and never has been. I am more interested in her incivility.

    Hey, I must really be very very careful with you guys…

  44. 50 gpuccio January 26, 2011 at 5:21 pm

    Petrushka,

    “You were wrong about this. Yes or no?”

    Very simply, I did not know that paper. I am not omniscient. And the paper is not a great proof of usefulness.

    I have no problem, anyway, to believe that synthetic genes can be useful. I just wanted to emphasize that synthetisizing useful synthetic genes, especiall;y in a top down way, is so difficult that we have not yet had great results in that field. But we will certainly succeed in that.

    Why should I have problems with the power of intelligent design? I believe in that power. So, I miss your point here.

  45. 51 gpuccio January 26, 2011 at 5:23 pm

    Petrushka,

    Frankly, I believed that the faous paper was presented as evidence of functionality in the random space. That was certainly Alan Fox’ implication.

    Well, it is not.

  46. 52 gpuccio January 26, 2011 at 5:24 pm

    errata corrige

    famous, not faous.

  47. 53 Petrushka January 26, 2011 at 6:05 pm

    And the paper is not a great proof of usefulness.

    ————————-

    At what point would usefulness be “great”?

    Evolution is about incremental change, not about finding a best or correct solution.

    You propose a class of solution to the problem of functionality that has never in the history of science proved correct or useful. When I point out this historical fact, you engage in name calling.

    You frequent a forum where mentioning this historical fact results in banning. It is courageous of you to post here, But I am somewhat dismayed that you engage in the same kind of taunting that is typical of the protected denizens at UD. At least half a dozen times you have characterized me personally.

    It really isn’t a useful tactic.

    If you wish to provide some positive evidence for the existence of a designer, or wish to provide some testable entailment, feel free. Otherwise you join a centuries old procession of people who have explained phenomena by reference to divine intervention.

    It’s not that you are wrong; it’s that your explanation leads nowhere. When one of your pronouncements is proved wrong, you are not capable of admitting that you were wrong. Isn’t this just a bit uncivil?

  48. 54 Petrushka January 26, 2011 at 7:20 pm

    The question of which sequences are useful and how rare useful sequences might be is a matter of chemistry and not something that can be decided without research.

    gpuccio: you have made pronouncements about how likely it is to find useful sequences. Your estimates are wrong. It’s really time to admit that you don’t know, and that you didn’t expect unamplified sequences to have function in living organisms.

    You have said it is up to mainstream biologists to demonstrate that incremental steps are possible. And that is what is being done. It’s difficult and tedious work, but it is being done.

  49. 55 Maya January 26, 2011 at 7:48 pm

    gpuccio writes:

    “and respect the fact that you have ventured out of a heavily moderated forum to discuss your views in a neutral venue.”

    Thank you. That, at least, is more than Maya has ever tried.

    Well, I would like to say that what I meant is simply that Maya has never tried (at least IMO) to respect that fact.

    Discussing one’s views in a neutral forum is what anyone with even pretensions to intellectual honesty simply does. You don’t get brownie points for it — such behavior is the bare minimum expected of people who claim to be able to support their positions.

    The fact that you, pretty much alone among the UD denizens, are participating here doesn’t demonstrate any particular courage on your part, but the failure of the other UDers to do so does reflect very badly on them.

    If you were really committed to open discussion of IDC and actually valued free speech, you wouldn’t participate at UD or, at the very least, you would publicly protest their policies. That I would find worthy of a compliment.

  50. 56 Maya January 26, 2011 at 7:52 pm

    gpuccio writes:

    “That’s fine. Except ID doesn’t propose a testable model. It has no entailments to compare to other models.”

    I don’t agree.

    You can disagree all you like, but unless you can propose a testable model with detailed entailments, your disagreement is meaningless.

    Yes, yes, I know you won’t respond to me because I somehow offended your delicate sensibilities. That doesn’t make me less correct.

  51. 57 Zachriel January 26, 2011 at 8:06 pm

    Zachriel: That’s fine. Except ID doesn’t propose a testable model. It has no entailments to compare to other models.

    gpuccio: I don’t agree. But we have already discussed that, and I have nothing new to add.

    Evolutionary theory is so full of entailments, it has spawned multiple fields of study. If there were entailments for ID, you would think there would be journals full of detailed research. But there’s not.

    Zachriel: But there is FSCI. Please explain why a design argument concerning the movements of the classical planets is not valid.

    gpuccio: I can’t see how such a design argument can be built.

    It was a common enough exercise in the Middle Ages to deduce design from the complex movements of the heavens and their obvious function concerning human lives. Where did they go wrong?

    gpuccio: As you should know, complexity is not enough. You have to compute the functional complexity, as I have done for proteins.

    So you’re saying that if we find a complex alien artifact with hundreds of carefully balanced gears and gizmos, which is essentially the Medieval model of the Solar System, we won’t be able to detect design?

    gpuccio: Again, you confound observable facts (which are in some way objective, although not in a perfect way), with explanatory theories (which are not objective, and are the true staff of empirical science).

    Science is objective and empirical. (Sometimes we use the term empirical science to distinguish it from the older use of the term science to refer to all forms of learning, including non-empirical fields such as mathematics.) When Mathgrrl said we are discussing objective empirical science, it means it’s not merely a matter of preference or opinion, but something that independent observers can verify. If you can’t show it, then it’s not science.

  52. 58 gpuccio January 26, 2011 at 10:38 pm

    Petrushka:

    No name calling. Just my judgemnent about your statements, strategies and style. I have all the rights to express that.

  53. 59 gpuccio January 26, 2011 at 10:40 pm

    Petrushka:

    ” When one of your pronouncements is proved wrong, you are not capable of admitting that you were wrong. Isn’t this just a bit uncivil?”

    That just means that I don’t think that my pronouncements have been proven wrong. Can you accept that?

  54. 60 gpuccio January 26, 2011 at 10:42 pm

    Petrushka:

    “gpuccio: you have made pronouncements about how likely it is to find useful sequences. Your estimates are wrong.”

    Which estimates? You are working with your imagination, again. I have made pronouncements about how likely it is to find naturally selectable sequences in random libraries, and nobody has proved me wrong.

  55. 61 gpuccio January 26, 2011 at 10:44 pm

    Just a general comment: I was not trying to be complimented for my “courage”. I just acknowledged that Mathgrrl had been kind to say what she said.

  56. 62 Petrushka January 26, 2011 at 10:58 pm

    That just means that I don’t think that my pronouncements have been proven wrong. Can you accept that?

    If the statements of yours that I quoted above are not wrong, then they are vacuous.

    You entire argument and your calculation of dFSCI depend on your ability to exclude incremental pathways.

    And that in turn depends on your ability to characterize the space of functional sequences.

    If randomly generated libraries having numbers amenable to laboratory investigation contain functional sequences having no similarity to natural sequences, then you have no basis on which to claim that no imaginable series of incremental steps could lead to the current set found in living things. You simply don’t know.

    Not only do you not know, but your bias has led you to make statements that have been disconfirmed.

    Not only did the synthetic genes make the difference between life and death, they also provided “specified” functionality. There is no telling from these experiments whether other functionality existed.

  57. 63 gpuccio January 26, 2011 at 11:21 pm

    Petrushka:

    I fully disagree with you on practically all.

    You conflate random libraries with designed libraries.

    You conflate artificial selection with natural selection.

    You blatantly ignore that you have given no example of the incremental pathways which must be proved to make your model even vaguely credible.

    You blatantoly ignore that you yourself have presented very strong evidence against those incremental pathways (the rugged landscape paper).

    And so on. Very simply, you ignore facts and truth and state follish things.

    And yes, this is a judgement, and I take full responsibility for it. You are not a fair interlocutor.

    And this is not name calling.

    • 64 Pachyaena March 4, 2011 at 11:15 am

      gpuccio said:

      “You blatantly ignore that you have given no example of the incremental pathways which must be proved to make your model even vaguely credible.”

      And you blatantly ignore that you have given no example of the pathway (incremental or otherwise) which must be proved to make the claim of your designer even vaguely credible.

      I have said on other sites that I think that ID of some sort by some sort of designer is possible, but that doesn’t mean I believe that a designer or design are probable or certain. There’s no absolute proof right now, one way or another. However, if ID assertions are to be taken seriously by science, it will take evidence that is scientifically verifiable (or falsifiable), and that includes that pathway mentioned above. It’s simply not enough to say that something appears to be designed but that you don’t have to show who, how, what, where, or when, or even a scientifically credible way to look for those things.

  58. 65 gpuccio January 26, 2011 at 11:29 pm

    Zachriel:

    “Evolutionary theory is so full of entailments, it has spawned multiple fields of study. If there were entailments for ID, you would think there would be journals full of detailed research. But there’s not.”

    There will be.

    “It was a common enough exercise in the Middle Ages to deduce design from the complex movements of the heavens and their obvious function concerning human lives. Where did they go wrong?”

    They did not go wrong. They were making a form of cosmological ID argument, which is still valid, but different. I am discussing the biological ID argument. The scenario is completely different.

    “So you’re saying that if we find a complex alien artifact with hundreds of carefully balanced gears and gizmos, which is essentially the Medieval model of the Solar System, we won’t be able to detect design?”

    Yes. probably. But for the artifact, not for the planets.

    “Science is objective and empirical. (Sometimes we use the term empirical science to distinguish it from the older use of the term science to refer to all forms of learning, including non-empirical fields such as mathematics.) When Mathgrrl said we are discussing objective empirical science, it means it’s not merely a matter of preference or opinion, but something that independent observers can verify. If you can’t show it, then it’s not science.”

    The usual mix of truth and wrong triviality. Science is not objective. It is, however, a non objective interpretation of somewhat objective facts. I believe you must understand that. I hope you are just playing a game.

    Or are you stating, like Mathgrrl, that scientific theories are objective and universally shared? Are you such a fool?

    Or, even worse, are you stating, like many of your friends, that the theory of evolution is a fact?

    Please, keep your intellectual integrity, for your own sake.

  59. 66 Petrushka January 26, 2011 at 11:43 pm

    You conflate random libraries with designed libraries.

    You conflate artificial selection with natural selection.
    ==============================

    I posted a link to a paper describing how the libraries are made.

    The criteria for their “design” can be stated in under ten bits. From this starting point the actual sequences are random, and yet the library contains sequences that can make the difference between life and death.

