Sunday, August 3, 2008

ID Research Themes

This is the fourth in a series of posts regarding themes in Darwin’s Black Box and The Design Matrix.


"The vast majority of scientists do not view Intelligent Design as science and I happen to agree with them. ... At best, Intelligent Design may only be a nascent proto-science..."
Mike Gene, Introduction, The Design Matrix

Interesting start to a post entitled "ID Research Themes", eh? However, it would appear that Gene switches gears from his introductory comments later on:


"Actually, the concept of design can be useful as a research guide. Several years ago, while reading some scientific articles describing the proofreading process of protein synthesis, it occurred to me that an important step of information flow appeared to lack proofreading. Already aware that the process of making DNA and protein synthesis was proofread, I wondered about transcription, the process of making RNA. I could not recall ever hearing anything about proofreading being associated with RNA polymerase activity ... It struck me that this was a great opportunity to use the hypothesis of design. Since the terminal step in information transfer (mRNA to protein) is proofread, could I use [ID] to infer that the earlier step in the information transfer (DNA to RNA) was likewise proofread? Yes.

... With this hypothesis in hand, I could go into a lab and design experiments to discover whether proofreading does indeed occur during transcription. ... If I had, in fact, performed these experiments, my prediction would have been borne out. A literature search I performed after coming up with this hypothesis provided support that there is good evidence that RNA polymerase can proofread. Thus, the suspicion of design was able to direct a line of thinking that not only could generate research, but could also uncover truths and further understanding of our biological world." (Emphasis mine)
"Mike Gene, Chapter 4, The Design Matrix*

Impressive, but Mike just keeps on giving. In Chapter 10, Mike Gene lists several testable hypotheses he developed from each of the four criteria within the Design Matrix (links provided where provided):

Rationality:
1. transcriptional proofreading (from Chapter 4)
2. lagging strand synthesis
3. use of cytosine as part of the DNA molecule

Discontinuity:
4. investigating the bacterial flagellum (here too)
5. investigating the eukaryotic flagellum

Analogy:
6. degradosome (an earlier hypothesis here)
7. use of nano-wheels in the cell

Foresight:
8. assisted in developing the hypothesis of front-loading evolution

There you go! Eight (8) working design hypotheses!

To the teleologist, go! Develop your own hypotheses (or use Mike's) and design your own experiments.

To the non-teleologist, please drop your argument about ID not being able to develop a viable research programme. Mike Gene has shown that it is an empty argument

*See link to #1 if you object to this prediction.

Source:
Gene, M., The Design Matrix: A Consilience of Clues, 2007
http://www.idthink.net/

Next: Engineering Thinking in Darwin's Black Box and The Design Matrix

96 comments:

  1. If these are indeed "working design hypotheses", they should lead to predictions about the mechanism. For example, can ID "theory" postulate HOW transcriptional proofreading (one of the examples you cite) come about? Evolutionary theory has a mechanism to explain this. What is the mechanism that ID folks have postulated to explain this? If it is the same old "think-poof" mechanism, please don't bother to answer this question.

    Secondly, it is abundantly clear that all of the observations and bits of evidence used by Mr(s) Gene were provided by scientists who were not laboring under the design paradigm. In fact, it is abundantly clear that no scientist who advocates design has ever contributed one bit of evidence for it. Does this parasitism bother you? Is it time for full-blooded ID scientists to get into a lab and generate data of their own rather than cherry-pick observations made by others that seem to fit into their own pre-conceived notions? If it is true that non-ID scientists found observations that did not fit into their pre-conceived notions, how is it possible for you and other IDists to constantly accuse "Darwinists" of being dogmatic and not open to following the evidence?

    Finally, in exactly NONE of these examples has anyone found any observation that cannot be accommodated by an evolutionary mechanism. The only thing that distinguishes ID from biology is the teleological bias of ID. IDists like to think that there is a higher purpose, a reason, for biological structures and mechanisms. Unfortunately NONE of their work ever leads to experimental evidence for that teleology. When ID scientists come up with an observation that clearly supports teleology and also cannot be accommodated by evolutionary thinking, you will have a real reason to blog about this stuff. Until then, it's just blowing smoke.

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  2. Welcome back Dave. Long time, no hear. :)

    "For example, can ID "theory" postulate HOW transcriptional proofreading (one of the examples you cite) come about?"

    "...in exactly NONE of these examples has anyone found any observation that cannot be accommodated by an evolutionary mechanism."


    You are treating design as a mechanism, and any engineer can tell you that is patently false. Engineers make use of mechanisms in their designs. So the question really is "Can a myopic tinkerer/Blind Watchmaker create natural objects that appear to be designed?" Depending on the object under investigation, the answer can be possible, plausible, or probable. If the answer is only possible, this could raise suspicions of a rational designer. Thus more experiments would be required.

    "Secondly, it is abundantly clear that all of the observations and bits of evidence used by Mr(s) Gene were provided by scientists who were not laboring under the design paradigm. In fact, it is abundantly clear that no scientist who advocates design has ever contributed one bit of evidence for it. Does this parasitism bother you?"

    In a word, no. Science builds on previous discoveries. Now "full-blooded ID scientists" still need to roll up their sleeves and do the legwork, but because they may use previous experiments to form their hypothesis does not mean they are "parasites".

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  3. Welcome back Dave. Long time, no hear.

    I've been out of the country, so I didn't have time to comment (here or elsewhere). I'm glad to hear that I was missed :-)

    "For example, can ID "theory" postulate HOW transcriptional proofreading (one of the examples you cite) come about?"

    "...in exactly NONE of these examples has anyone found any observation that cannot be accommodated by an evolutionary mechanism."

    You are treating design as a mechanism, and any engineer can tell you that is patently false.


    Perhaps I can persuade you to head over to this thread on Amazon, where an engineer named Brent Mortimer has continually claimed that design IS a mechanism. He could use a dose of your wisdom...

    Engineers make use of mechanisms in their designs. So the question really is "Can a myopic tinkerer/Blind Watchmaker create natural objects that appear to be designed?" Depending on the object under investigation, the answer can be possible, plausible, or probable. If the answer is only possible, this could raise suspicions of a rational designer. Thus more experiments would be required.

    Suspicions are not evidence. Indeed it is true that "more experiments would be required", just because NO experiments have been done by ID folks. But let's explore your position a little more closely. You say that observations have raised suspicions of a "rational designer". You say that more experiments are then required. Taking the example of transcriptional processing, WHAT experiments would you propose that might give you support for those suspicions of a rational designer? How do you approach these questions, and design experiments which test the teleological assumptions that you are making? I submit that there are no such experiments that could be designed, primarily because this is a mechanism-free set of notions. But if you have some additional experiments in mind, let's hear 'em. I'd be happy to be wrong in this instance.

    "Secondly, it is abundantly clear that all of the observations and bits of evidence used by Mr(s) Gene were provided by scientists who were not laboring under the design paradigm. In fact, it is abundantly clear that no scientist who advocates design has ever contributed one bit of evidence for it. Does this parasitism bother you?"

    In a word, no. Science builds on previous discoveries. Now "full-blooded ID scientists" still need to roll up their sleeves and do the legwork, but because they may use previous experiments to form their hypothesis does not mean they are "parasites".


    Science does indeed build on previous discoveries. But there is a difference between science and ID, and this statement makes it very clear. Scientists use previous observations to generate hypotheses and design experiments to test those hypotheses. The results of these experiments are used to refine or reject the hypotheses, and can also be used by other scientists in the same manner. ID folks DON'T DO EXPERIMENTS. They do not build on previous discoveries; they merely comment on them. Even Behe, the paragon of scientific credibility in the ID pantheon, hasn't done an experiment in years. Why is that? I submit that it is because, as noted above, there are no experiments that can be done to test the teleological assumptions of ID. If you can't do experiments, you are reduced to commenting on them, and cherry-picking the observations that fit your preconceived notions. That is not science. That is not "building" on previous discoveries. It is parasitism, pure and simple.

    We've heard, for over a decade now, that ID scientists will be doing these experiments. We've just heard it from you again. Pardon my skepticism, but after a decade or so in which no ID adherent has published one peer-reviewed paper based on ID notions, or even attempted one experiment to test the telelogical underpinning of the whole enterprise, I am not quite willing to accept your optimism that will be "rolling up their sleeves" anytime soon.

    But tell me some specific experiments that would comprise the next step toward showing that transcriptional processing has a teleological basis, and I might get more optimistic. And get over to Amazon to straighten out your fellow engineer about design and mechanism, please!

    thanks

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  4. "Perhaps I can persuade you to head over to this thread on Amazon, where an engineer named Brent Mortimer has continually claimed that design IS a mechanism. He could use a dose of your wisdom..."

    This is why I like, Dave. You spend all of your free time looking up stuff for me to read.

    Seriously, it was interesting, but I do believe Brent Mortimer is mistaken. If design is a "mechanism", then it is an all-encompassing mechanism that utilises/manipulates other mechanisms. I find that definition lacking. IMHO, design is not a mechanism, but a means to utilise mechanisms, and in order to do that, a designer needs some sort of rationality and foresight.

    "You say that observations have raised suspicions of a "rational designer". You say that more experiments are then required. Taking the example of transcriptional processing, WHAT experiments would you propose that might give you support for those suspicions of a rational designer? How do you approach these questions, and design experiments which test the teleological assumptions that you are making? I submit that there are no such experiments that could be designed, primarily because this is a mechanism-free set of notions. But if you have some additional experiments in mind, let's hear 'em. I'd be happy to be wrong in this instance."

    First, I will never claim to have all the answers. I only posted eight starting points for experiments to be developed. Second, it is not testing for the "design mechanism" but rather gaining more understanding on the properties (and thus limits) of the mechanisms and determining what these mechanisms can do unguided. After 150 years, I think we have a good database of knowledge to make the case for rational design and set up experiments for it, but...

    We've heard, for over a decade now, that ID scientists will be doing these experiments. We've just heard it from you again. Pardon my skepticism, but after a decade or so in which no ID adherent has published one peer-reviewed paper based on ID notions, or even attempted one experiment to test the telelogical underpinning of the whole enterprise, I am not quite willing to accept your optimism that will be "rolling up their sleeves" anytime soon."

    Point taken that no (or very few) experiments have been done. This is a huge target on the back of ID, and a deserved target, too, may I add.

    Mike Gene and myself are NOT saying that ID is at the same level as the Modern Synthesis, but it has to start somewhere. It would appear that ID scientists have been caught in a "war of words" rather than doing the experiments. That does not take away from the point that the experiments are not impossible to draw up and perform. I may not have those answers, but someone may (and if you do, post your comment here or somewhere SOON!)

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  5. I am finding this to be a very interesting and helpful site. Well done! I very much appreciate any such hints as to the nature of reality.

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  6. Thank you for the kind comments, William B., and welcome to EE.