    Aside from the pointless dispute over the definition of random, how is it that humans can produce sequences from scratch that have specifiable biological function, in a universe that you claim contains virtually no functional sequences?

    The sequences certainly aren’t designed as copies of any natural sequences. They have no bases in common with natural sequences. As stated above, the specification that defines their similarity is under 10 bits.

    Surely that says something about sparseness.

  60. 67 Petrushka January 26, 2011 at 11:53 pm

    The claim that there is some fundamental difference between artificial and natural selection is completely bogus. All experimentation narrows the variables. It’s why we use the term “controlled.”

    The functionality or non-functionality of a sequence is a matter of chemistry. What you and I dispute is the cause of the mutations that are functional or non-functional. You assert that uncaused mutations cannot supply the raw material for selection of any kind.

    Function is always determined by context. Natural selection is different from artificial only in the fact that it applies a fitness value based on the totality of an organism in its environment. Based on the practices of humans, artificial selection tends to produce overspecialized organisms that cannot survive and compete in the wild.

    I would like to see you attempt to describe a process of artificial selection that could produce a balanced ecosystem.

  61. 68 Petrushka January 27, 2011 at 12:35 am

    They did not go wrong. They were making a form of cosmological ID argument, which is still valid, but different. I am discussing the biological ID argument. The scenario is completely different.

    Science is not objective. It is, however, a non objective interpretation of somewhat objective facts. I believe you must understand that. I hope you are just playing a game.

    —————————–

    That is just so sad.

    You’d think, if science is not objective, that communist science would produce theories of particle physics that are incompatible with those produced by capitalists, or that Adventists would produce different theories of disease than those produced by atheists. And that it would be impossible to settle disputes by research and experiment.

    I have yet to see an ID argument that could not be characterized by asserting that gaps in our knowledge of history can be filled by positing the existence of a gap filler.

    I have personally observed the claim of the demise of evolution since about 1956. It would be funny if it weren’t so sad.

  62. 69 Zachriel January 27, 2011 at 1:05 am

    Zachriel: So you’re saying that if we find a complex alien artifact with hundreds of carefully balanced gears and gizmos, which is essentially the Medieval model of the Solar System, we won’t be able to detect design?

    gpuccio: Yes. probably. But for the artifact, not for the planets.

    You don’t seem capable of explaining the difference. No matter. The point is made.

    gpuccio: Science is not objective. It is, however, a non objective interpretation of somewhat objective facts.

    A scientific theory is an explanatory framework, a number of interrelated claims that have objectively testable entailments.

    gpuccio: Or are you stating, like Mathgrrl, that scientific theories are objective and universally shared? Are you such a fool?

    You seem to be trying to make a distinction, but just because you can’t doesn’t make others fools. Perhaps Mathgrrl just needs a more complete explanation. She seems quite capable of following a chain of thought.

    Scientific theories are universally *sharable*, because the entailments are objectively and empirically demonstrable.

  63. 70 gpuccio January 27, 2011 at 8:53 am

    Petrushka:

    “Aside from the pointless dispute over the definition of random, how is it that humans can produce sequences from scratch that have specifiable biological function, in a universe that you claim contains virtually no functional sequences?”

    By design. By understanding the biochemical rules of folding and by applying them, in this particular case. That implies conscious understanding and conscious purpose. Design.

    “The sequences certainly aren’t designed as copies of any natural sequences. They have no bases in common with natural sequences. As stated above, the specification that defines their similarity is under 10 bits.”

    That is foolish. Those 10 bits summarize a very long intelligent enquiry into reality by conscious intelligent beings. Exactly the kind of knowledge and information which allows designing efficient algorithms to obtain a purpose.

    “Surely that says something about sparseness.”

    No, Sparseness has nothing to do with that. It says something about the power of intelligent design, of conscious identification of meanings and purposes.

  64. 71 gpuccio January 27, 2011 at 9:00 am

    Petrushka:

    “The claim that there is some fundamental difference between artificial and natural selection is completely bogus. All experimentation narrows the variables. It’s why we use the term “controlled.””

    An so? All experimentation is obviously artificial.

    “You assert that uncaused mutations cannot supply the raw material for selection of any kind.”

    A really cryptic statement.

    “Based on the practices of humans, artificial selection tends to produce overspecialized organisms that cannot survive and compete in the wild.”

    And natural selection tends to produce almost nothing.

    “I would like to see you attempt to describe a process of artificial selection that could produce a balanced ecosystem.”

    You must decide yourself. One moment you seem to state that I believe that human intelligent design cannot achieve anything, and then you seem to state that I believe that it can do anything.

    Neither is true. Human intelligent design, at present, can do very much, and cannot do a lot of other things. That is, and has always been, my position.

    Obviously, what humans can do is not in any way a limit of what intelligent design can do.

    • 72 Pachyaena March 4, 2011 at 12:27 pm

      gppucio said:

      “All experimentation is obviously artificial.”

      I’m curious. If humans are designed, and human intelligence is designed, and if humans are not artificial, how can humans do anything that is artificial, especially if we are designed with the complex specified function of being able to conduct experiments?

      When a deer or a monkey tastes different plants to see if they’re palatable, is it experimenting? Is it being artificial? Are some or all actions artificial just because it’s humans doing them? Isn’t it natural for humans to experiment? When a bird builds a nest or a beaver builds a dam, is it being artificial? What about a human building a house or a vaccine or an experiment?

      You said:

      “And natural selection tends to produce almost nothing.”

      What exactly does natural selection produce?

  65. 73 gpuccio January 27, 2011 at 9:11 am

    Zachriel:

    “A scientific theory is an explanatory framework, a number of interrelated claims that have objectively testable entailments.”

    And remains subjective anyway. All scientific theories are more or less supported by facts, but that does not make them objective and universally shared.

    “Perhaps Mathgrrl just needs a more complete explanation. She seems quite capable of following a chain of thought.”

    Quite so, until she has to face conclusions she does not like. Then her fanaticism seems to obstruct her reasoning. My personal opinion, obviously.

    “Scientific theories are universally *sharable*, because the entailments are objectively and empirically demonstrable.”

    They are certainly “sharable”, because we can put them into words. They are certainly not universally “shared”, in the sense of considered true.

    Moreover, and “entailment” is at best objectively “observed”, as a predicted fact, but that does not in any way “demonstrate” the explanatory framework; it just supports it. Again, be careful with your epistemology.

  66. 74 Alan Fox January 27, 2011 at 9:13 am

    Petrushka:

    The question of which sequences are useful and how rare useful sequences might be is a matter of chemistry and not something that can be decided without research.

    Exactly.

    Gpucciu, this sis the simple point I have tried to make up-thread. Gordon M. makes much of his concept of “small islands of functionality” but this is unjustified because we do not know what functional sequences await discovery by mutation or experiment. What work that has been done shows that functionality is far from rare.

    I have no reason to change my mind. If you want, we could leave that oint [sic, I’m reading “out”] as still undecided (it truly is).

    But, until there is some evidence that functional proteins are rare in search space, the whole FCSI argument is unsupported assertion.

  67. 75 Alan Fox January 27, 2011 at 9:17 am

    Obviously, what humans can do is not in any way a limit of what intelligent design can do.

    Not to derail the thread, but, since you mention it, this is a meaningless statement. Until someone decides what”Intelligent Design” means, it is impossible to evaluate what “Intelligent Design” might do.

  68. 76 Alan Fox January 27, 2011 at 9:19 am

    Sorry, I should have written ‘what “Intelligent Design” is…

  69. 77 Zachriel January 27, 2011 at 1:42 pm

    gpuccio: They are certainly not universally “shared”, in the sense of considered true.

    They can be shared because they can be objectively supported.

    What is interesting is that you consider this so obvious, that you called Mathgrrl a fool for not knowing it. It would be better if you explained clearly what you meant.

    Empiricism in science refers to data collected by the senses, and by extension, through the use of instrumentation. Objectivity in science refers to observations that can be shown to be independent of the individual observer. This can be done by using different observers, different perspectives and methodologies, and through the use of instrumentation. In modern science, it also means publication.

    The natural sciences are empirical and objective. Theories are supported by objective evidence because they make specific empirical predictions that can be verified by independent observers.

    Other than that, it’s not clear what distinction you are making when you say “Empirical science is not objective.”

  70. 78 Petrushka January 27, 2011 at 2:43 pm

    You must decide yourself. One moment you seem to state that I believe that human intelligent design cannot achieve anything, and then you seem to state that I believe that it can do anything.

    ————————–

    I believe humans can isolate mechanisms found in nature and perform experiments to verify specific mechanisms. One can experiment with evolution, but living systems cannot be designed without using evolution as a tool. Evolution itself is not designed.

    One of the greatest and best known intellectual leaps in the history of human thought was Newton’s realization that the falling of objects on earth could be extrapolated to account for the orbits of planets.

    Another great idea was the realization that changes brought about by animal and plant breeders could be extrapolated to account for natural changes in populations.

    The objections you bring to the problem of incremental change are hardly new. They have been and continue to be addressed by research.

    But they will not be addressed by ID scientists like Douglass Axe. If you are looking for incremental pathways, it is easy to produce an experiment that fails to produce positive results, just as it would be easy to do an experiment in physics that fails to produce atomic fusion.

    The question of incremental pathways is not one of interpretation. The history of molecular evolution may be lost, but potential pathways can be constructed. Whether the gaps can be crossed by known, regular mechanisms is something that can be objectively determined.

    I know it is futile trying to convince you, but the reality is that incremental pathways are either possible or not possible. The question can be objectively resolved. It makes no difference whether the steps are designed or whether they occur in nature. The only question is the minimum size of the necessary steps.

    It’s interesting to observe ID science at work. The standard thought process seems to involve asking how can we present the most improbable scenario, rather than how can we construct a scenario involving regular processes.

    This can be seen in Behe’s thinking about the evolution of the flagellum. He looks at knockout experiments and notes that knocking out a gene disables motility. He doesn’t consider that genes do not evolve from a knockout state to a fully functional state.

    He also fails to look for diversity in similar living things. He says that all the genes required for a flagellum must be present or the whole thing is useless. He lacks the curiosity to look around and discover that there are dozens of organisms happily surviving with partial sets of his irreducible genes.

    ID combines a failure of imagination with a willful sabotage of research. It asks the wrong questions and performs boneheaded experiments, designed to fail.

  71. 79 Petrushka January 27, 2011 at 3:15 pm

    I’m going to digress a bit from biology to discuss something I recently discovered that I think is relevant to how research is conducted.

    I’ve been playing a game called Freecell, a version of solitaire that comes with every installation of Windows.

    When I first started playing, I won about 60 percent of the games and gave up on the rest. I got curious about what percentage were winnable, so I looked around for information.

    Freecell has some “deals” that are difficult for humans to win, but the “search space” is small enough that computer programs can exhaust all possibilities. It turns out that out of 32757 possible deals, only one is unwinnable.

    The game shares with evolution the necessity that you cannot make large leaps between position. The entire space between the deal and a win must be traversed by single steps, following a few simple rules.

    When you encounter a difficult deal it is easy to believe that winning is impossible. It would be easy to conclude that you could only get from A to B by cheating, by introducing a saltation event.

    But the possibility or impossibility of winning is an objective fact. It just so happens that every deal has been exhaustively examined and the facts are not in dispute.

    But what I notice is that after finding out that virtually deal is winnable, my behavior changed. I found that I could win almost every deal, and that if I failed on the first attempt, I could win on the second or third.

    I find in this an analogy to scientific research. For centuries mainstream science has proceeded on the assumption that every hand is winnable, every phenomenon can be expressed as the result of regular processes, there is no cheating, no divine intervention. There are no cases where the assumption of intervention has been fruitful.

    So I ask, what is the point of assuming intervention explains anything? The objective fact is that every phenomenon can be explained by regularity, or it can’t. But asserting the negative produces no increment in knowledge. It merely means you are too lazy to look at the possibilities.

    There are problems too large to be examined in toto. The history of life is one of these. But we can look at small cases and see if regularity can explain them. If it can, we are justified in having confidence that larger cases can be explained.

    Certainly more justified than leaping to the conclusion that an historically sterile explanation, with no precedents for usefulness, will suddenly prove correct.

  72. 80 Petrushka January 27, 2011 at 4:55 pm

    AF: But, until there is some evidence that functional proteins are rare in search space, the whole FCSI argument is unsupported assertion.
    ———————————

    The question is not just rarity.

    The biggest conceptual problem that ID proponents have is assuming that evolution or the designers are searching for something. This is implicit in everything Dembski writes and most of what Behe writes.

    Evolution as seen by biologists is not searching; it is simply a term applied to denote change and differential reproductive success. ID proponents retrospectively attribute intention to nifty structures.

    It is conceptually no different than attributing intentionality to the moon and its size and orbit (without which we would most likely not be here).

    But rarity is an important issue, and it is not being ignored. It is essential that current configurations be reachable by regular processes. If it were a done deal, there would be no need for further research.

    It is somewhat amusing (and sad) to see people look at a difficult problem and assume it will be solved by positing sky fairies. It’s not that they are wrong, but that their hypothesis can never contribute to human knowledge.

    Even if a designer existed, one must do research on the assumption of regular processes. An MD must know that you reach a diagnosis by searching among natural alternatives, not by assuming demons. At least I hope that’s what they do.

  73. 81 Alan Fox January 27, 2011 at 6:31 pm

    Evolution as seen by biologists is not searching; it is simply a term applied to denote change and differential reproductive success.

    Apologies if I gave a wrong impression. Of course the process of mutation is random and hitting on a better (in the context of the niche environment) sequence is “stumbling upon” and not any form of active search.

    ID, I suggest, uses the “Sherlock Holmes” method to arrive at its conclusions. Eliminate all other explanations and the remaining hypothesis, however unlikely must therefore by correct. Dismiss your straw-man understanding of evolutionary theory and ID wins!

  74. 82 Alan Fox January 27, 2011 at 6:33 pm

    BE correct!!!

  75. 83 Petrushka January 27, 2011 at 11:55 pm

    Apologies if I gave a wrong impression.
    __________________

    My comment at that point wasn’t directed at you.

    But Sherlock didn’t spend much time considering spooks and spirits as possible perpetrators, even though his author did in real life.

  76. 84 Petrushka January 28, 2011 at 2:49 pm

    I see that Casey has a response to the antifreeze paper up on rvolutionnews.org.

  77. 85 gpuccio January 28, 2011 at 4:07 pm

    Alan Fox:

    “But, until there is some evidence that functional proteins are rare in search space, the whole FCSI argument is unsupported assertion.”

    Exactly as, until there is some evidence that functional proteins are frequent and connected in search space, the whole neo darwinian model is unsupported assertion.

    However, I remain convinced, for all the reasons I have discussed in detail, that the existing evidence points clearly to the rarity and separateness of functional islands, especially if we refer to naturally selectable functions, and not to artificial ad hoc definitions of functional proteins.

  78. 86 Petrushka January 28, 2011 at 4:15 pm

    especially if we refer to naturally selectable functions, and not to artificial ad hoc definitions of functional proteins.
    ________________________

    Keeping an organism alive under adverse conditions is an ad hoc definition?

    Functional sequences having no bases in common with natural sequences say nothing about the rarity of function?

    How about if you simply admit you are wrong about no new folds having function in living organisms?

  79. 87 gpuccio January 28, 2011 at 4:16 pm

    Alan Fox:

    “Not to derail the thread, but, since you mention it, this is a meaningless statement. Until someone decides what”Intelligent Design” means, it is impossible to evaluate what “Intelligent Design” might do.”

    I am afraid you don’t understand the point.

    What intelligent design means is very clear: it’s the procedure by which conscious intelligent beings output specific objects using their representations of meaning and purpose to determine, at list in part, the form of the object. I find that concept very simple.

    The problem is that Petrushka and others were using the example of what humans can or cannot do as a gold standard of what a design procedure can or cannot do. That is incorrect.

    First, what humans can or cannot do today is very different from what they could or could not do 100 years ago, or will be able to do in 10 years.

    Second, other conscious intelligent beings could certainly be better than present humans in their design procedures.

    The point is not what humans can or cannot do today, but what intelligence and purpose can do in principle. Today, human protein engineers have limited capabilities, but in 30 years they could have developed their understanding, knowledge and purposes so that they can attain completely different results.

    That was my simple point, as usual misunderstood.

  80. 88 gpuccio January 28, 2011 at 4:30 pm

    Zachriel:

    “Empiricism in science refers to data collected by the senses, and by extension, through the use of instrumentation. Objectivity in science refers to observations that can be shown to be independent of the individual observer. This can be done by using different observers, different perspectives and methodologies, and through the use of instrumentation.”

    I perfectly agree on that. And you are right, I consider it obvious. But the fact that science uses some objective contents does not make it objective.

    “In modern science, it also means publication.”

    I don’t agree. That is, at best, naive.

    “The natural sciences are empirical and objective.”

    No. They are certainly empirical (a point I have never denied). But they are not objective. I deny that firmly.

    “Theories are supported by objective evidence because they make specific empirical predictions that can be verified by independent observers.”

    Theories are supported by objective evidence because they:

    a) can explain existing facts

    b) can predict new facts to be observed

    Your insistence on b) only is at best suspicious.

    And anyway, neither of those “supports” makes theories objective.

    “Other than that, it’s not clear what distinction you are making when you say “Empirical science is not objective.””

    It should be simple: empirical science is not objective, because it is an inference based on facts, either known or predicted, but still is and remains an inference.

    An inference is not logically implied by facts. It is never “demonstrated”. Different inferences can be made from the same facts and, while an inference can sometimes be falsified, it can never be objectively proven true. No intelligent person has necessarily to “accept” an inference as true. The best we can do is to try to decide what is the best available inference, and even that is almost always controversial. A “majority” criterion, the so called scientific consensus, is never proof of a correct judgment, although it may have some practical utility.

    It is simple.

    • 89 The whole truth May 14, 2011 at 1:13 pm

      While it’s true that many inferences are made in science, and that some are controversial, unsupported, or even ridiculous, it’s certainly true that many are objective and provable.

      For instance, if science says that a temperature of -100 degrees Fahrenheit is cold, and that it would kill an unprotected human within a short time, it is true, it can be observed, it’s objective, and it’s provable.

      If science says that poured and dried concrete is hard, and that a 100 pound block of it falling directly onto an unprotected human’s head from a height of 100 feet would kill that human, it’s true, it’s observable, it’s objective, and it’s provable.

      If science says that the the moon or Mars are a certain distance away from the Earth at a particular time (within a minuscule margin of error), it’s true, it’s observable, it’s objective, and it’s provable.

      These are very simple examples of facts. Facts that are easily provable or have already been proven. Many other things are just as easily provable or already proven.

      It it crazy to say that nothing is provable or that “facts” are never anything but subjective inferences.

      Do you realize that everything you said about inferences and a lack of objectivity is applicable to your position?

  81. 90 gpuccio January 28, 2011 at 4:34 pm

    Petruahka:

    “I know it is futile trying to convince you, but the reality is that incremental pathways are either possible or not possible. The question can be objectively resolved. It makes no difference whether the steps are designed or whether they occur in nature. The only question is the minimum size of the necessary steps.”

    Why would you try to convince me of something that I already believe?

    You can certainly show an incremental path to existing complex functions which was designed, but which can credibly occur by random search and NS. I am waiting. I have asked for that many times.

  82. 91 gpuccio January 28, 2011 at 4:40 pm

    Petruahka:

    “Keeping an organism alive under adverse conditions is an ad hoc definition?

    Functional sequences having no bases in common with natural sequences say nothing about the rarity of function?

    How about if you simply admit you are wrong about no new folds having function in living organisms?”

    Good examples of artificial ad hoc questions. Which, by the way, I have already answered.

  83. 92 Petrushka January 28, 2011 at 4:57 pm

    The problem is that Petrushka and others were using the example of what humans can or cannot do as a gold standard of what a design procedure can or cannot do. That is incorrect.

    ————————–

    That is not a fair characterization of my criticism of design.

    I’m saying the problem of big numbers is just as much a problem for design as it is for evolution. If the number of coding sequences is greater than the number of atoms in the universe, then where does the designer store his database of sequences? How was the database developed in less than infinite time?

    You assert that functional spaces are isolated. That implies that each and every sequence must be tested.

    Evolution requires that functional sequences must be connected by the kind of changes actually observed in nature. That’s an entailment. It’s testable.

    When I asked you about this at UD, you mumbled something about designers using directed evolution. I’d sure like to see you follow up on this.