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  7. Seriously, it was interesting, but I do believe Brent Mortimer is mistaken. If design is a "mechanism", then it is an all-encompassing mechanism that utilises/manipulates other mechanisms. I find that definition lacking. IMHO, design is not a mechanism, but a means to utilise mechanisms, and in order to do that, a designer needs some sort of rationality and foresight.

    Thanks for wandering over there and posting a comment. Indeed Mortimer is wrong; I have asked him many times how he would build a house using only the design and no toolkit, but he routinely ignores that and continues to insist that design=mechanism. He might be giving engineers a bad name :-)


    First, I will never claim to have all the answers. I only posted eight starting points for experiments to be developed. Second, it is not testing for the "design mechanism" but rather gaining more understanding on the properties (and thus limits) of the mechanisms and determining what these mechanisms can do unguided. After 150 years, I think we have a good database of knowledge to make the case for rational design and set up experiments for it, but...

    We've heard, for over a decade now, that ID scientists will be doing these experiments. We've just heard it from you again. Pardon my skepticism, but after a decade or so in which no ID adherent has published one peer-reviewed paper based on ID notions, or even attempted one experiment to test the telelogical underpinning of the whole enterprise, I am not quite willing to accept your optimism that will be "rolling up their sleeves" anytime soon."

    Point taken that no (or very few) experiments have been done. This is a huge target on the back of ID, and a deserved target, too, may I add.

    Mike Gene and myself are NOT saying that ID is at the same level as the Modern Synthesis, but it has to start somewhere.


    A small correction - it should have started by now. Here's an example from the world of real science. In 1982 Stanley Prusiner published a paper that advanced the heretical idea that proteins, free of any nucleic acid, could be infectious agents for diseases such as kuru or bovine spongiform encephalopathy (aka Mad Cow Disease). This was greeted with much skepticism, but other scientists went to work and generated hypotheses, did experiments, published papers etc. It turned out that Prusiner was right. In 1997 he received the Nobel Prize. That's 15 years after he caught a lot of flak for this heretical notion.

    ID was advanced as a notion sometime in the early 1990's. A decade and a half later there are not only no Nobel Prizes in the coffers, there are also NO PUBLISHED PAPERS AT ALL. Why is that?

    I maintain that this is because the testable hypotheses cannot be generated and experiments cannot be done to validate the teleological assumptions of ID. All that ID folks can do is cherry-pick the work of real scientists, philosophize in books (not peer-reviewed papers), take pot shots at evolutionary theory, and help pass disingenuous laws to help them teach creationism in public schools. They can't do experiments. It's a crippled paradigm from the scientific perspective, but it works well as a political tool.

    You can maintain that they should be starting any time now. Over the long term one of us will be proven correct...

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  8. Thanks for the example of Stanley Prusiner. My personal favourites are the discovery of solar wind (of which I learned a few details from the documentary series, The Planets) and Brentz's "megaflood" theory to explain the Scablands of the US Northwest.

    As for Mortimer, just like other professions, there are engineers who have "interesting" ideas, but I've found that it usually doesn't affect their technical knowledge. An example I can recall are engineers who seriously think that vaccinations are dangerous and kill children. This is obviously bogus when one objectively looks at the evidence, but the viewpoint does not affect the engineer's technical ability to put out a sound design.

    Bottom line: Mortimer is wrong about design being a mechanism. Also, I think he puts too much faith in Dembski's Explanatory Filter.

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  9. "You can maintain that they should be starting any time now. Over the long term one of us will be proven correct..."

    I remain optimistic that ID-favourable scientists will break away from DI and the IDM to start work on their own.

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  10. Bottom line: Mortimer is wrong about design being a mechanism. Also, I think he puts too much faith in Dembski's Explanatory Filter.

    Any faith in the EF is too much. They don't call it the Nixplanatory Filter for nothing; it has never been used to assess design for any biological process or structure. But it has made a bunch of money for Dembski...

    "You can maintain that they should be starting any time now. Over the long term one of us will be proven correct..."

    I remain optimistic that ID-favourable scientists will break away from DI and the IDM to start work on their own.


    That's fine. But if you were a working biological scientist, you would seriously wonder why this hadn't already happened. Science is a very competitive field. Any testable idea, no matter how wacky, usually attracts LOTS of people hoping to prove or disprove it. Look at the example of cold fusion!

    Ideas which are not testable don't usually do so well. There's a clue here; hopefully it will become apparent over time.

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  11. JJS wrote:
    "There you go! Eight (8) working design hypotheses!"

    Based on what I read here (my copy of The Design Matrix has not yet arrived) your claim goes beyond what Mike Gene claims. You passed him while he was shifting gears :-)

    His hypotheses are not design hypotheses and he does not claim that they are. The hypotheses do not say anything about any object or process being purposefully built.

    What he is claiming is that a suspicion of design may inspire someone to formulate useful and workable scientific hypotheses. He does not (as you have pointed out) consider the ID proposition itself to be scientific.

    Like Dave, I too consider Mike's actual claim to be weak, but I'll save that topic for another comment.

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  12. JJS P.Eng., I'm sorry, but I don't see a single empirical prediction from any of the hypotheses you listed. Are you aware that scientific predictions are about what will actually be observed--that the point is that predicting keeps us honest by forcing us to do all of the interpretation before the prediction, instead of interpreting after we have the results in hand? I've found that when ID proponents claim to have predictions, they dishonestly and/or ignorantly conflate them with hypotheses.

    Dave wrote:
    "In 1982 Stanley Prusiner published a paper that advanced the heretical idea that proteins, free of any nucleic acid, could be infectious agents for diseases such as kuru or bovine spongiform encephalopathy (aka Mad Cow Disease)."

    Dave, it's worth mentioning that when Prusiner first advanced that hypothesis in Science (which IMO is now a theory), he included new data from testing it.

    "ID was advanced as a notion sometime in the early 1990's. A decade and a half later there are not only no Nobel Prizes in the coffers, there are also NO PUBLISHED PAPERS AT ALL. Why is that?"

    It's also worth noting that by "published papers," we mean papers that include new data (primary literature), not reviews (secondary).

    "I maintain that this is because the testable hypotheses cannot be generated and experiments cannot be done to validate the teleological assumptions of ID."

    I disagree, Dave. I maintain that this is because ID proponents are AFRAID to test an ID hypothesis. In their hearts, they know that ID is hooey.

    JJS P.Eng. wrote:
    "I remain optimistic that ID-favourable scientists will break away from DI and the IDM to start work on their own."

    How optimistic? How much would you bet, and at what odds? The benchmark here is a paper with new data derived from testing an empirical prediction of an ID hypothesis.

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  13. In the extensive comments at TT (re your previous post), you wrote: "Behe implied indirect evolutionary pathways were possible but not plausible, but he lacked the words and the framework to avoid falling into the traditional role of dissenter, thus opening a door for his detractors to stall the development of the IC concept."

    Do you really believe this? How can detractors "stall the development of a concept"?

    Were they in Behe's lab, sabotaging his experiments?

    Did he submit papers that were arbitrarily rejected?

    What, exactly, do you think a "detractor" could do that would "stall the development" of a truly scientific concept?

    I'm really interested to hear more about this, and the evidence that it occurred...

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  14. Dave, let me see if I can re-phrase:

    "Behe implied indirect evolutionary pathways were possible but not plausible, but he lacked the words and the framework to avoid falling into the traditional role of dissenter, thus opening a door for his detractors to assume their traditional role of showing "Yes, it is possible for evolution to do this". Thus, completely unintended by Behe, the IC concept ended up being stalled."

    I find it interesting you were the only one to catch this! Raevmo, Todd B. and Zachriel never commented on this. You must be hell on your grad students! Every draft they give you is probably covered in red! ;)

    I never meant that there was a "conspiracy" to halt the development of IC; I only meant to convey that the Traditional Template stalled it. I am not one for conspiracy theories. I still think Oswald acted alone. ;)

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  15. "Behe implied indirect evolutionary pathways were possible but not plausible, but he lacked the words and the framework to avoid falling into the traditional role of dissenter, thus opening a door for his detractors to assume their traditional role of showing "Yes, it is possible for evolution to do this". Thus, completely unintended by Behe, the IC concept ended up being stalled."

    I still don't understand WHY you try to pin this on the anonymous "detractors" rather than on Behe. Detractors are everywhere in science; when we submit a paper for publication they are called "reviewers". When we give seminars at other institutions, they are called "audience members". But they don't stop me, and shouldn't stop Behe, from continuing to work on a good idea.

    So I'd submit that it is Behe's fault, unintended or not, that the concept "stalled". Maybe it just isn't such a good idea after all...

    Additionally, and unfortunately for your argument, in this case the detractors were right. Evolution can result in IC systems. IC is not a hallmark of design. Nobel Prize-winning geneticist Herman Muller wrote in 1918(!) - "Most present day animals are the result of a long process of evolution, in which at least thousands of mutations must have taken place. Each new mutant in turn must have derived its survival value from the effect which it produced upon the "reaction system" that had been brought into being by the many previously formed factors in cooperation; thus a complicated machine was gradually built up whose effective working was dependent upon the interlocking action of very numerous elementary parts or factors, and many of the characters are factors which, when new, where originally merely an asset finally become necessary because other necessary characters and factors had subsequently become changed so as to be dependent on the former. It must result, in consequence, that a dropping out of, or even a slight change in any one of these parts is very likely to disturb fatally the whole machinery;"

    source - "Genetic Variability, Twin Hybrids and Constant Hybrids, in a Case of Balanced Lethal Factors", Hermann J Muller, Genetics, 3(5):422-499, 1918, online here.

    Why would you call them "detractors" when they are right? Why do you assume that it is their fault that Behe never did any experiments to test his notions?

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  16. Dave, let me be clear. It was not my intention to "pin" the stalling of IC on its detractors. The stalling occurred, in part, because Behe unintentionally fell into the "dissenter" role of the Traditional Template. IC does have merit, and IMO, Mike Gene demonstrated that in The Design Matrix.

    Staying on the topic of Behe, that was an interesting quote from Muller. He used words like "must have" and "had been". Behe (successfully IMO) criticised use of these words without support details in Darwin's Black Box (Chapter 4, I believe).

    Now, is Muller talking about a direct pathway to IC, which has already been admitted by Thornhill and Ussery (Journal of Theoretical Biology, 2000) or an indirect pathway? If indirect, then the only mechanism that can account for the origin of IC systems is gradual cooption. If indirect, then the latter portions of Chapter 8, The Design Matrix hold and these precursors need to be found for gradual cooption to progress from possible to plausible.

    And who says the detractors are necessarily right? All they did was show a possible evolutionary route for IC systems.

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  17. It was not my intention to "pin" the stalling of IC on its detractors. The stalling occurred, in part, because Behe unintentionally fell into the "dissenter" role of the Traditional Template. IC does have merit, and IMO, Mike Gene demonstrated that in The Design Matrix.