    It makes the problem of design even more difficult, because artificial selection tends to be one dimensional (rewarding only one trait at a time), whereas natural selection involves all traits simultaneously, in environments that change, and including predation, parasitism, disease and such.

    The combinations that would have to be cataloged would be the number of coding sequences times the number of possible environments.

    Evolution avoids the problem of big numbers simply by not testing the entire sequence space. It only tests the vicinity available through mutation. Bearing in mind that some types of mutation produce larger changes than simple point mutations.

    So the choice is between the working assumption that functional sequence space is bridgeable, or that some mysterious entity has more database capacity than there are particles in the universe.

    Note I said working assumption. If we knew everything about this, there would be no need for further research.

  84. 93 Petrushka January 28, 2011 at 5:04 pm

    You can certainly show an incremental path to existing complex functions which was designed, but which can credibly occur by random search and NS. I am waiting. I have asked for that many times.

    ————————————-

    If an incremental path exists, it can be found by natural selection.

    By definition, and incremental path is one in which every sequence change allows the organism to live and reproduce.

    I think your conceptual blindness is the result of thinking that evolution is tending toward a goal, rather than simply branching.

  85. 94 Petrushka January 28, 2011 at 5:32 pm

    The kind of mathematics done by ID proponents is no different than calculating the odds of you parents meeting, marrying, and conceiving at exactly the right time to produce your specific genome, and multiplying this probability times the number of generations of humans.

    It assumes that the production of you was a target.

    Similarly, Behe and Dembski define the current configurations of living genomes as targets.

    They ignore the simple fact that there are an infinite number of possible targets, and a huge number of *needed* adaptive changes that never happen.

    For every instance of a drug resistance mutation, there are fare more failures to adapt. Most organisms, confronted with the *need* to adapt, simply die. Most populations, faces with sudden environmental change, or a new and more efficient predator, simply go extinct. We have many examples of extinctions resulting from the superior hunting abilities of humans, and many examples caused by the transport of species from one part of the world to another.

    If adaptation were *front loaded* we would expect to see adaptations occur with more regularity. Instead, the fossil record indicates entire families of organisms wiped out by environmental change.

    So our hypothetical designer either doesn’t care about extinction, or has motives too inscrutable for us to divine.

  86. 95 Alan Fox January 28, 2011 at 9:18 pm

    I am afraid you don’t understand the point.

    I certainly don’t understand what is meant by “Intelligent Design”.

    What intelligent design means is very clear: it’s the procedure by which conscious intelligent beings output specific objects using their representations of meaning and purpose to determine, at list in part, the form of the object. I find that concept very simple.

    I certainly don’t understand this. What beings? What procedure? Are you sayin’… Whadda you sayin’? This really makes no sense! Is this a process(?) that is anything to do with biology?

    Second, other conscious intelligent beings could certainly be better than present humans in their design procedures.

    What makes you say (I can’t imagine that you really think this!) that other intelligent beings designed humans? Wasn’t it just God?

    Or were you just speculating idly?

  87. 96 Zachriel January 29, 2011 at 2:59 am

    Zachriel: Other than that, it’s not clear what distinction you are making when you say “Empirical science is not objective.”

    gpuccio: It should be simple: empirical science is not objective, because it is an inference based on facts, either known or predicted, but still is and remains an inference.

    So? The inference is based on objective support.

    gpuccio: An inference is not logically implied by facts. It is never “demonstrated”. Different inferences can be made from the same facts and, while an inference can sometimes be falsified, it can never be objectively proven true.

    Being proven True™ is not the question.

    gpuccio: No intelligent person has necessarily to “accept” an inference as true.

    No, just that it is objectively supported. For instance, take the theory of universal gravitation, that the force which causes the apple to fall is the same force that causes the planets to trace complex orbits across the sky. The theory may be an abstraction, but the science of verifying it is based on objective empiricism.

    It still isn’t clear what you mean by “Empirical science is not objective.”

  88. 99 Alan Fox March 1, 2011 at 8:16 am

    Here is another research paper demonstrating functionality in artificial gene sequences.

    Those “islands of functionality” seem to be linked by sand bars! Amazingly, I came across the paper because it was referred to here in a thread at UD. “ID wins again!”

  89. 101 Alan Fox March 2, 2011 at 6:13 pm

    Oops, Petrushka! I promise I do try and follow links but I can’t always devote as much time to following ID’s fortunes as I’d like.

    Good job we have people such as yourselves who are less dilletante about it!

  90. 102 MathGrrl March 3, 2011 at 1:37 pm

    I’ve been trying to get a mathematically rigorous definition of CSI from the ID proponents at UD, without much success. I just realized that I’m spending too much time there when I saw that I own the recent comments:

  91. 103 Eugen March 3, 2011 at 4:58 pm

    Mathgrrl?

    Hi is this the right blog?

  92. 104 Petrushka March 3, 2011 at 5:01 pm

    UD seems to have no interest in discussing this topic, even though it speaks to the heart of their argument.

    How can you assert that functionality exists only in isolated islands if you ignore evidence to the contrary? How can you use the big numbers argument if it’s possible to find functional sequences in random libraries?

  93. 105 MathGrrl March 3, 2011 at 7:17 pm

    Hi Eugen!

    Thanks for joining us!

  94. 106 Eugen March 3, 2011 at 8:08 pm

    Hello boys and “grrls”

    This is obviously the blog ,then. I didn’t read all the posts yet. I’ll try later today. I really am here to learn, not to argue heavily. If I’m not sure about something I’ll be honest and say it.

  95. 108 Eugen March 5, 2011 at 2:02 am

    Hi everybody,

    I work on automated systems so i like to visualize problems mechanistically and pick them apart bit by bit.. Looking at a codon table I notice:

    a– The redundancy of codon to amino acid mapping is typical of forward error correcting (FEC) methods. These methods are absolutely critical in modern digital data transfer and streaming. They are used in one way data transfers and that is exactly what we have in this case.

    b—There is variable strength to error correction capability in codon to amino acid map. Some amino acids are assigned 6 codons as if there was need to make sure these are properly translated. It’s possible some amino acids are more important or critical than others. There is some optimization at work here.

    c— Property of the group of amino acids that uses the most codons is polar and small sized. There has to be a good reason why they get the largest share of codon assignments but I don’t know why for now.

    d— If error rate is high there could be another layer of redundancy.There are several groups of amino acids ,each group have the same property .Possibly any amino acid of the same property group will do the same job in the chain which will make protein.

    e— If error rate is low than this layer of redundancy by group property could be used to fine tune protein by modulating folding tension. This could be done by selecting different sized amino acid from the same property group.

    Does this make some sense to anybody here?

  96. 109 MathGrrl March 6, 2011 at 11:00 pm

    Eugen,

    I understand that you can model some aspects of what we observe in biological organisms using the concepts of information theory. It’s important to remember that what you are constructing is a model and that the underlying biochemistry is much messier.

    I think you are at risk of assuming your conclusions when you make statements like “Some amino acids are assigned 6 codons”. That’s not an assignment, it’s just the way the chemistry works out. This leads to a more general point that we shouldn’t be surprised to see that evolutionary mechanisms take advantage of biochemical reactions and structures that have particular interesting characteristics.

    I’ll stop speculating about your ultimate point now and wait for you to make it.

  97. 110 Eugen March 7, 2011 at 5:13 pm

    Hi Math

    OK ,I will accept correction on “assigned codons”. I should rather say there is a relation of 6 codons to an amino acid ( in only few cases). One AA is represented by 6 codons, according to codon to AA relation rules. Really interesting bit is that codon table seems unchanged across species and over the long periods of time.

    This is probably more frustrating to me than to you. I’m trying to understand if it’s possible for this system to organize itself by forces of chemical reactions only. I don’t want to preach design because I’m not qualified to do so.

    There are couple more cases which I examined this way. One is DNA replication and the other signal transduction. I won’t bore you with the details because it would be similar to above. But let me assure you “the devil is in the details”.

    I’m playing with DNA Skittle these days (when I have time). http://www.biomedcentral.com/1471-2105/10/452
    Web site where you can download it looks hacked ,unfortunately.

    I see few very interesting things but it will take more playing. Also ,they would probably sound quite outrageous to you. All this is more like following series of clues and hints than direct “in your face” evidence.

    At the end ,my basic point is :there is resemblance between cell and human designed systems.

    I think you will laugh to hear I’m in moderation on UD. Go figure.

  98. 111 MathGrrl March 7, 2011 at 8:04 pm

    Did you use a naughty word, Eugen?

  99. 112 Eugen March 7, 2011 at 8:16 pm

    I called you and Dr Bot ninjas.

    Sorry if that was inapropriate.

    Hiyaaa!

  100. 113 Alan Fox March 7, 2011 at 11:23 pm

    Really interesting bit is that codon table seems unchanged across species and over the long periods of time.

    Indeed! That (with a very few exceptions) the genetic code is universal across all known lifeforms on Earth is an amazing fact. It nests very well with other evidence suggesting common origins.

  101. 114 MathGrrl March 8, 2011 at 10:42 am

    Ninja? I’m a pirate! No wonder you were banned. 😉

  102. 115 Eugen March 8, 2011 at 1:56 pm

    Mathgrrl

    How about ninja/pirate. http://tinypic.com/r/dv4m0/7

    Hi Alan

    it makes sense to use standardized components. It’s much easier to modify system in that case. Also , I would expect to see modularity and optimization as part of well engineered setup. Not only hardware should be modular and standardized but also software.

    One of the exceptions to codon table is in found in mitochondria. That ‘s understandable because it is a cell power plant. Those power plant bastards always have special safety and security requirements. It’s not easy to get contract there.

  103. 116 Petrushka March 8, 2011 at 8:36 pm

    This is probably more frustrating to me than to you. I’m trying to understand if it’s possible for this system to organize itself by forces of chemical reactions only.

    That would include you, Szostak, and lots of biochemists. It would seem to be a problem in biochemistry rather than in systems analysis. Chemistry does things like protein folding so much more efficiently than software.

  104. 117 MathGrrl March 8, 2011 at 10:20 pm

    Eugen,

    I’m still participating on that thread at UD and I’m afraid you might have company in the room of the banned soon. Someone using the handle lastyearon posted this:

    Haha! I actually read this entire thread…in one sitting. I’m convinced that this thread is now the best evidence we have of the lack of scientific merit of Intelligent Design.

    “That was designed”.
    “How do you know”.
    “Because it contains a lot of CSI”
    “What is CSI and how do you measure it”
    “Go away”.

    Awesome.

    From now on, rather than linking to the Kitzmiller decision, I’m going to link straight here.

    That may violate the “civility” guideline more than ninjas did.

  105. 118 Eugen March 9, 2011 at 3:33 am

    Thanks Mathgrrl,

    Fantastic save.Post is probably gone by now.

    that thread is interesting but it’s buried under dozens of others.
    Actually,my posts usually wait between few hours to few days before they get published. Looks like I’m not banned ,rather on “iffy” list.

  106. 119 Eugen March 9, 2011 at 1:00 pm

    Hi Petrushka

    thanks for mentioning Szostak. I remember reading about him while ago.

    “It would seem to be a problem in biochemistry rather than in systems analysis.”

    Yes,I could be overdoing it with my mechanistic analogies.OTOH, there is place for analogies. Maxwell, Thomson,Faraday used them heavily to help them explain electro magnetism. Maxwell was encouraging his students by saying how analogies are not about resemblance but about relation.

  107. 120 Petrushka March 9, 2011 at 6:38 pm

    Electromagnetism is a simpler and more lawful phenomenon than evolution, whether chemical, biological, or modeled in software.

    The key concept that eludes the ID crowd is the fact that evolution does not preserve its history.

    Looking at current structures, whether characterized as simple or complex, one cannot reconstruct the steps leading to their existence.

    So as with any forensic investigator, one looks for footprints, or one asserts divine intervention. Sometimes there will be no footprints.

  108. 121 Eugen March 10, 2011 at 3:01 am

    Petrushka

    “So as with any forensic investigator, one looks for footprints, ….”

    You used analogy there and that’s fine. We learn almost everything through analogies without even realizing that. It helps us grasp new concepts by comparing new with the old knowledge and then establishing logical similarities. Of course this doesn’t work in every case. Also using visual tools, my other favorite is very helpful when learning something new.

    How do you learn something new?

    Anyway I came here to convert you 🙂 …not.

    I checked UD thread Mathgrrl mentioned. It’s pandemonium there.

  109. 122 Petrushka March 10, 2011 at 2:32 pm

    I don’t object to people disagreeing with me, or even people trying to convert me.

    To me the issue is not who’s right and who’s wrong, but who has a process and methodology for advancing knowledge.

    If you read these four threads you may find that there are some who reject arguments based on the historical success of methodologies.

    Personally, I find that there’s been a long history of attributing phenomena to intelligent agency, and a long history of explaining phenomena as regular processes. Sometimes it takes centuries to elucidate regularities.

  110. 123 Eugen March 10, 2011 at 7:28 pm

    Just kidding about conversion.

    I can’t do that because I’m not 100% sure what’s going on. You could call me ID sympathizer rather than proponent. Did Designer use nano tweezers to manipulate molecules? I don’t even know how to imagine that ,especially not to model, prove or convince somebody.

    But I must tell you there are precise,regular,repetitive and controlled events/processes we can observe at the cell level.By using latest science and our logic we can try to understand details of these events.

    This is not very scientific but my intuition is telling there is more to it. I get the same feeling when I troubleshoot complex system I’m not familiar with.

    At first approach, brain is trying to form general logical concepts. After that ,one continues to modularize the system into operational groups. Next, within the group you try to find sub groups , relation between them and sequence of operation. Sub group is broken into tasks, each task is examined as deep as possible, down to the last component.

    All along ,at every level you must look for dependencies, patterns , loops, general stops,
    redirects etc. It’s quite a process.

  111. 124 Petrushka March 10, 2011 at 9:27 pm

    But I must tell you there are precise,regular,repetitive and controlled events/processes we can observe at the cell level.

    But that says nothing about their history.

    My argument is that ID cannot say anything about history, because it makes no attempt to imagine and test theories about history. It’s not simply wrong. It’s a vacuous approach.

    Which is why ID advocates never stick around to discuss research indicating that randomly produced libraries of sequences contain significant numbers of functional sequences.

    There is no point in arguing that evolution cannot accumulate functional changes. That has been demonstrated both in software and in the biochemical laboratory. At least one former ID icon, Hubert Yockey, has conceded that evolution can in principle produce any string. That is to say there is no data string that is irreducible or unreachable by evolutionary algorithms or processes.

    So when someone is sympathetic to ID,I would like to know what the attraction is. Historically, every phenomenon has started with an ID explanation which has gradually been eroded.

    I will grant that we have no detailed, step by step history for every gene. But we have many reasons to believe that the actual history was step by step, and not a single instance of an observed intervention.

  112. 125 Eugen March 11, 2011 at 2:09 pm

    “There is no point in arguing that evolution cannot accumulate functional changes. That has been demonstrated both in software and in the biochemical laboratory.”

    Would you please point me to a fair experiment done without continuous guidance by engineers.

  113. 126 MathGrrl March 11, 2011 at 3:00 pm

    Eugen,

    You can find links to ev and Tierra in some of my posts on this thread. I’d also suggest looking into Avida and the Steiner Problem solutions posted at The Panda’s Thumb a few years back.

    If you really want to blow your mind, look up John Koza’s work on Genetic Programming.

    Let me know if you have trouble finding the links.

  114. 129 MathGrrl March 11, 2011 at 3:53 pm

    Sorry, didn’t close the tag. I told you I was confused.

  115. 130 Eugen March 11, 2011 at 6:27 pm

    Oops, I wasn’t clear. I meant fair bio chemical experiments without continuous guidance by engineers (and scientists).

    Mathgrrl

    I read on GA you mentioned. Those are fully programed, controlled environments with results which are expectable. They lead horse to the water and make him drink.

    You created quite a pandemonium on UD. I’ll make popcorn and watch.

  116. 131 Petrushka March 11, 2011 at 6:39 pm

    Those are fully programed, controlled environments with results which are expectable.

    That’s simply untrue. In every possible sense of the word it’s untrue.

    For a very simple example, the traveling salesman problem can be “solved” by GAs with 10,000 stops. That meets the 10^150 search space criterion.

    There is no way to know the best solution, just a way to find incrementally better solutions.

    That is the fundamental misunderstanding of ID advocates, the notion that there is a goal or target, as opposed to incremental improvement.

    Evolution does not search for a target. The only thing that could ever be considered a target is an incremental step that is equal or better than the starting point.

    Which is why ID advocates drop out of the discussion when it is demonstrated that random sequences can be functional. that is the baseline from which you can get incremental improvement.

  117. 132 Zachriel March 11, 2011 at 9:48 pm

    Mathgrrl: I’m a little confused by what’s going on over at the UD thread. vjtorley seems to be refuting Dembski at 283. My only option at 295 was to agree with him.

    Great stuff, Mathgrrl. CJYman is weighing in on the thread, too. Brings back fond memories. Chaos≠Random!

  118. 133 Eugen March 11, 2011 at 11:57 pm

    “Evolution does not search for a target.”

    How evolution then finds a target?

    “Which is why ID advocates drop out of the discussion when it is”

    Petrushka

    I’m not really ID advocate if UD keeps me in moderation. I’m a drifter looking for new home 🙂

    Hi Zachriel

    long time no see.

  119. 134 Petrushka March 12, 2011 at 3:29 am

    How evolution then finds a target?

    Evolution doesn’t find targets. Evolution accumulates changes.

    ID advocates paint a bull’s eye around the current condition and call it a target, as if that were something that evolution were aiming for.

    Researchers can have a target. They can, for example, force a condition whereby a population will benefit from a specific function. An ecosystem can also create a situation whereby a specific functional change is required for the survival of the population.

    Outside the laboratory, the expected response would be extinction. Most species that have existed are extinct.

    Successful change generally requires a permissive environment in which drift can occur. That is why most new species occur after a mass extinction, when competition is reduced.

  120. 135 Pachyaena March 12, 2011 at 6:00 am

    Alan, I was banned at Pharyngula, Panda’s Thumb, The Bathroom Wall, and ATBC under a different user name than the one I’m using here (please don’t ask). Both ‘sides’ of the ID vs. evolution argument are deaf in advance and vehemently expect everyone to agree that their ‘side’ is the one with all the evidence in their favor.

    There’s some compelling evidence on the ‘side’ of evolution, but it’s far from absolute, and there are many unsupported inferences. Hopefully, some of those inferences may become facts in the future. Some aspects of ID are interesting but it’s mostly based on wishful inferences and religious proselytizing. The inferences in ID are not likely to ever become facts. I have a strong feeling that the debate will go on and on and on…….

    I’d like to add that kairosfocus and bornagain77 (along with most others on UD) are doing ID more harm than good, at least from a scientific standpoint. Those guys are so wrapped up in their religious beliefs that they wouldn’t know reality if it slapped them in the face. Of course there are some scientists who are driven more by their beliefs (and other agendas) than by actual evidence, but the religious kooks who push ID (even though they say ID and religion are not connected) are making sure that ID is always thought of as a religious agenda.

    • 136 Alan Fox March 13, 2011 at 1:57 pm

      Alan, I was banned at Pharyngula, Panda’s Thumb, The Bathroom Wall, and ATBC under a different user name than the one I’m using here (please don’t ask).

      It’s rather unfair to complain about being banned at AtBC and then not be prepared to justify the complaint. I can’t take your claim seriously.

  121. 138 Eugen March 12, 2011 at 1:59 pm

    Pachyena

    ” I have a strong feeling that the debate will go on and on and on…….”

    That’s guaranteed as nobody is sure what the truth is. I have moderate views on evo/ID debate, similar to yours.

    Petrushka

    ” Evolution doesn’t find targets. Evolution accumulates changes ”

    Great. Please direct me to fair bio chemical experiment which starts with only basic chemical components. These components will then continue unguided to produce amino acids, proteins, protein machines etc

    • 139 Pachyaena March 13, 2011 at 8:36 pm

      Eugen, you’re right, no one knows everything for sure, but there sure are a lot of people who think they know everything for sure.

      Ya know, it really doesn’t matter how life originated or whether evolution is strictly material or influenced by a designer, except to possibly satisfy the curiosity of the humans who would like to know. I’m curious, but I realize that I’ll probably never know. Frankly, I don’t understand why so many people are so determined to have their minds made up right now about things that haven’t actually been figured out yet (if ever). I wonder why people don’t just wait for more answers from more research, and see what happens. Anyone can do whatever research they want to, and if they have good evidence it will probably be taken seriously. If all they have is inferences and beliefs, it probably won’t be taken seriously, at least by people who aren’t easily fooled.