    Borrowing a point from your rhetorical toolkit, Gene can only argue that this MIGHT have been part of the explanation. It is equally likely (far more likely, IMHO) that the stalling occurred because, as pointed out numerous times before, ID cannot generate predictive hypotheses, controlled experiments, and new observations. That explanation is consistent with all the facts, and also predicts that ID will continue to be non-productive in the realm of real science. Gene's explnation (and yours too, presumably) is that ID will start to produce results any time now. We'll see how that works out, won't we?

    Staying on the topic of Behe, that was an interesting quote from Muller. He used words like "must have" and "had been". Behe (successfully IMO) criticised use of these words without support details in Darwin's Black Box (Chapter 4, I believe).

    I consistently find it baffling that IDists weep, wail and gnash their teeth when confronted with possible explanations from the evolutionary perspective. You and others seem to demand iron-clad step-by-step explanations for every biological structure. In the first place, that is NOT science; science is always tentative and no true scientist will ever tell you that his/her explanation is the only possible one. Muller was behaving prudently, scientifically, and you need to recognize that.

    Secondly, and most importantly, if you demand certainty from your opponents, you need to provide it for them. Where is the certainty re mechanisms, timing, entity, or location of the think-poof explanation that is ID? Isn't is just a tad hypocritical to bemoan your opponents' failure to provide certainty while simultaneously espousing the most vaporous notions yourself?

    Now, is Muller talking about a direct pathway to IC, which has already been admitted by Thornhill and Ussery (Journal of Theoretical Biology, 2000) or an indirect pathway? If indirect, then the only mechanism that can account for the origin of IC systems is gradual cooption. If indirect, then the latter portions of Chapter 8, The Design Matrix hold and these precursors need to be found for gradual cooption to progress from possible to plausible.

    Ah, the God of the Gaps argument again. What will you do when these precursors are found and your gap gets smaller?

    Sadly for your perspective, the precursors have been found in the case of blood clotting cascades and the bacterial flagellum, just to name two of Behe's favorite examples. Obviously, the exact pathway and timing whereby these (known and hypothesized) precursors became integrated into the currently known biological systems will probably never be known to the satisfaction of Gene et al. But again, satisfying that sort of criticism needs to be accompanied by a demand for equal clarity re the ID pathway and mechanism. Where is the ID explanation for the blood clotting cascade that matches the current level of detail in support of the evolutionary scenario? Can you point me to a citation? I thought not.

    And who says the detractors are necessarily right? All they did was show a possible evolutionary route for IC systems.

    Granted. But that route, as pointed out innumerable times before, at least has some evidence supporting it, and it can lead to predictive hypotheses and controlled experiments and new observations. The ID route to an IC system has none of the above. What's the attraction there?

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  18. "Gene's explnation (and yours too, presumably) is that ID will start to produce results any time now. We'll see how that works out, won't we?"

    Yup, we sure will. You bring the popcorn, I'll bring the beer. We'll be like those old dudes from the Muppet Show, heh heh

    Also, I like how you debated your point within the Explanatory Continuum. Now if I can get everyone else to do so, then we'll have some fun!

    "I consistently find it baffling that IDists weep, wail and gnash their teeth when confronted with possible explanations from the evolutionary perspective. You and others seem to demand iron-clad step-by-step explanations for every biological structure. In the first place, that is NOT science; science is always tentative and no true scientist will ever tell you that his/her explanation is the only possible one."

    I propose the reason there is weeping, wailing and gnashing of teeth is that evolution is not presented as tenative, but rather as fact. This is the mainstream position taken that I (and others) object to. The real weeping, wailing and gnashing of teeth is when it is publically acknowledged that the Modern Synthesis is not a fact but our best explanation.

    "What will you do when these precursors are found and your gap gets smaller?"

    That only gets you to the plausible stage; more evidence is required to get to the probable stage (and no I don't know what it would take other than lots more circumstantial evidence).

    "Granted. But that route, as pointed out innumerable times before, at least has some evidence supporting it, and it can lead to predictive hypotheses and controlled experiments and new observations. The ID route to an IC system has none of the above. What's the attraction there?"

    IMHO, so can IC. The working hypotheses listed in the above post are a starting point, which was the point of this post all along.

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  19. I propose the reason there is weeping, wailing and gnashing of teeth is that evolution is not presented as tenative, but rather as fact. This is the mainstream position taken that I (and others) object to. The real weeping, wailing and gnashing of teeth is when it is publically acknowledged that the Modern Synthesis is not a fact but our best explanation.

    Perhaps that is how it is presented in your church, but not how it is presented in scientific journals. Try to read some and see if you can understand that scientists DO understand that evolutionary theory is the current best explanation. There is no gnashing of teeth in the scientific community over the reality that the Modern Synthesis is a working, changing, and yes, evolving, explanation. Any field of science where the reigning theory is static is a boring field of science.

    Furthermore, there is a subtle distinction that needs to be made more explicit. Evolution, defined as descent with modification, IS A FACT. It happened, and continues to happen. The evidence for that is incontrovertible. Evolutionary theory, the current best explanation for that observed fact, is tentative, dependent on new observations and insights. So please don't confuse evolution the fact) with evolutionary theory (the current best explanation for that fact). That will help a lot.

    Finally, I note that you slide right around the problem that I mentioned with ID. If evolution is derided as a "just-so story", how much further down the scale would you rank ID? Why is sauce for the goose not sauce for the gander in your treatment of these alternative explanations for the diversity of life on the planet?

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  20. "Try to read some and see if you can understand that scientists DO understand that evolutionary theory is the current best explanation."

    And I find it commendable that you do see MS as tenative. What is presented in science journals and what is being presented in MSM are two different things, and I find it dishonest (at best) by the MSM.

    "Furthermore, there is a subtle distinction that needs to be made more explicit. Evolution, defined as descent with modification, IS A FACT. It happened, and continues to happen. The evidence for that is incontrovertible."

    If you mean microevolution (i.e. beak changes in finches, colour changes in moths, etc.), we are in agreement. My point is this distinction is NOT made to the public, and instead of the extrapolation to macroevolution being put forward as the best explanation, it is being put forward as fact.

    "Finally, I note that you slide right around the problem that I mentioned with ID. If evolution is derided as a "just-so story", how much further down the scale would you rank ID? Why is sauce for the goose not sauce for the gander in your treatment of these alternative explanations for the diversity of life on the planet?"

    I didn't mean to sidestep it. Is ID a "just-so" story, or is it the first step in the teleologist's attempt to gain back 150 years of lost ground in a 2500-year old debate? Let it grow. Let it develop. I, Mike Gene, and others like us are NOT saying ID is at the same level as MS. All we are saying is give ID a chance.

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  21. And I find it commendable that you do see MS as tenative. What is presented in science journals and what is being presented in MSM are two different things, and I find it dishonest (at best) by the MSM.

    If by MSM you mean "main-stream media", that is a far different thing than saying that scientists are responsible for the misconceptions that you and your fellow church-goers have. Sure, the media distort things. So what? When did that become news? And when did those distortions change reality?

    If ID wants to be considered to be scientific, it will have to start paying a lot less attention to the media and a lot more attention to the scientific journals...

    If you mean microevolution (i.e. beak changes in finches, colour changes in moths, etc.), we are in agreement. My point is this distinction is NOT made to the public, and instead of the extrapolation to macroevolution being put forward as the best explanation, it is being put forward as fact.

    No, macroevolution is also a fact. The evidence that chimps and humans have a common ancestor is overwhelming. The evidence that fish are an ancestor to humans is overwhemlming. It's a fact. Furthermore, saying that you know that microevolution happens but you don't think macroevolution happens is analogous to saying that you believe in inches but you don't think they can ever add up to a mile. Illogical.

    Evolution (descent with modification) is a fact. The current best explanation for it (evolutionary theory) is, like all scientific approaches, tentative, provisional, and subject to change if new observations come along. It is powerfully supported by the available evidence. In that regard it is substantially more useful (and scientific) than ID.

    I didn't mean to sidestep it. Is ID a "just-so" story, or is it the first step in the teleologist's attempt to gain back 150 years of lost ground in a 2500-year old debate? Let it grow. Let it develop. I, Mike Gene, and others like us are NOT saying ID is at the same level as MS. All we are saying is give ID a chance.

    It had a chance. It was the accepted framework for several thousand years. It fails the test of explaining the evidence. It fails the test of being a predictive framework. It fails the test of results; no useful processes or products have resulted from ID/creationism. It fails, period. And shows no signs of strengthening in the future, sorry.

    Game over.

    ReplyDelete
  22. flipping through my previous posts...

    Ah, here we go! From the fine folks at Evangelical Dialogue on Evolution...

    "Evolution Meanings Group#1: Extremely high degree of scientific certainty
    ...E-2) Common ancestry. This is central to what scientists usually mean by “evolution.” Common ancestry (or common descent) means that life has branched out, so dogs and wolves are distant cousins, dogs and cats are more distant cousins, and if you go back far enough dogs and fish, or dogs and trees, had a common ancestor. You can put humans in the family tree as well – related to chimpanzees, more distant from other mammals, and so forth.

    Evolution Meanings Group#2: Less Scientific Certainty
    ...E-4) Mechanisms (E-3) account (physically) for common descent. This is typically what scientists mean by “the theory of evolution.” We know these mechanisms produce changes in species, but do they account for all the evolution (in the E-2 sense) that has happened through the history of life on Earth? Most biologists, including most Christians working in these areas, would say “yes,” but it is certainly not as 100% established as the previous meanings."


    And from my earlier post, The Explanatory Continuum...

    "E2. Common ancestry: According to the scientific world and Evangelical Dialogue, this would fall under probable, but why? It would appear that E2 is closer to the boundary of probable and plausible since much of the evidence appears circumstantial and any “hard” evidence either appears to be lacking or is controversial. That said there are two reasons for E2 to be in the probable category: no competing hypothesis and the shear weight of the accumulated circumstantial evidence. Both lend credibility for E2 to be considered probable.

    E4. Mechanisms (E3) account for (physically) common descent: Charles Darwin argued for the possibility of natural mechanisms to describe the history of life. 150 years later, there is only circumstantial evidence to support Darwin’s hunch. Therefore, E4 falls in the plausible category."


    And I still see zero comments/objections to the post. Perhaps you missed this one while overseas.

    Let's face it: I ain't gonna convince you common descent is probable at beast, and you ain't gonna convince me it's a fact (for the reasons stated above). To convince me, you need more than circumstantial evidence.

    ReplyDelete
  23. And I still see zero comments/objections to the post. Perhaps you missed this one while overseas.

    Indeed I did. I'd caution you against concluding, from a lack of comments, that your arguments must be air-tight.