  122. 140 Petrushka March 13, 2011 at 2:27 am

    Great. Please direct me to fair bio chemical experiment which starts with only basic chemical components. These components will then continue unguided to produce amino acids, proteins, protein machines etc

    I’m afraid you are beginning to sound like the denizens of UD. when the argument against evolution goes badly, switch to abiogenesis.

    What’s next? Get your own dirt?

    I suppose when Szostak or someone in his field demonstrates a pathway to chemical replicators, you will assert the because it requires laboratory manipulation, it is “assisted.”

    We are very unlikely to find the one true history of the origin of life. At best we will find scenarios that require a minimum of manipulation, and which involve conditions and processes consistent with what we know about planetary formation and prebiotic history.

  123. 141 Alan Fox March 13, 2011 at 2:04 pm

    @ Mathgrrl

    Congratulations on your tour de force!

  124. 142 Toronto March 13, 2011 at 3:12 pm

    Petrushka:

    “I’m afraid you are beginning to sound like the denizens of UD. when the argument against evolution goes badly, switch to abiogenesis.

    What’s next? Get your own dirt?”

    Every now and then I come across a line I wish I had written myself!

  125. 143 Petrushka March 13, 2011 at 5:26 pm

    Every now and then I come across a line I wish I had written myself!

    I kind of wish I had thought of it first myself.

  126. 144 Eugen March 13, 2011 at 10:39 pm

    ” I’m afraid you are beginning to sound like the denizens of UD. when the argument against evolution goes badly, switch to abiogenesis.

    What’s next? Get your own dirt?”

    Every now and then I come across a line I wish I had written myself! ”

    Petrushka

    I think we were talking about different things. I’m mostly interested in processes inside a cell. I selected few of the processes and studied them in some detail. I’m finding that multidisciplinary approach is the most promising. Scientists trained in biology and robotics/automation ( my field) or biology/electronic communications will be able to apply their multidisciplinary skills in this area. When these different science fields are combined a new and surprising findings will emerge. I only have a slightest glimpse into unlimited possibilities at this time. I tried to share one of the ideas with you ( and others) in my post on March 5 but you must have an open mind to grasp these possibilities. Forget about the dirt,study these issues.

    Toronto

    hello neighbor. You think Leafs will make the playoffs this year?

  127. 145 Petrushka March 13, 2011 at 10:49 pm

    I think we were talking about different things. I’m mostly interested in processes inside a cell.

    Fine enough. Biologists do this.

    But if you are interested in the history of these processes you are discussion evolution.

    You are being disingenuous when you switch from the study of change over time in populations to the origins of first replicators.

    Simply noting that current structures are complex does not reveal anything about their history.

  128. 146 Eugen March 13, 2011 at 11:05 pm

    You are being disingenuous when you switch from the study of change over time in populations to the origins of first replicators.

    10-4 on that

    I possibly misunderstood you were talking about the first cell evolution. I’m mostly interested in the issues just described above. Also I’m programmer not a scientist in my field.

  129. 147 Petrushka March 13, 2011 at 11:19 pm

    I possibly misunderstood you were talking about the first cell evolution.

    You are the one who steered the discussion to “…bio chemical experiment which starts with only basic chemical components…”

    I have been discussion evolution as change in populations of replicators.

    Perhaps it would be a good idea for you to read through these four threads so we could avoid going in circles.

  130. 148 Toronto March 13, 2011 at 11:22 pm

    Eugen:

    How close of a neighbour are you?

    I stopped following the Leafs after 1967. 🙂

    Evolution is a study of change. Whether poofed into existence or arrived at by some biochemical accident, the origins of life are of no concern to evolution.

    Evolution versus creationism is what this debate is about.

  131. 149 Eugen March 14, 2011 at 12:21 am

    Petrushka

    Quoting Toronto:
    ” the origins of life are of no concern to evolution.”

    That’s the source of misunderstanding. I constantly mix OOL and evolution.

    Toronto

    I live between TO and Hamilton. Thanks for reminding me about OOL in the quote above.

    “I stopped following the Leafs after 1967”

    I don’t blame you. 🙂

    I always joke with other Leafs fans how they need to have backup team to support.

  132. 150 Alan Fox March 14, 2011 at 8:50 am

    Alan, I was banned at Pharyngula, Panda’s Thumb, The Bathroom Wall, and ATBC under a different user name than the one I’m using here (please don’t ask).

    It’s rather unfair to complain about being banned at AtBC and then not be prepared to justify the complaint. I can’t take your claim seriously.

    Reply
    Pachyaena
    March 13, 2011 at 8:09 pm
    Suit yourself.

    Still pretty sure nobody but spammers have been banned at AtBC recently. If you adopted this attitude to being asked to support a claim, then I am not surprised if other commenters gave you short shrift. The convention is on any rational or science site is that if you make a factual claim that you can’t or won’t support with evidence, you withdraw it.

    There was another character who posted for a while at AtBC under the name of Kris. That couldn’t have been you, of course, because he wasn’t banned, although he acted like that was his goal.

  133. 151 MathGrrl March 14, 2011 at 12:53 pm

    Alan,

    @ Mathgrrl

    Congratulations on your tour de force!

    Thank you, but I think vjtorley deserves a huge amount of credit for his intellectually honesty and willingness to follow the evidence, even when it led to a conclusion completely at odds with the claims of his fellow ID proponents.

  134. 152 Petrushka March 14, 2011 at 2:14 pm

    I wonder why people don’t just wait for more answers from more research, and see what happens. Anyone can do whatever research they want to, and if they have good evidence it will probably be taken seriously.

    Perhaps you could assist the ID movement by describing how ID research could be carried out. What are the testable entailments of ID that would suggest research?

  135. 153 Pachyaena March 14, 2011 at 3:13 pm

    I didn’t say ID research. I said research. As far as what kind of research, that’s up to the people doing it.

    It’s abundantly clear that both ‘sides’ of this endless debate believe they are on the right track and have strong evidence to back up their claims. No matter what they’re looking for in the way of further (and convincing) evidence, it’s going to take more research to find it. Therefor, whether it’s ID proponents or materialistic evolution proponents, they’re going to have to fill in important gaps in current knowledge with REAL evidence if they want to persuade skeptical or undecided people that their claims are valid.

    Any agenda is in the same boat. Of course many people are easily convinced of just about anything, whether there’s any evidence or not, but intelligent, sensible people like to see actual evidence of claims, and especially if the claims are big.

    For thousands of years (or longer) many people have claimed that they have all the answers and that their way is the only right way, whether they had any actual evidence or not. Why are so many people in such a FUCKING hurry to think and claim that they KNOW things that they DON’T know?

    While some people spend all their time trying to talk others into believing that their agenda and beliefs are the only ‘truth’, there are many people (fortunately) who are actually looking for real, observable, verifiable evidence of how nature works. Many things have been figured out but many things have not. More information will undoubtedly be found and many gaps in current knowledge will be filled. All ‘sides’ should just say “I don’t know.” when it comes to things that have not been verified, and if they want convincing evidence they should get out there and find it.

    And most of all, the ID proponents should shut the fuck up about their religious beliefs and stop saying that ID is scientific while they’re preaching sermons. Even if ID is true, and that’s a HUGE if, it will never be proven by spouting a bunch of religious crap. Unverifiable beliefs and inferences, whether religious or not, are not proof.

  136. 154 Petrushka March 14, 2011 at 3:25 pm

    And most of all, the ID proponents should shut the fuck up about their religious beliefs and stop saying that ID is scientific while they’re preaching sermons.

    What else do they have? What is the positive evidence for ID?

    Any sightings of the designer? Any observed instances of intervention?

    As far as I can tell, ID consists entirely of claims that we don’t know everything.

    For several centuries science has consisted of hypothesizing about regularities and testing those hypotheses.

    What alternative methodology do you recommend?

  137. 155 MathGrrl March 14, 2011 at 4:01 pm

    Mark has very kindly opened a new thread to discuss CSI, in light of the recent admissions at UD that CSI is not a good metric for detecting intelligent agency.

    I hope some of the UD folks will participate there.

  138. 156 Eugen March 14, 2011 at 4:23 pm

    “Why are so many people in such a FUCKING hurry to think and claim that they KNOW things that they DON’T know? ”

    Pachyena, you rebel!

  139. 157 Toronto March 14, 2011 at 5:27 pm

    Pachyaena:

    You make it sound like both positions have the same amount and weight of evidence, and that therefore it’s some sort of close neck-to-neck race.

    That isn’t the case at all.

    If you took all the evidence for the evolution side off the table and left just pure ID evidence, you’d have a bare table.

    ID as it exists is an exercise in doubt, not a science.

    I’d like to see the ID position presented without any sort of reference to evolution.

    • 158 Pachyaena March 14, 2011 at 9:26 pm

      Toronto, when it comes to some things, both positions do have the same amount and weight of evidence, and that is none. And since those things are often what the debates focus on, it’s incumbent on either party to gather and show actual evidence of their claims.

      It wasn’t my intention to make it sound like both positions have the same amount and weight of evidence, and that therefore it’s some sort of close neck-to-neck race, but unless and until either side connects all the relevant dots, it’s not a done deal.

      Consider this:

      There’s a murder. There’s a suspect. A lot of evidence points to that suspect as the perpetrator, but there’s no smoking gun. The suspect goes on trial. The evidence is presented and the jury is instructed to consider the evidence and come back with a verdict. Some of the things presented are inferences and can be interpreted in more than one way. The law requires that the evidence must be beyond a reasonable doubt to convict the suspect. Reasonable doubt is a vague term. The suspect is convicted. Later, more evidence is found that absolutely proves that the convicted person didn’t commit the murder. Or, more evidence is found that absolutely proves that the convicted person did commit the murder.

      A murder case is important, but the question of what’s behind the origin of life and whether it evolves in a strictly materialistic way or with the help of a designer/creator may be the most profound question ever asked. Before the jury is told to deliberate, I think that more evidence should be gathered. A decision does not have to be made right mow. What’s the rush?

      Maybe one of the reasons some people argue so much is because the critical evidence hasn’t all been discovered. The smoking gun needs to be found, if possible.

  140. 159 Toronto March 14, 2011 at 9:47 pm

    Pachyaena:

    “Maybe one of the reasons some people argue so much is because the critical evidence hasn’t all been discovered.”

    ID has no evidence of its own. Every single talking point ID has is an improbability statement targeting some facet of evolution.

    Show me some stand-alone ID evidence. If science had never investigated this thing that came to be known as evolution, what would you present to the world?

    Where is ID’s stand-alone evidence?

  141. 160 Pachyaena March 14, 2011 at 9:55 pm

    Toronto, I too would like to see the ID position presented without any sort of reference to evolution, and without ANY reference to Gods or religious beliefs. I would also like to see evolution presented without any sort of reference to ID or creationism.

    In many instances, both sides obviously think that bashing the other side is all they need to do to prove their own case. Even if the Toe is crap, that doesn’t make ID true, and even if ID is crap that doesn’t make the Toe true. Each one has to stand on its own merits. And the first thing the proponents of each side ought to do is agree on exactly what those merits are. It’s pretty tough to have ‘faith’ in any theory where even the devotees disagree on the important particulars.

  142. 161 MathGrrl March 14, 2011 at 10:00 pm

    Pachyaena,

    I would also like to see evolution presented without any sort of reference to ID or creationism.

    I refer you to a Pubmed search for “evolution” that returns 153188 articles meeting your criteria.

    • 162 Pachyaena March 14, 2011 at 10:41 pm

      MathGrrl, I meant all the time. I guess I should have said that specifically but I thought it was implied by other things I said.

      I realize that no mention is made of ID or creationism in many papers and books that concern evolution. I was thinking more along the lines of blogs and public debates and the like.

  143. 163 Pachyaena March 14, 2011 at 10:34 pm

    “ID has no evidence of its own. Every single talking point ID has is an improbability statement targeting some facet of evolution.”

    I’m pretty sure there are some ID proponents who would disagree with that. Personally, I think that some of the things they propose are somewhat interesting, but not convincing.

    “Show me some stand-alone ID evidence.”

    It would probably be better if you asked an ID proponent for that.

    “If science had never investigated this thing that came to be known as evolution, what would you present to the world?”

    I likely wouldn’t present anything at all to the world. To acquaintances or friends I might present some personal observations or actual evidence of some things, if they were interested.

    “Where is ID’s stand-alone evidence?”

    Well, I suppose that some of the ID proponents would say their stand-alone evidence is in their mathematical formulas and in their observations of organisms. Others would quote the Bible or some other religious hooey and claim that it is absolute stand-alone proof. I would have to see a lot more than that to be convinced.

    Here’s a question for you:

    Where is evolution’s stand-alone evidence, without any inferences, probabilities, or improbabilities?

  144. 164 Petrushka March 14, 2011 at 11:31 pm

    I realize that no mention is made of ID or creationism in many papers and books that concern evolution. I was thinking more along the lines of blogs and public debates and the like.

    If an argument is to be made against evolution, it needs to be made against the published literature, not against news articles and blogs. Even if an argument has been made in a blog, the counter-argument needs to cite the relevant literature, not just weaknesses in the way a blogger presented the case.

    Where is evolution’s stand-alone evidence, without any inferences, probabilities, or improbabilities?

    See Lenski, et al. See the literature on animal and plant breeding.

    Science is full of inferences. No one has seen a full orbit of Neptune or Pluto.

    • 165 Pachyaena March 15, 2011 at 6:29 pm

      “If an argument is to be made against evolution, it needs to be made against the published literature, not against news articles and blogs. Even if an argument has been made in a blog, the counter-argument needs to cite the relevant literature, not just weaknesses in the way a blogger presented the case.”

      Does that apply to all sides of an argument? And who decides what the “relevant literature” is?

      By the way, here are some definitions of “published”:

      Definition of PUBLISH
      transitive verb
      1
      a : to make generally known b : to make public announcement of
      2
      a : to disseminate to the public b : to produce or release for distribution; specifically : print 2c c : to issue the work of (an author)
      intransitive verb
      1
      : to put out an edition
      2
      : to have one’s work accepted for publication

      “See Lenski, et al. See the literature on animal and plant breeding.”

      I’m well aware of the “literature”. If Lenski or anyone else had proof of evolution, the debate wouldn’t be happening. There is some evidence, but it isn’t absolute, and it doesn’t prove either strictly materialistic or intelligence derived, ultimate causes.

      “Science is full of inferences. No one has seen a full orbit of Neptune or Pluto.”

      Yeah, science is full of inferences, and many of them are no more supported than the ones in ID theory.

      The origin and/or evolution of life are a lot more complex and harder to figure out than the orbit of Neptune or Pluto.

  145. 166 Toronto March 15, 2011 at 2:43 am

    Pachyaena:
    “I would also like to see evolution presented without any sort of reference to ID or creationism.”

    There is no ID science to refer to. There is no stand-alone evidence for ID, at all.

    If I’m wrong, you should be able to show it to me.

  146. 168 Petrushka March 15, 2011 at 3:16 am

    Patrick doesn’t post much at UD, but somehow I got banned for arguing with Patrick. I was completely banned for maybe two years, and one dy I just tried to post and it worked.

    Then I got banned again for arguing wit KF.

  147. 169 Eugen March 15, 2011 at 12:10 pm

    What are ideas about evolution after the first cell is formed. Lets say we have one cell split into two. What could possibly happen with two cells? Sorry if this sounds naive but I like to visualize these mechanisms.

  148. 170 Petrushka March 15, 2011 at 2:07 pm

    What are ideas about evolution after the first cell is formed. Lets say we have one cell split into two. What could possibly happen with two cells? Sorry if this sounds naive but I like to visualize these mechanisms.

    Szostak has worked out specific biochemical scenarios for your perusal. There’s even a video that someone has made illustrating his ideas.

    Feel free to visualize.

  149. 171 Petrushka March 15, 2011 at 3:55 pm

    The video is hypothetical, but it invokes ongoing research.

    I’m curious how an ID proponent would approach testing OOL scenarios. Would they dump a bunch of chemicals in a beaker and draw conclusions from the failure of life to emerge, or would they try to imagine plausible scenarios and test them?

    To me it goes to the utility of ideas.

    Ideas can either be productive or sterile.

  150. 172 Eugen March 15, 2011 at 5:27 pm

    Thanks for the link. I’ll check it later.

  151. 173 Toronto March 15, 2011 at 11:00 pm

    Pachyaena:

    “Why should I be able to show it to you? Why don’t you ask an ID proponent?”

    You have positioned yourself in the middle of the debate, taking no firm position in favour of either side.

    In order to do this, you must have evaluated the evidence of each side fairly.

    You must have found and evaluated that stand-alone evidence for ID, in order to take the middle-ground position you’ve taken in the debate.

    Where is the stand-alone ID evidence you evaluated to come to your position?

  152. 174 Pachyaena March 16, 2011 at 9:39 am

    There is nothing I “must” do to convince you or anyone else of a damn thing. I didn’t come up with the theory of evolution or ID, and I’m not promoting either one.

    Actually, my “position” of keeping an open mind about the ultimate causes and processes of things, that haven’t been verified, let alone even discovered in many cases, is the most reasonable and patient position.

    You and some others apparently want me to say ‘The ToE is absolutely right in every way and that’s a proven fact! Science never makes mistakes and knows everything about everything, and agrees on everything! ID sucks and the people who promote it are a bunch of retards!’ Would that make you happy?

    You’re obviously displeased that I don’t take a “side” and then defend only that side while condemning the other side. This isn’t a sporting event with a time limit. It’s an ongoing endeavor that will likely never end as long as there are human beings. There may even be beings on other planets who are asking the same questions and looking for the answers too. If so, I wonder if they’re as impatient and eager to be right, whether the evidence is all in or not, as humans are.

  153. 175 Petrushka March 16, 2011 at 11:02 am

    You’re obviously displeased that I don’t take a “side” and then defend only that side while condemning the other side.

    Perhaps you could illuminate your position by stating what elements of mainstream science you accept as well established.

  154. 176 Toronto March 16, 2011 at 1:25 pm

    Pachyaena:

    A reader trying to get up to speed on the ID/evolution debate is going to think that both sides have very little stand-alone evidence to back up their position which is very misleading.

    In order to come to your conclusion about lack of evidence for either position, you must have evaluated and judged some evidence.

    What stand-alone evidence for the ID side did you evaluate and find lacking in merit?

  155. 177 Petrushka March 17, 2011 at 12:50 am

    The origin and/or evolution of life are a lot more complex and harder to figure out than the orbit of Neptune or Pluto.

    Sure the details are tough. Gravity took 200 years between Galileo and Newton, and another 200 between Newton and Einstein. Gravity is still an incomplete theory.

    But that doesn’t mean that after Galileo, there was any reasonable doubt about the general configuration of the sun and planets.

    One can see the forest before every tree is cataloged.

  156. 178 Pachyaena March 17, 2011 at 7:24 pm

    “One can see the forest before every tree is cataloged.”

    Isn’t that what an ID proponent would say about ID?

    Why is it okay for materialistic evolutionists to infer (speculate) but not for IDists?

  157. 179 Pachyaena March 17, 2011 at 7:39 pm

    Remember what I said about the murder case? A lot of evidence can seemingly point to something, using inferences, but the amount of evidence isn’t what matters. What matters is the quality of the evidence. One short video of the murder would trump any amount of circumstantial evidence, inferences, or verbal testimony.

    The ToE has a lot of circumstantial evidence, and inferences, but it does not have the smoking gun. Neither does ID theory. On that basis they are equal, unless and until either side can produce the smoking gun that actually shows the ultimate causes/processes behind life and evolution.

    • 180 Pachyaena April 11, 2011 at 11:53 am

      I want to expand a bit on what I said directly above. Again referring to a murder case, circumstantial evidence can be thought of as ‘entailments’. Entailments (circumstantial evidence) pointing to a particular suspect could be plentiful and quite convincing and could keep detectives and prosecutors real busy trying to put it all together and tie up all the loose ends, but a newly discovered video of the murder showing that a different person committed the crime would override all those entailments. Entailments aren’t necessarily proof of an ultimate act or cause, especially when it comes to the origin of life or evolution.