    Let's simplify things. Evolution is most parsimoniously defined as "descent with modification". That descent with modification is a fact. No matter how blindered you are, the evidence for descent with modification is overwhelming. Our previous conversation re chimpanzee chromosomes is part of that evidence. The data indicating that chimps (and other Old World primates) have identical nucleotide changes that inactivate a gene in the pathway to vitamin C is part of that evidence. Moving away from the prickly topic of chimps and humans, the phylogenetic linkages between bacterial species and eukaryotic organelles such as mitochondria and chloroplasts is part of that evidence. Each individual bit of evidence may not convince you by yourself. But you have to be massively delusional to ignore all of the incredible number of individual observations, all of which are consilient with the "descent with modification" explanation. It's a fact. And its factuality allows scientists to make predictions which are borne out by experiment. Its factuality allows scientists to make progress in understanding, to design new processes and products which benefit mankind. Denying that factuality would return us to the biomedical Dark Ages.

    What is tentative is the completeness of our understanding of the mechanisms whereby this fact came about. That is evolutionary theory, and it is a vibrant, dynamic, thriving scientific enterprise. No reasonable person claims that we understand it completely, and no reasonable person considers all of these explanations to be completely accurate.

    Let's face it: I ain't gonna convince you common descent is probable at beast, and you ain't gonna convince me it's a fact (for the reasons stated above). To convince me, you need more than circumstantial evidence.

    I'm not going to convince you. Only evidence can convince you, if you are a thinking person. So please familiarize yourself with the evidence. If you don't understand it, please familiarize yourself with the basic concepts that you need for that understanding. It is not circumstantial evidence, it is a powerful and massive bloc of observations that only make sense if descent with modification occurred. If you can't see that, it is for reasons beyond my (and probably your) understanding.

    ReplyDelete
  24. From your last comment, I find this most interesting:

    "Evolution is most parsimoniously defined as "descent with modification". That descent with modification is a fact. ... What is tentative is the completeness of our understanding of the mechanisms whereby this fact came about."

    How can you call "descent with modification" a FACT when you don't completely understand the mechanisms involved? IOW, you sound an awful lot like this:

    "Evolution is true because it must have happened"

    I'm not a "church-boy-hick" who refuses to see what's in front of him. I see for myself the circumstantial evidence assembled and remain unconvinced that macroevolution is NOT a fact. Possible, maybe even plausible, but not a fact.

    ReplyDelete
  25. How can you call "descent with modification" a FACT when you don't completely understand the mechanisms involved?

    It's pretty simple, really. Science is our attempt to explain observations (facts) as the outcome of natural and understandable mechanisms. So all science would be DOA if your objection was valid.

    Here's an analogy that may not hurt so much as admitting that evolution is a fact.

    It is a fact that the earth travels in an elliptical orbit around the sun.

    The mechanism which we use to explain that fact is known as gravitational theory. Gravitational theory a la Newton has been shown to be incomplete; it explains most of the facts, but not all observations can be accounted for by this framework. Gravitational theory a la Einstein explains more of the observations. But I, as a real scientist, would never state that our understanding via this framework is complete. It is the best we have right now.

    Descent with modification is a fact. Evolution by natural selection (and other mechanisms) offers the current best explanation for that fact.

    I never said that you are a "church-boy-hick" who refuses to see what's in front of him. I wouldn't spend any time here if I thought that was the case. I think you are an intelligent rational person who is capable of understanding the evidence, and you are honest. That's a cut above the average IDC blogger, for sure.

    At the same time you yourself admit that you are not a biologist. In some of your previous posts that lack of basic knowledge was made quite clear. So I do think, if you are really serious about understanding the evidence, that you need to get more familiar with the basics of biology. Then you can get to the point where you understand that the evidence for evolutionary theory is a) overwhelming, b) useful, and c) not circumstantial at all.

    At that stage you may have a crisis of faith, if, as I suspect, your antipathy toward evolution is based on religious grounds. I can't help you with that; we all have to traverse that divide in our own fashion. But I can help you see the evidence, if you are prepared to change your mind based on a new understanding of the evidence. If you are not prepared to change your mind, let me know that now, and I'll not darken your comment pages any longer.

    As I said before, I can't convince you. But the evidence might, if you make an honest attempt to understand it, and if you quit misconstruing it on the basis of incomplete knowledge.

    ReplyDelete
  26. "I'm not a "church-boy-hick" who refuses to see what's in front of him. I see for myself..."

    I'm skeptical. How many amino-acid sequence alignments have you done?

    "...the circumstantial evidence assembled..."

    Your claim that the evidence is merely "circumstantial" is utterly false. Every time a real scientist (like me) compares/contrasts a new sequence against the databases constitutes an empirical test of common descent.

    So, how many have you done?

    You're looking like an aggressively ignorant hick from where I stand.

    ReplyDelete
  27. JJS,

    It's not clear to me if you are doubting common descent, or the mechanisms that caused it. In The Edge of Evolution, Behe argues that the evidence for common descent is overwhelming. If the leading proponent of ID argues for it, I think we can pretty much take it as the closest thing we'll get to fact.

    ReplyDelete
  28. Bilbo,

    It seems to me that you are saying that appeals to authority are valid if you already agree with the authority.

    Is that an accurate description of your position?

    ReplyDelete
  29. Oh, who to address first?

    How about Smokey?

    "I'm skeptical. How many amino-acid sequence alignments have you done?

    Nice touch. Ignore the engineer. What does he know about science anyway?

    From WordNet:
    engineer

    noun
    engineer ... (a person who uses scientific knowledge to solve practical problems)


    You're looking like an elitist from where I'm sitting.

    ReplyDelete
  30. Bilbo said:

    "It's not clear to me if you are doubting common descent, or the mechanisms that caused it."

    Dave said earlier:

    "Let's simplify things. Evolution is most parsimoniously defined as "descent with modification". That descent with modification is a fact. ... What is tentative is the completeness of our understanding of the mechanisms whereby this fact came about."

    Perhaps an analogy will make my position clearer.

    If I design a structure without detailed knowledge of how the loads can be safely transferred to the foundation/ground, then I have a faulty design. Before I apply my stamp of approval, I had better have confidence that I know and understand how this load transfer will actually occur. This entails detailed knowledge of the applied load and resisting mechanisms involved. If I don't have a complete understanding of the mechanisms and despite that allow the design to be stamped, I am playing Russian roulette with people's lives. Therefore, I had better be right when it comes down to the mechanisms and loads involved.

    IMHO, when I see Dave's statement, it is analogous to stamping a design without full knowledge of the loads and mechanisms involved. Detailed knowledge of how you get from A to B to C to D is important to an engineer.

    To qualify, I would have no problem with the following statement:

    "Common descent with modification as a means to describe macroevolution is probable."

    ReplyDelete
  31. Mike has a good post regarding my post here.

    ReplyDelete
  32. "Nice touch. Ignore the engineer. What does he know about science anyway?"

    What? I'm not ignoring you, I'm challenging the veracity of your claim that you are familiar with the evidence.

    "You're looking like an elitist from where I'm sitting."

    How so? You claim to have objectively looked at the evidence. I'm asking if you've looked at any of the gigabytes of freely available evidence. There's nothing elitist about my challenge at all.

    The fact is that the sequences and the tools for aligning them are available to everyone, so if you've examined the evidence, you should have done this quite often.

    Questions:

    1) Have you examined the sequence evidence for yourself?
    2) What is elitist about asking if you have done so?

    ReplyDelete
  33. Smokey wrote: It seems to me that you are saying that appeals to authority are valid if you already agree with the authority.

    Is that an accurate description of your position?


    No. My position would be that if both authorities that you agree with and authorities that you don't agree with, agree on a position, then the position is probably correct. And if you choose to disagree with them, you had better have a very good reason.

    ReplyDelete
  34. "My position would be that if both authorities that you agree with and authorities that you don't agree with, agree on a position, then the position is probably correct."

    I don't get it. The authorities are agreeing with you on common descent. Did you mean "authorities that you don't agree with on OTHER matters"?

    ReplyDelete
  35. "IMHO, when I see Dave's statement, it is analogous to stamping a design without full knowledge of the loads and mechanisms involved."

    I don't see any analogy there. You seem to be assuming the antecedent (design).

    "Detailed knowledge of how you get from A to B to C to D is important to an engineer."

    Really? Then why don't any of the engineers who endorse ID offer any hypotheses of how and when the designer designed A to B to C to D?

    ReplyDelete
  36. Smokey: Did you mean "authorities that you don't agree with on OTHER matters"?

    Yes. In other words, if both authorities who reject ID and authorities who accept ID agree on common descent, then one better have good reasons for disagreeing with them, or even doubting them.

    ReplyDelete
  37. OK, Bilbo.

    So at least you and Dave and I agree that descent with modification (i.e., the fact of evolution) occurred and is occurring in real time.

    With that out of the way, wouldn't the only people who could truly be considered authorities in this context be people who actually either:

    1) Do evolutionary biology, or
    2) Produce new data relevant to predictions of evolutionary (or ID) hypotheses?

    ReplyDelete
  38. If I design a structure without detailed knowledge of how the loads can be safely transferred to the foundation/ground, then I have a faulty design. Before I apply my stamp of approval, I had better have confidence that I know and understand how this load transfer will actually occur. This entails detailed knowledge of the applied load and resisting mechanisms involved. If I don't have a complete understanding of the mechanisms and despite that allow the design to be stamped, I am playing Russian roulette with people's lives. Therefore, I had better be right when it comes down to the mechanisms and loads involved.

    IMHO, when I see Dave's statement, it is analogous to stamping a design without full knowledge of the loads and mechanisms involved. Detailed knowledge of how you get from A to B to C to D is important to an engineer.


    That is not analogous at all, sorry.

    I'm talking about EXPLAINING observations made in the natural world. Those facts (in this case the diversity AND similarity of life on the planet) will be there whether you can explain them or not.

    You are talking about designing new structures. That structure won't be there if you don't design and build it. If it is not there then you have nothing to explain. That's flamingly obvious.

    Bilbo gets it, and Smokey gets it; why can't you see the difference? Facts are different than explanations for those facts, but the facts will be there in the presence or absence of any explanation. Science wants to explain those facts, and strives to do so via hypothesis-building and experimentation. But the facts don't depend on your explanation; your structure does depend on your design.

    Evolution is a fact; it will be there if we have a good explanation of how it happened, or if we don't.

    ReplyDelete
  39. Mike has a good post regarding my post here.

    I beg to differ. Here is a short translation of that long-winded non-rebuttal of my arguments.

    1) The Design Matrix (DM) is a way to determine teleology, but you need to keep in mind that "science is incapable of determining whether or not life was designed." In other words, you can claim to be using the work of real scientists even while admitting that science can't do what you say you want to do.

    2) DM is not ID. In other words, the decade-and-a-half failure of the ID crowd to come up with even a single peer-reviewed paper based on ID "theory" can't be associated with the DM crowd. How very convenient. But what will you be calling this non-scientific hopeful teleology a decade from now when neither Mike nor anyone else has succeeded in producing a peer-reviewed paper based on DM theory? Oh, I forgot. DM isn't science, so you don't have to publish any papers. That is incredibly convenient, but only for those who like to publish books rather than contribute new knowledge or new processes or new products. Somehow I have the feeling that the rest of us won't reap the benefits like Mike will...

    3)Mike writes "With regard to the transcriptional proofreading, predictions about mechanisms are not needed from the investigative perspective." Funny, that sounds suspiciously like Dembski's "ID is not a mechanistic theory, and it's not ID's task to match your pathetic level of detail in telling mechanistic stories." Tell me again how this is different from ID??? Tell me again how you can gain a better understanding of anything useful if you don't have a mechanistic explanation????

    I'd have to conclude that DM is just ID in an even cheaper tuxedo.

    I'll say it again, Mike. Get into a lab and do some real work if you want your recycled notions to garner any real respect outside of the ID/creationist echo chamber. And publish it under a real name, not a pseudonym, please.

    ReplyDelete
  40. Smokey: With that out of the way, wouldn't the only people who could truly be considered authorities in this context be people who actually either:

    1) Do evolutionary biology, or
    2) Produce new data relevant to predictions of evolutionary (or ID) hypotheses?


    I would say authorities are people who know enough about a subject that they don't have to depend upon authorities to know it.

    "Produce new data"? What if they just intepret the data?

    ReplyDelete
  41. "I would say authorities are people who know enough about a subject that they don't have to depend upon authorities to know it."

    But how does one learn about doing science? A bunch of classes, or an apprenticeship?

    ""Produce new data"? What if they just intepret the data?"

    In science practice, we make predictions--that keeps us much more honest than you, because the process of prediction makes us do the interpretation before seeing the data. Your side is obviously afraid to do this; hence, the gross misrepresentations of science and scientific expertise to laypeople.

    Science is about producing new knowledge, and even false hypotheses can be useful in doing so. But if you're afraid to produce any new knowledge, you aren't really doing science by merely "interpreting" the new knowledge produced by others (who aren't really testing the hypotheses you advocate anyway).

    ReplyDelete
  42. Smokey: In science practice, we make predictions--that keeps us much more honest than you,

    Oh don't hold back, Smokey. Just come right out and call me a lying s.o.b.


    because the process of prediction makes us do the interpretation before seeing the data.

    Imagine it's the beginning of the 20th century. You're a physicist trying to come up with an experiment to show that Newtonian physics is compatible with the Michelson-Morley results. Suddenly, you read a paper by a non-physicist who says Newton got it wrong. Your first reaction: "Obviously a dishonest quack who is ignores all the previous data supporting Newton and is afraid to do the experiments necessary to support his whacko theory."

    That's exactly what you sound like, Smokey.

    Let's face it, scientists do experiments and get data. Right now that data tells us that we have a sub-cellular world of complex molecular machines acting in synchronized co-ordination as a giant factory. We have two ways of interpreting this data: non-teleological or teleogical. So far, it looks to us teleogists as if the data is beginning
    to fit the teleological interpretation much better.

    ReplyDelete
  43. Bilbo wrote: Let's face it, scientists do experiments and get data. Right now that data tells us that we have a sub-cellular world of complex molecular machines acting in synchronized co-ordination as a giant factory. We have two ways of interpreting this data: non-teleological or teleogical. So far, it looks to us teleogists as if the data is beginning to fit the teleological interpretation much better.

    If some of the teleologists were actually working biological scientists, that might start to be an impressive argument. But since most of them are engineers (sorry, JJS), lawyers, philosophers, and other assorted folks who are blissfully ignorant of the evidence or how to interpret it, it's not so impressive. Sorry, Bilbo, but nearly everybody who actually generates and interprets the data on which you depend is convinced that non-teleological explanations are sufficient. That should count for something, even in the fantasy land of ID and TT.

    As has been pointed out a few million times before, if the teleological explanation is ever to have any respect in the scientific community where the teleologists think it is relevant (biology), then somebody is going to have to do develop some testable hypotheses, do some controlled experiments, and publish (in a peer-revieweed journal) some new observations that cannot be explained by the current evolutionary framework AND which are consistent with a teleological explanation. Until you do that, all you have is smoke, mirrors, lawyers and biological ignoramuses like Joy .

    And I honestly don't understand how it is even theoretically possible to determine teleology in a situation where you have no idea about who, when, where, how, and why a particular design was developed. If you have a theoretically possible answer to that, however, please save it until it gets past the theoretical stage. In other words, get into a lab and practice what you preach before you preach any more.

    ReplyDelete
  44. Bilbo wrote:
    "Oh don't hold back, Smokey. Just come right out and call me a lying s.o.b. "

    Nice evasion. I'm pointing out that the scientific method compensates for our human tendencies to see what we want to see.

    "Imagine it's the beginning of the 20th century. You're a physicist trying to come up with an experiment to show that Newtonian physics is compatible with the Michelson-Morley results. Suddenly, you read a paper by a non-physicist who says Newton got it wrong."

    And the paper contains empirical predictions, which destroys your attempt at analogy.

    "Your first reaction: "Obviously a dishonest quack who is ignores all the previous data supporting Newton and is afraid to do the experiments necessary to support his whacko theory."

    My real reaction: test the predictions.

    "That's exactly what you sound like, Smokey."

    Not at all, Bilbo, and you know it.

    "Let's face it, scientists do experiments and get data."

    Yes. Pseudoscientists spin existing data and avoid making empirical predictions.

    "Right now that data tells us that we have a sub-cellular world of complex molecular machines acting in synchronized co-ordination as a giant factory."

    No, that's a metaphor. I work on one class of those "machines," and I know that every metaphor breaks down.

    "We have two ways of interpreting this data: non-teleological or teleogical."

    If you're interpreting the data scientifically and teleologically, you should be able and willing to make discrete empirical predictions. You're afraid to.

    "So far, it looks to us teleogists as if the data is beginning to fit the teleological interpretation much better."

    Really?
    Hypothesis: molecular motors were designed.
    Prediction: there won't be an evolutionary trail showing how motors evolved from nonmotor precursors.

    Whaddaya think, Bilbo?

    ReplyDelete
  45. Let's see, I'm evasive, dishonest, afraid...I'll skip the ad hominems and get to the substance: Empirical predictions. If the teleological view is correct, and someone designed the original cells, then our predictions will be different than we find in hard science. Why? Because we're dealing with a mind, and trying to understand how that mind worked. Minds are not easily (if at all) subject to the hard sciences. Even in the neurosciences, we largely rely on the subjective reports of the people we are studying. So what sort of predictions can a teleologist make? Predictions based on how our minds work.

    Let's take proofreading as an example. Mike Gene found out that there is a proofreading mechanism for transcription, and predicted that we would find a proofreading mechanism for translation. Why? Because that would be the rational thing to do. Turns out he was right and there is one. Interestingly, it works very much like the one for transcription, even though it is not homologous to it. He didn't predict this. We don't know enough about nanotechnology to make more specific predictions. Just general ones.

    Let's take a case where analogical thinking has probably gone wrong. We teleologists thought the genetic code was conventional, just like our codes. If Art is right, then Yarus et al. have shown that the genetic code isn't conventional, but has some sort of physico/chemico basis. Score one for non-teleologists. Does it weaken or falsify the teleological view? Perhaps. What we need to find out is if there is a good design reason for using a physico/chemico basis for the genetic code. If we don't find one, then yes, it weakens the teleological view. If we find a good design reason, does it strengthen it? Perhaps. But we also have to keep in mind that the blind watchmaker, given enough trials can come up with good design, also.

    Now let's get to your example, Smokey:
    Hypothesis: molecular motors were designed.
    Prediction: there won't be an evolutionary trail showing how motors evolved from nonmotor precursors.


    Yeah, I'll buy that. Mike Gene makes it even easier. We don't even need an evolutionary trail. Most of the precursors to the parts of the molecular motors just have to be missing.

    I'll be gone for a few days. Probably back next week.

    One last word, I think we need both teleologists and non-teleologists, to keep each other honest, and to understand the biological world. Enough personal attacks, guys. How about a group hug? :)

    ReplyDelete
  46. Bilbo

    The transcriptional processing "prediction" has already been dealt with here. Furthermore there is no a priori reason to discard an evolutionary explanation for it. Teleology cannot be used as an explanation until the who, what, when, where, how and why of the "design" is made explicit. Until you do that, all you are doing is hand-waving (and selling books to rubes).

    I did enjoy this last bit, though. One last word, I think we need both teleologists and non-teleologists, to keep each other honest, and to understand the biological world.

    I initially misread it as something I could agree with. So I fixed it for you.

    I think both teleologists and non-teleologists need to understand the biological world, especially before they pontificate on the meaning of other people's observations.

    Maybe you can pass that along to Joy...

    ReplyDelete
  47. "Let's see, I'm evasive, dishonest, afraid...I'll skip the ad hominems..."

    You're employing a straw man. I said that your response was an evasion. That's not an ad hominem at all.

    "... and get to the substance: Empirical predictions. If the teleological view is correct, and someone designed the original cells, then our predictions will be different than we find in hard science."

    False dichotomy. One can do hard science with minds.

    " Why? Because we're dealing with a mind, and trying to understand how that mind worked."

    But you're just wanking if you are afraid to hypothesize when the mind worked and to whom it belonged.

    "Minds are not easily (if at all) subject to the hard sciences. Even in the neurosciences, we largely rely on the subjective reports of the people we are studying."

    Bilbo, you're a joke. You're now conflating "neuroscience" with "psychology." I do hard neuroscience myself, studying the fuzzy logic underlying LTP.

    "Let's take a case where analogical thinking has probably gone wrong. We teleologists thought the genetic code was conventional, just like our codes."

    It's not a code within biology at all, because there's nothing symbolic about it. It's only a code in our discussions of it because we symbolize the bases and amino acids with letters.

    "If Art is right, then Yarus et al. have shown that the genetic code isn't conventional, but has some sort of physico/chemico basis. Score one for non-teleologists."

    You're only scoring in your dreams.

    "Now let's get to your example...Yeah, I'll buy that. Mike Gene makes it even easier. We don't even need an evolutionary trail. Most of the precursors to the parts of the molecular motors just have to be missing."

    Then which precursors are missing, IYNSHO?

    ReplyDelete
  48. Sorry it took me so long to get back here. I forgot what the exact address of JJS's blog was.

    Let's see, Dave says,

    "The transcriptional processing "prediction" has already been dealt with here.

    Yeah, but I'm on a time limit and read too slow to got back and find it. My point is that teleological predictions will have a different character to them than non-teleological ones. Why? Because we are dealing with minds, which aren't very predictable. And because we are dealing with a new technology -- nanotechnology. If we had an expert nano-engineer, we could ask him to predict what type of proofreading system the designer was likely to use, and he could make a prediction.