      I’m not saying that ID ‘theory’ is valid or that there’s any credible evidence of a designer, but I think it’s fair to say that a strictly materialistic origin of life and evolution (as they’re typically promoted by science) haven’t been proven. There’s some inferential evidence for a materialistic origin of life and evolution but there are some very important gaps that leave some big questions unanswered. I doubt that ID proponents will ever be able to fill any gaps with actual evidence, and I wonder if I’ll live long enough to see if science will fill the critical gaps with actual evidence, and not just inferences or probabilities. ID proponents certainly won’t fill any gaps with actual evidence if all they do is spout religious crap.

      I realize that some inferences in science are or seem to be reasonable but some things could be discovered that make a lot of current inferences look stupid. Which inferences will hold up to future discoveries and the test of time remains to be seen. It’s actually an exciting time to be alive because we may find some answers to some really big questions in the near future.

  158. 181 Petrushka March 17, 2011 at 8:00 pm

    Why is it okay for materialistic evolutionists to infer (speculate) but not for IDists?

    You can speculate to your heart’s content, but it isn’t worth a damn if you speculations have no entailments. ID is not wrong. It is sterile. There are no sightings of the designer, no observations of design intervention.

    There is no precedent in recorded history of a design hypothesis leading to a useful scientific finding.

    There have been plenty of such speculations. Newton invoked angles to tweak the orbits of planets, keeping them stable. Prior to science, design was the default hypothesis to explain everything that lacked an obvious cause. Earthquakes, storms, disease, etc.

    What is not OK is claiming that untestable speculations, and speculations that are merely sciency sounding restatements of “we don’t know yet,” are on the same playing field as testable hypotheses and established theories.

    But your last statement is factually incorrect. There are innumerable smoking guns pointing to evolution.

    Evolution has been observed in controlled laboratory experiments, “sports” (mutations) have been the subject of innumerable plant and animal breeding experiments, ERVs are an undeniable smoking gun.

  159. 182 Petrushka March 17, 2011 at 8:08 pm

    Angles = Angels

    I think.

  160. 183 Petrushka March 17, 2011 at 8:34 pm

    There is no precedent in recorded history of a design hypothesis leading to a useful scientific finding.

    By “design hypothesis” I mean an explanation that invokes a cause that is outside regular and observable causes. Unobserved agents doing unobserved things at unspecified times and places for unspecified reasons.

    Anthropology is not a good analogy, because everything that we attribute to ancient humans is attributed because we can observe humans at work and can observe their products and methods. We know their motives and their capabilities. All this detailed knowledge is factored into the design inference when examining a potential artifact.

  161. 184 Alan Fox March 18, 2011 at 4:35 pm

    The ToE has a lot of circumstantial evidence, and inferences, but it does not have the smoking gun.

    I think you’ll find it does if you are prepared to make the effort to look. The continuing confirmation of a nested hierarchy of relatedness is beautifully (yes, beautifully!) confirmed by the pattern of homologies in DNA sequences.

    Neither does ID theory.

    ID does not yet have a theory!

    “Easily the biggest challenge facing the ID community is to develop a full-fledged theory of biological design. We don’t have such a theory right now, and that’s a real problem. Without a theory, it’s very hard to know where to direct your research focus. Right now, we’ve got a bag of powerful intuitions, and a handful of notions such as “irreducible complexity” and “specified complexity”—but, as yet, no general theory of biological design.”

    Paul Nelson, interviewed in Touchstone vol 17, July/August, 2004.

    Notions but no theory – and nothing’s changed since 2004.

    • 185 Pachyaena March 20, 2011 at 7:26 pm

      I have looked, and the alleged “… continuing confirmation of a nested hierarchy of relatedness is beautifully (yes, beautifully!) confirmed by the pattern of homologies in DNA sequences.” is highly debatable and incomplete. There’s a big difference between inferences and a smoking gun.

      I’m sure that many ID proponents would argue that ID does have a theory and that it’s a very viable one. One person doesn’t speak for all ID proponents.

      Neither ‘side’ has absolute proof of their ultimate contentions. Neither ‘side’ has the smoking gun. If either ‘side’ did, they could show it, without inferences, probabilities, improbabilities, religion, beliefs, agendas, or speculation.

  162. 186 Toronto March 19, 2011 at 12:46 am

    Pachyaena:

    “The ToE has a lot of circumstantial evidence, and inferences, but it does not have the smoking gun. Neither does ID theory.

    “Smoking gun”?

    I think a better metaphor for ID would be, “unarmed”.

  163. 187 Toronto March 20, 2011 at 8:00 pm

    Pachyaena:

    You keep referring to an ID theory. I would like to know what you yourself, not any ID proponent means by that.

    Since you bring up the existance of a theory, you should be able to describe the theory that you yourself, refer to.

    Show me the stand-alone evidence for ID that you refer to when you make statements regarding comparisons between ID and evolution.

    I’m not asking you to find something new, just simply explain the stand-alone ID theory that you have already examined, in order to come to the conclusions that you have arrived at.

    • 188 Pachyaena March 21, 2011 at 6:50 pm

      Well, I used the word “theory” because ID proponents refer to it that way and because it could be described that way, even if rather loosely.

      It seems clear that you don’t think ID qualifies as a “theory” and I’m sure there are lots of other people who feel that way too. I do wonder though; what exactly is a “theory”?

      I’ve had discussions with others about it before but like so many other words it has a different meaning to different people.

      For the sake of discussions I don’t think it matters much if “theory” is used in a somewhat loose, general sense. To me it’s the evidence in a theory (or hypothesis, or claim, etc.) that matters the most.

      Something I think about a lot is:

      Who decides whether a theory is a theory or not? What exactly does it take to differentiate a hypothesis or claim from a theory? Where precisely is the dividing line between which word should be used to label a claim?

      Are there theories that are ‘official’, and if so, who decides on whether they’re official?

      Is there an ‘official’ version of the theory of evolution? When additions or changes are made to the ToE, is there an official body of certain people who give their official stamp of approval to those additions and/or changes?

      Is there a certified copy of the official ToE, containing all the necessary evidence to support it, somewhere on the web that anyone can access at any time to see what the official status and evidence currently is?

      Seems to me that the ToE is a highly variable theory that has no single, certified, official version, and is open to myriad interpretations. You know, like the Bible is open to myriad interpretations. 🙂

      And, is there a certified copy of the ‘official’ ID theory containing all the necessary evidence to support it, somewhere on the web that anyone can access at any time to see what the official status and evidence currently is?

      It’s kind of frustrating to discuss or debate things that are so variable and ‘un-official’.

  164. 189 Petrushka March 21, 2011 at 1:37 pm

    Neither ‘side’ has absolute proof of their ultimate contentions. Neither ‘side’ has the smoking gun. If either ‘side’ did, they could show it, without inferences, probabilities, improbabilities, religion, beliefs, agendas, or speculation.

    I’m not aware of any science that deals in absolute truth. All of science is based on inferences and probabilities.

    At some point the probabilities reach a point where ordinary people trust their lives to them on a daily basis.

    The general outline of the history of life (the age of the earth, the sequence of change over time, the basic mechanism of variation and selection and descent with modification are that well established). One can always doubt, but doubt is not always justified or reasonable.

  165. 190 Petrushka March 21, 2011 at 5:26 pm

    Could I point out that concluding anything from a literal smoking gun requires inference?

    What is this business with asserting that inference is somehow tainted? Just about everything we do in life, form moment to moment, is based on inferences and probabilities.

  166. 191 Toronto March 21, 2011 at 7:20 pm

    Pachyaena:

    “And, is there a certified copy of the ‘official’ ID theory containing all the necessary evidence to support it,..”

    I think what you’ve shown educators here, is that the “Teach The Controversy” idea will be a failure.

    For instance, despite being exposed to both “sides”, you can’t make up your own mind about any single point, never mind knowing what the two “sides” actually are.

  167. 192 Alan Fox March 21, 2011 at 9:59 pm

    Something I think about a lot is:

    Who decides whether a theory is a theory or not? What exactly does it take to differentiate a hypothesis or claim from a theory? Where precisely is the dividing line between which word should be used to label a claim?

    Are there theories that are ‘official’, and if so, who decides on whether they’re official?

    It’s very simple. Is a theory useful? If so, it gets used. Newton’s model on the behaviour of large bodies in space is still useful. The predictions are still good enough to be used in planning space flights. Relativity is more accurate but, in practice, Newtonian mechanics prevail.

    • 193 Pachyaena March 22, 2011 at 1:50 am

      I’m sure there are a lot of people who would say that the ToE is not useful in any way at all, and even some scientists would say that its usefulness is limited or nil. Some would say that it’s very useful and necessary to understand the diversity of life.

      ID proponents would say that ID ‘theory’ is very useful and completely necessary to understand life, the diversity of organisms, and the universe. Some people would say that ID ‘theory’ is useless.

      The debate will go on and on and on and….

  168. 194 Petrushka March 21, 2011 at 10:33 pm

    It’s very simple. Is a theory useful? If so, it gets used.

    For example, evolution can be used to predict the location of fossils, including intermediate fossils that are previously unknown.

    I would be curious whether in the 300 years since Paley, ID has predicted the existence of any type of living thing not previously known.

  169. 195 Petrushka March 22, 2011 at 12:55 pm

    “Useful” doesn’t mean you can make money with it.

    In science, useful means it suggests lines of research.

    What research has ID inspired?

  170. 196 Toronto March 22, 2011 at 3:24 pm

    Pachyaena: The debate will go on and on and on and….

    ..without any contribution from you.

    On the other hand, I might just be wrong.

    Who’s to say?

    Does any one of us actually know?

  171. 197 Petrushka March 22, 2011 at 5:00 pm

    I don’t see any debate. Just a bunch of people trying to pass laws without doing science.

    • 198 Toronto March 22, 2011 at 5:34 pm

      Petrushka:

      I think that’s what scares me the most, that legislators are enacting laws allowing creationism into schools under the guise that ID is a scientific concept.

      There can only be a pretence of debate, since ID has no evidence of it’s own, but this sham debate will be enough to swing votes to the creationist side and force students to “make up their own minds”.

  172. 199 Petrushka March 22, 2011 at 5:51 pm

    I’d love to see evolution taught from a historical perspective.

    I learned about it by reading Gould’s essays in Natural History, as they came out. I personally love reading about the old debates in their historical context. I appreciate the fact that for at least 80 years after Darwin, there were serious arguments against evolution, and that serious people had serious questions.

    Those debates were conducted by honest and intelligent people. I’d love to see Behe and Dembski placed in context.


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