    Furthermore there is no a priori reason to discard an evolutionary explanation for it.

    Agreed.

    Teleology cannot be used as an explanation until the who, what, when, where, how and why of the "design" is made explicit.

    Sort of agree and disagree. We can make hypotheses about the designer, as Mike Gene has done -- Human-like mind, rational, very knowledgeable about biochemistry, cell biology, genetics, etc., and designed the first cells, front-loaded to exploit Darwinian processes. Then we see how well the data fits the hypotheses.

    Until you do that, all you are doing is hand-waving (and selling books to rubes).

    Mike has done it, so buy the book and read it.

    Smokey writes,

    You're employing a straw man. I said that your response was an evasion. That's not an ad hominem at all.

    Oh, thank goodness. I'm only dishonest and afraid. I was nervous that I was evasive, also.

    False dichotomy. One can do hard science with minds.

    How?

    But you're just wanking if you are afraid to hypothesize when the mind worked and to whom it belonged.

    I'm not afraid to hypothesize. I'll go with Mike Gene's hypothesis, for now. It worked 3.5 billion years ago, and belonged to someone very intelligent and rational, with foresight about how the first living cells could evolve.

    Bilbo, you're a joke.

    Oh darn. Now I'll have to add that to the list of my faults.

    You're now conflating "neuroscience" with "psychology." I do hard neuroscience myself, studying the fuzzy logic underlying LTP.

    Not sure what "LTP" is, but it sounds intriguing. Am I mistaken in thinking that the ultimate goal on neuroscience is to subsume psychology?

    It's not a code within biology at all, because there's nothing symbolic about it. It's only a code in our discussions of it because we symbolize the bases and amino acids with letters.

    I argued with Art about this. I think it's a code in exactly the same way a computer code is a code. Certain characters act as instructions for the computer to perform operations. Likewise, certain nucleic acids act as instructions for the cell to perform certain operations.

    "If Art is right, then Yarus et al. have shown that the genetic code isn't conventional, but has some sort of physico/chemico basis. Score one for non-teleologists."

    You're only scoring in your dreams.

    Yeah, but I was scoring for your side. Is that a problem for you?

    Then which precursors are missing, IYNSHO?

    Another one of those mysterious letter thingys. I wonder what IYNSHO means. Or is that another attack on my character?

    Since I'm just a member of the peanut gallery, I'm relying on Mike Gene's book for a lot of my information. So far, he's only covered the Genetic Code, for which there seem to be no precursors. That by itself doesn't mean much, since it could just be a frozen accident. The significance comes in considering that the Code is one of the most reliable possible, and has served organisms well for over 3 billion years. In terms of Rationality and Foresight, this would be a strong indicator of design.

    Now Art has suggested that the Code's redundancy for stop codons is a sub-optimal design, since it creates more nonsense DNA than a Code with just one stop codon would. If he's right, this would count against design. So this would be an interesting feature to investigate. A teleological perspective would predict that there is a good design reason for 3 stop codons. A more specific prediction? Sorry, don't have one. But a researcher with a teleological perspective might find out why it's a good design sooner than a researcher with a non-teleological perspective.

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  49. I wrote: Until you do that, all you are doing is hand-waving (and selling books to rubes).

    Bilbo responded: Mike has done it, so buy the book and read it.

    No thanks. I'm not a rube. But please give me a holler when you or mike publishes a peer-reviewed scientific paper.

    I might live that long, I'm only 58...

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  50. Oops. What I meant, Dave, was that Mike had done what you required, or most of it:

    Teleology cannot be used as an explanation until the who, what, when, where, how and why of the "design" is made explicit.

    Now buy his book. It's a very good read. Since Mike says that ID isn't science, I doubt you will find peer-reviewed papers on ID. What he does say is that ID can use hard science to help investigate whether or not features of living organisms were intelligently designed, much the way detectives use hard science to determine if a murder has been committed.

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  51. Bilbo: Now buy his book. It's a very good read. Since Mike says that ID isn't science, I doubt you will find peer-reviewed papers on ID.

    Well, that's certainly convenient. Since I am a scientist, that means I won't have all those ID papers to plow through in the future.

    What he does say is that ID can use hard science to help investigate whether or not features of living organisms were intelligently designed, much the way detectives use hard science to determine if a murder has been committed.

    Well, then, here's a puzzle for you. Send it to Mike if it is too hard.

    Go to this URL, where you can read about an interesting bone artifact discovered in Slovenia. Some authorities suggest that it is a flute; if so, it is the earliest example of a musical instrument. Other authorities suggest that it is merely a bone that a cave bear chewed on. If you use the ID approach (either Dembski's version where the who, what, when, where, how and why of the "designer" are not allowed to be discussed, or Mike's recently mutated version), how would you test the inference that this is a flute?

    thanks in advance

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  52. Dave asked, how would you test the inference that this is a flute?

    Not sure. I don't think all cases of ID are unambiguous. And the case of the ID of living cells may turn out to be ambiguous as well. On the other hand, the evidence may become so overwhelming as to convince even diehard skeptics, oldtimer (I'm only 54, but not a scientist). Mike's book begins by looking at data that would make us suspect ID, which is enough to justify an investigation. What the results of that investigation will turn out to be he leaves for the future (or part II and III of The Design Matrix?)

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  53. Bilbo writes: Mike's book begins by looking at data that would make us suspect ID, which is enough to justify an investigation.

    Apparently it is not enough to "justify an investigation", because none of your teleologist crowd can be motivated to do that and publish the results in peer-reviewed journals. That is amazing hypocrisy!

    If it truly justifies an investigation, then you need to investigate it. If you don't have the courage of your convictions, then you are no better than Dembski and Behe and all of the other ID folks who refuse to generate one testable hypothesis or do one experiment.

    There will always be data which make scientists "suspect" some explanation or the other. But they don't stop there! They actually test that suspicion by doing experiments. Apparently the mere suspicion is good enough for you and Mike and all the rubes who bought the book.

    It's a great scam you guys have come up with. And you can probably keep it up for a long time. But from the perspective of actually accomplishing anything at all, it will be a big fat zero unless you actually put some effort into looking past your suspicions. The simple observation that you are unwilling to do that implies, to me at least, that you really do know that it is a scam, and that testing your suspicions can't be done.

    Sad.

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  54. Sheesh, Dave, just because I called you an oldtimer is no reason to get especially grumpy. Good thing I'm not in your neighborhood or you might try to club me with your walker. ;P I can't test ID because I'm not a scientist. If I were, one of the things I would want to test is whether or not having 3 stop codons is a good design. Not sure how I would go about doing that. I might try computer simulations, to see what happens if we go with 1 stop codon, instead of 3. If possible, I would try an in vitro experiment, where I alter the code to 1 stop codon. Since your a scientist, maybe you can think of some other ways of testing it.

    Now once we test it, let's suppose we get results that suggest 3 codons are a good design strategy. Does that prove ID? No. Again, it could just be a frozen accident. But it would strengthen the ID hypothesis. If we continue to test various features we hypothesize were designed for things we associate with intelligent design -- analogy (with things we know are designed); discontinuity (with non-teleogical processes); rationality (the design makes sense); or foresight (it appears to have been designed with the future in mind) -- and we continue to get positive results, it continues to strengthen the ID hypothesis.

    But what if we get negative results? Then it would weaken the ID hypothesis. If we're stubborn scientists (I hear they exist), we won't give up (at least, not right away), and will continue to look for other ID hypotheses that will explain the apparent negative results. But the more negative results, the less likely ID will look.

    Hmmm...meanwhile, I'll have to add "rube" to the list of my faults. It's getting rather long.

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  55. Bilbo wrote: If I were (a scientist), one of the things I would want to test is whether or not having 3 stop codons is a good design. Not sure how I would go about doing that. I might try computer simulations, to see what happens if we go with 1 stop codon, instead of 3. If possible, I would try an in vitro experiment, where I alter the code to 1 stop codon. Since your a scientist, maybe you can think of some other ways of testing it.

    No, actually, I can't figure out a way to test it. That's because the hypothesis is not scientific. What is a "good design"? How do we recognize it? How do we quantify it? Furthermore, since the alleged entity that did the alleged designing is either invisible or long-dead, how do we know that our vague notions about "good design" correspond to the entity's notions? How do we know what tools and materials were used in this design, since limitations in tools and materials can have a dramatic effect on "good" design?

    The point of this, which still seems to be whizzing right past your head, is that your ill-formed teleological notions about the design of living things are not hypotheses, and are thus inherently untestable. The reason you can't figure out how to test them is not because you are not a scientist. It is because they are untestable.

    Why is that so hard to understand?

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  56. Bilbo,
    Let's set aside about the number of stop codons and look at the mere existence of a single stop codon.

    Can we agree that by our criteria, having a stop codon is a good design because it allows proteins to end with any one of the twenty residues?

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  57. smokey: "Can we agree that by our criteria, having a stop codon is a good design because it allows proteins to end with any one of the twenty residues?"

    Sounds good to me.

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  58. Dave: "No, actually, I can't figure out a way to test it. That's because the hypothesis is not scientific. What is a "good design"? How do we recognize it? How do we quantify it?"

    Smokey and I agree that at least one stop codon is a good design -- "because it allows proteins to end with any one of the twenty amino acids" --, so now your argument is with one of your fellow critics.

    "Furthermore, since the alleged entity that did the alleged designing is either invisible or long-dead, how do we know that our vague notions about "good design" correspond to the entity's notions?"

    Part of our hypothesis is that the designer had a human-like mind, which means its ideas of rationality and foresight would correspond to ours.

    "How do we know what tools and materials were used in this design, since limitations in tools and materials can have a dramatic effect on "good" design?

    Agreed. But in this case, even though I'm not a scientist, it seems reasonable that if the designer had the capability to design three stop codons, designing one stop codon probably wouldn't have been that difficult.

    "The point of this, which still seems to be whizzing right past your head, is that your ill-formed teleological notions about the design of living things are not hypotheses, and are thus inherently untestable. The reason you can't figure out how to test them is not because you are not a scientist. It is because they are untestable."

    Disagree. If it turns out that 3 stop codons results in more nonsense DNA, and we can't find any good reason for having 3 stop codons, it weakens our hypothesis -- that there was a designer with a human-like mind.

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  59. Bilbo asserted: If it turns out that 3 stop codons results in more nonsense DNA, and we can't find any good reason for having 3 stop codons, it weakens our hypothesis -- that there was a designer with a human-like mind.

    This sentence indicates fractal ignorance about biology and DNA. The relationship between nonsense DNA and stop codons is, as far as I can tell, nonexistent. Thus any "prediction" about nonsense DNA increasing or decreasing in a genome with one or more than one stop codons is a non sequitur. I cannot imagine continuing a discussion where one of the discussants maintained this level of ignorance about the topic being discussed. Get a biology book, take a molecular biology course, and maybe someday you will understand just how laughable that sentence appears...

    I can see that further discussion with you about biological science or experimental design would simply be frustrating.

    I'll leave it to Smokey to discuss your hypotheses. BTW, I am not sure if you defined "good design", so it really doesn't matter to me if you think Smokey agrees with you about this or not.

    Carry on.

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  60. Bilbo,

    1) We agree that having a stop codon is a good design because it allows proteins to end with any one of the twenty residues.

    2) Stop codons do not "code" (metaphorically) for amino acids.

    3) Therefore, you also must agree that NOT having a start codon(s) that doesn't code for an amino acid is a bad design, because (remember you agreed with this reason) it does not allow proteins to begin with any one of the twenty residues.

    4) Therefore, either your intelligent designer didn't design both the start and stop mechanisms, or you have just demonstrated beyond any doubt that you can't recognize an intelligent design.

    You wrote:
    "Smokey and I agree that at least one stop codon is a good design -- "because it allows proteins to end with any one of the twenty amino acids" --, so now your argument is with one of your fellow critics."

    You're either lying or mistaken, Bilbo, as I don't have any argument with Dave. Your hypothesis is utterly unscientific, and you don't have a clue about predictions (they are about what you will directly observe, not about how you will interpret it). My point is that you are a flaming hypocrite. Don't you agree?

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  61. I quite agree that I know very little about biology. But I wasn't the one who suggested that 3 stop codons results in more nonsense DNA than 1 stop codon. It was Art, who knows a whole lot about biology, here:

    http://evolutionengineered.blogspot.com/2008/08/design-matrix-revealed.html

    And thanks for another avenue of research, Smokey. Now if I were a scientist, I would want to study why there are stop codons that don't code for amino acids, but there are start codons that do. A very good question, that a teleologist should want to discover the answer to.


    Meanwhile, let me add all those extra faults to my list. Let's see hypocrite...oh I forget, there were so many of them. Could you remind me?

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  62. Art's exact words: "I need only point out that one stop codon is all that is needed. Three stop codons = much more "opportunity" for nonsense mutation."

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  63. Bilbo

    Art's statement made sense. You just can't read with comprehension, because you don't even know what it is you think you are discussing...

    Take a biology course. Then you will understand the difference between a nonsense mutation (a coding change for a single codon) and nonsense DNA (long stretches of noncoding DNA with no apparent function).

    crikey.

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  64. "I quite agree that I know very little about biology."

    So what makes you think that you understand it better than those of us who devote our lives to studying it?

    "And thanks for another avenue of research, Smokey."

    What avenue of research, Bilbo? I simply pointed out your hypocrisy.

    "Now if I were a scientist, I would want to study why there are stop codons that don't code for amino acids, but there are start codons that do."

    You aren't a scientist, and if you were, you'd understand that science is about how, not why. The reason why is that this mechanism evolved--it wasn't intelligently designed."

    "A very good question, that a teleologist should want to discover the answer to."

    But this is a lie, because teleologists in biology don't try to discover answers to anything, how or why.

    "Meanwhile, let me add all those extra faults to my list. Let's see hypocrite...oh I forget, there were so many of them. Could you remind me?"

    So are your criteria for judging intelligent design faulty, or was translation not intelligently designed? I don't see any other way out of your cognitive dissonance.

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  65. Bilbo:
    "But I wasn't the one who suggested that 3 stop codons results in more nonsense DNA than 1 stop codon. It was Art, who knows a whole lot about biology, here: "

    Art's exact words: "I need only point out that one stop codon is all that is needed. Three stop codons = much more "opportunity" for nonsense mutation."

    Oh, the irony, Bilbo. You held up "Art's exact words" but you couldn't be bothered to read and/or understand them.

    I call that hypocrisy.

    Why do so many of your responses consist of false claims that Dave's position conflicts with those of other scientists?

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  66. Smokey, I think the key comes down to your statement: "You aren't a scientist, and if you were, you'd understand that science is about how, not why. The reason why is that this mechanism evolved--it wasn't intelligently designed."

    Well, yes, if this mechanism was not intelligently designed, then asking why it was designed this way wouldn't make much sense. But your assertion that it wasn't intelligently designed is what I question. How do you know that?

    And I realize that Art was talking about more opportunities for nonsense mutations. I assume that he wouldn't have said that unless he believed those opportunities have been used. Or was it the nonsense "mutations" your quibbling about, instead of nonsense "DNA"?

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  67. Bilbo

    You're floundering. I'd stick a fork in you to let you know that you are done, but I doubt you would be able to detect it.

    Besides the problem you have with not being able to figure out if you (or anyone else) can define "good design", you are clueless about the things you think you are discussing here.

    Here's a clue.

    Nonsense mutations are POINT MUTATIONS, i.e. single base changes in DNA.

    Nonsense DNA (by which I assume you mean the stuff that creationists call "junk DNA") are vast stretches, many thousands of nucleotides.

    There is no relationship between the two, just as there is no relationship between your "hypothesis" and real science.

    Please stop. I can't take any more of this without laughing until I weep.

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  68. "Smokey, I think the key comes down to your statement:..."

    No, Bilbo, the key is never anyone's statement or argument. The key is the evidence, something you ignore when it doesn't support your desire to think that life was designed.

    "Well, yes, if this mechanism was not intelligently designed, then asking why it was designed this way wouldn't make much sense."

    You missed the point--science is not about why, it's about how. Your reluctance to address how is a rejection of science.

    "But your assertion that it wasn't intelligently designed is what I question. How do you know that?"
    Because by the criteria you claimed illustrated design, it isn't designed.

    "And I realize that Art was talking about more opportunities for nonsense mutations. I assume that he wouldn't have said that unless he believed those opportunities have been used. Or was it the nonsense "mutations" your quibbling about, instead of nonsense "DNA"? "

    As Dave noted, you don't know what you are talking about. Most people view that as a problem.

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  69. Smokey:
    "Because by the criteria you claimed illustrated design, it isn't designed."

    Ooh, now we're getting somewhere. Could you fill in some of the details?

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  70. From Dave's Wikipedia cite: "a nonsense mutation is a point mutation in a sequence of DNA that results in a premature stop codon, or a nonsense codon in the transcribed mRNA, and possibly a truncated, and often nonfunctional protein product. A missense mutation is a point mutation where a single nucleotide is changed to cause substitution of a different amino acid. Some genetic disorders, such as thalassemia and DMD, result from nonsense mutations."

    I don't understand the laughter, Dave. This supports Art's contention that 3 stop codons risk more nonsense mutations than 1 stop codon. So Art's objection that this is irrational looks like a good one. So if I were a scientist, I would want to research this area, to see if there is a rational reason for 3 stop codons. Whether I erred in calling nonsense mutations, "nonsense DNA", isn't clear from the article, and is irrelevant to the point. Perhaps you should try understanding the point before objecting to it so quickly. We could make more headway in this discussion.

    Which reminds me, I still don't get why I'm a "hypocrite." Stop codons seem like a good design, since it allows the translation process to stop at any of the 20 amino acids. Having a start codon that is one of the 20 amino acids seems -- on the face of it -- like bad design. If I were a scientist, I would want to investigate this also.

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  71. Bilbo hoped: Whether I erred in calling nonsense mutations, "nonsense DNA", isn't clear from the article, and is irrelevant to the point.

    You absolutely erred; there is no "whether" in this equation. No, it isn't clear from the article; that's asking an author to anticipate every stupid error that someone could make, and I'm sure that author (like me) had no clue that anyone could come up with a misunderstanding of this sort. The author also does not mention unicorns, or fishing lures, or spastic colons, all of which have as much relation to nonsense mutations as anything you hve brought to the table.

    No, it is not irrelevant; an error in the basic facts surrounding what you think you are discussing is very relevant.

    And yes, the fact that you still don't seem to see the problem is a serious indicator that you are either completely clueless about molecular biology, or completely dishonest and trying to pretend that you don't know you have been pwned.

    Is it possible for you to admit that? Do you think that this charade is fooling anyone at all, with the possible exception of Larry?

    Your "hypothesis" was predicated on your error that nonsense mutations (single base changes that lead to the generation of a premature stop codon in a protein coding sequence) somehow are positively related to nonsense (aka "junk" DNA, long stretches of non-coding DNA).

    Please tell me a plausible mechanism whereby a single base change leads to the generation of long stretches of junk DNA in the genome. That would help me "understand the point" you think you are trying to make.

    Or perhaps you can be honest with yourself, and with the rest of us, and admit what is obvious - you really don't know squat about molecular biology, and your attempts at proposing hypotheses and designing experiments are as pathetic as would be my attempts to play first violin in the Boston Symphony.

    Can you be that honest with yourself? Please?

    If not, smokey's description of you as a hypocrite rings pretty true with me.

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  72. Dave,

    I perfectly understood Art's point, that premature stop codons would result in truncated, functionaless proteins. Perhaps I erred in calling this nonsense DNA, but I did not mean that this would account for all so-called "junk" DNA.

    More to the point, Art was offering a challenge to the view that the Genetic Code was rational. According to Art, it would be much more rational to have only one stop codon, since it would reduce the chances of nonsense mutations. And that seems like a fairly good challenge that a teleological view needs to answer.

    I freely admit that I know next to nothing about molecular biology. However, I was trying to imagine how a molecular biologist would go about testing Art's assertion. It seems reasonable that computer simulations, or in vitro experiments, where only one stop codon exists -- if such an experiment is possible (is it?) -- might be a way of testing the assertion. What would happen if we only had one stop codon? Would there be deleterious consequences? Are there reasons why the risk of nonsense mutations is better than something else? What happens if we lose stop codons? These are some of the questions I would want to know. No doubt, if I were a molecular biologist, I would have better quesions, and perhaps better methods for testing them.

    As to being a hypocrite, since I admit that having a start codon that codes for an amino acid looks irrational to me, I still don't see how I have been hypocritcal.

    Are there any other invectives you wish to hurl at me? Let's get them all off your chest so we can then have a meaningful discussion.

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  73. Bilbo

    I'm sorry to offend you, but that explanation is just not holding water. If you didn't take nonsense DNA to be equivalent to junk DNA, then you need to explain this part of your "hypothesis"

    If it turns out that 3 stop codons results in more nonsense DNA,

    I requested this explanation in my previous comment. You didn't provide it. Your alleged explanation, it would be much more rational to have only one stop codon, since it would reduce the chances of nonsense mutations moves the goal posts to pretend that you really really didn't mean nonsense DNA. So if you now assert that you really didn't mean nonsense DNA to mean junk DNA, what did you mean? Can you explain the relationship between multiple or single stop codons and more or less "nonsense DNA", the words in your original hypothesis? Please?

    Secondly, all of this discussion is a smokescreen to deflect attention from the real problem - you have no criteria for detecting "good design". Smokey suggested one to you, you agreed to it, and it turns out that if it is a criteria for good design, the designer blew it when he designed the start codons and the genetic code.

    That's the whole point of this discussion, and focusing on the insults is avoiding that question. You and Mike/Julie have no criteria for "good design". You can't generate any hypotheses involving the dismebodied telic entity without those criteria. You can't do experiments without hypotheses. All you can do is blow smoke and complain when somebody points out that you are merely blowing smoke.

    So answer the question, and please acknowledge that you can't recognize good design in this instance, or any other instance. Then it may be possible to believe that you are not a complete hypocrite. Insults are only insults when they are unsubstantiated. You have provided lots of evidence that allows me to use that word. Denying that reality is, unfortunately, also hypocritical.

    Sorry.

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  74. Dave,

    Let's assume, for the sake of argument that I thought "nonsense DNA" was the same as "junk DNA." Let's assume that when I looked at the Wikipedia site I realized my mistake. Now, how does this affect what Art -- an outstanding critic of ID, in my opinion -- had to say, which was that designing the Genetic Code with 3 stop codons, instead of only 1 would be irrational, since it would increase the opportunity for nonsense mutations? Art was using Mike Gene's criteria against Mike. I think he did it rather effectively. I think a teleologist needs to provide an answer to Art's objection. I've suggested ways a scientist might go about doing research to find out if there is a rational reason for designing the Genetic Code with 3 stop codons. If our hypothetical scientist isn't able to find a rational reason, then Art's objection still stands, and remains strong argument against the rationality of the Genetic Code, thus weakening the ID hypothesis.

    You write: "Secondly, all of this discussion is a smokescreen to deflect attention from the real problem - you have no criteria for detecting "good design". Smokey suggested one to you, you agreed to it, and it turns out that if it is a criteria for good design, the designer blew it when he designed the start codons and the genetic code."

    I agree that Smokey presented a good argument. I think our hypothetical scientist would also need to research the question of what advantage there would be to using a start codon that codes for an amino acid. If he couldn't find one, then I think Smokey has presented a good objection to the rationality of the Genetic Code. I don't think it is a strong as Art's since there doesn't seem to be a big disadvantage to it (though perhaps there is, and I just don't know about it). Nevertheless, I think it would provide a good objection to the rationality of the Genetic Code.

    However, could we wait until after our teleological scientist tries to find a rational reason for the start codon coding for an amino acid? Do we teleologists have to give up before we even start to look for a reason?

    Dave, besides calling me a hypocrite, do you have anything of substance to add to this discussion? Otherwise, I think we've said enough. I was hoping that Smokey would have provided some of the evidence that convinces him that he knows that life wasn't designed. I'm sure there's plenty of evidence that suggests that it wasn't. My point would be that this would a good place for a teleological scientist to begin research. And since the title of this thread is "ID Research Themes," I think I would have made my point.

    Now if all you're going to do is reiterate that I'm a hypocrite, don't bother. I think we all understand your point by now.

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  75. Bilbo - Let's assume, for the sake of argument that I thought "nonsense DNA" was the same as "junk DNA." Let's assume that when I looked at the Wikipedia site I realized my mistake. Now, how does this affect what Art -- an outstanding critic of ID, in my opinion -- had to say, which was that designing the Genetic Code with 3 stop codons, instead of only 1 would be irrational, since it would increase the opportunity for nonsense mutations? Art was using Mike Gene's criteria against Mike. I think he did it rather effectively. I think a teleologist needs to provide an answer to Art's objection. I've suggested ways a scientist might go about doing research to find out if there is a rational reason for designing the Genetic Code with 3 stop codons. If our hypothetical scientist isn't able to find a rational reason, then Art's objection still stands, and remains strong argument against the rationality of the Genetic Code, thus weakening the ID hypothesis.

    It is not much of a prediction to say that if you have more stop codons, you have a potential for more nonsense mutations, since stop codons are the ONLY site where nonsense mutations originate. It is like saying that you will have more potential for flat tires if you have three tires rather than one. It is merely common sense.

    If that is the best ID hypothesis you can launch, it is the Titanic.

    Furthermore it does not follow at all from ID or teleological principles. Proving it or disproving it via an experiment is not worth your while.

    So if that is what you are saying you predicted, thanks for nothing. If you actually did conflate nonsense mutation with nonsense DNA, you have to provide a linkage between cause (mutation) and effect (more nonsense DNA). So far, despite repeated requests, you haven't done that. You have merely retreated into a nonsense argument which, frankly, you should be ashamed of.

    As for the rest of your latest comment, it still fails to acknowledge what we all can see with our own eyes. You have no criteria for a good design. That is not something you generate after starting an experiment. It is an integral part of your hypothesis, and must come prior to the experiment.

    Then Bilbo wrote: Otherwise, I think we've said enough. I was hoping that Smokey would have provided some of the evidence that convinces him that he knows that life wasn't designed.

    That's completely backward. And inconsistent. Allow me to explain. You are the one who has a "suspicion" that life is designed. Even though you have failed miserably to define design, or make a non-trivial prediction that can be tested, you want others to show you how they know that life is not designed.

    Sorry. You have the burden of proof; it's your assertion that life is designed. All of the evidence available to biologists and others who understand what they are talking about indicates that we can explain life's diversity without invoking the supernatural. That is not anywhere close to "knows it is not designed", but it is a lot more evidence-based than anything you've shared here or elsewhere.

    If you want others to share your suspicion, and particularly if you want it to come closer to the "knows" that you demand from others, you'll need to do a lot better than you've done so far with regard to generating testable and non-trivial hypotheses, doing experiments, etc. Most of all you need to show that you understand how science is done, and that mere suspicions are going to get no attention from anyone in that business.

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  76. Smokey, please re-post sans insults (see here for new moderation policy).

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  77. Dave wrote: "It is not much of a prediction to say that if you have more stop codons, you have a potential for more nonsense mutations, since stop codons are the ONLY site where nonsense mutations originate. It is like saying that you will have more potential for flat tires if you have three tires rather than one. It is merely common sense.

    If that is the best ID hypothesis you can launch, it is the Titanic."


    Apparently I'm a miserable communicator, Dave. Let's move back a little in history. In his book, The Design Matrix, Mike Gene tried to argue that the Genetic Code showed evidence of design. One of his criteria of design is rationality, and he tried to show that there is evidence that the Genetic Code is rational.

    Art responded by trying to show that there is evidence that the Genetic Code is not rational. And the evidence he cited is the fact that there are 3 stop codons, instead of 1 stop codon. This would result, Art said, in more chances for nonsense mutations. Therefore, Art was saying, according to Mike's criteria, the Genetic Code is not rational. Therefore his ID hypothesis is weakened.

    That looks like a good argument to me -- for YOUR side, Dave. Do you get it? I was bringing up Art's point NOT because it supported ID, but because it challenged ID.

    Before we go any further in this discussion, do you understand that? If you don't, then there is no point in continuing the discussion, since we will merely be talking past each other.

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  78. Bilbo

    That's baloney. It doesn't jibe with this:

    Now once we test it, let's suppose we get results that suggest 3 codons are a good design strategy. Does that prove ID? No. Again, it could just be a frozen accident. But it would strengthen the ID hypothesis. If we continue to test various features we hypothesize were designed for things we associate with intelligent design -- analogy (with things we know are designed); discontinuity (with non-teleogical processes); rationality (the design makes sense); or foresight (it appears to have been designed with the future in mind) -- and we continue to get positive results, it continues to strengthen the ID hypothesis.

    or this:

    If it turns out that 3 stop codons results in more nonsense DNA, and we can't find any good reason for having 3 stop codons, it weakens our hypothesis -- that there was a designer with a human-like mind.

    Looks to me like you are saying that the single stop codon can be an argument for design, or it can be an argument against design.

    But again, that's enough of this smokescreen. It merely brings me back to the point that you have consistently ignored throughout all your comments. You don't have any criteria for recognizing "good design". When smokey presented you with one possible criteria, you jumped at it, but failed to recognize that a similar criteria applied to start codons would be a criteria for bad design.

    I don't think that this is about me failing to understand anything. I don't think our discussion hinges on that, however. It hinges on your inability to define criteria for generating hypotheses and doing experiments. Period.

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  79. Dave: "Looks to me like you are saying that the single stop codon can be an argument for design, or it can be an argument against design."

    Then I'm failing to communicate properly, for which I apologize. Let me try again: Art has argued that it would make more sense to design the Genetic Code with one stop codon, since it would reduce the chances for nonsense mutations. The fact that the Genetic Code that we do have has 3 stop codons would then be an argument against its rational design. Why design a Genetic Code with 3 stop codons, since it increases the chances of nonsense mutations? Wouldn't 1 stop codon have made more sense?

    This is Art's objection. And it makes perfectly good sense to me. Likewise, Smokey has also presented a good objection: If the advantage of using stop codons is that they don't code for amino acids, and that means that the gene has the freedom to end with any amino acid, followed by a stop codon, then it doesn't make sense to have a start codon that does code for an amino acid (if I remember, it's methionine). A designer would have found a more rational way to design the start codon.

    This also looks like a good objection to ID. I think Art's is a stronger objection, since one can see an obvious deleterious effect from nonsense mutations. Whereas I'm not sure there are any deleterious effects from having a start codon that codes for an amino acid. But it could be that I'm just ignorant, and that there all sorts of disadvantages to it that I don't know about.

    So Art and Smokey have presented two objections to the Genetic Code being rationally designed. It could be that there are lots more besides these, also, but let's stop there for now.

    Now let's get back to your objection: I have no objective criteria for good design. In part that's true. I don't have an explicit general criteria or definition for good design. I think it depends in large part upon the context. In the present context, Mike Gene has argued that our Genetic Code is rationally designed, because experiments with computer simulations show that it faithfully transmits the information in the DNA to the Protein formation more often 999,999 out of a million other possible codes. Does that prove it's a good design? Not necessarily. We don't know the motives of the hypothetical designer. Perhaps the designer was trying to design a Genetic Code that would be very unfaithful, but failed. However, if our hypothesis is that the designer was trying to make sure the information was transmitted faithfully (and this would be consistent with other things, such as the proofreading machinery for Transcription and Translation), then Mike's evidence would support it.

    So no, I don't have a really good definition of "good design." However, we can make hypotheses about what the designer was trying to accomplish, and then see if the data fits it.

    In this case, we have conflicting data. Mike's data seems to support the hypothesis of good design in this context. Art's and Smokey's data seems to weaken the hypothesis.

    Before I proceed further, I'll give you a chance to comment.

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  80. Bilbo

    I don't need to comment further. This statement of yours -

    Perhaps the designer was trying to design a Genetic Code that would be very unfaithful, but failed.

    sums up the futility of this discussion.

    When you arrogate to yourself this sort of escape hatch for all of your "hypotheses", they cease to be hypotheses. Design, by your definition or the classic Behe/Dembski definition, becomes unfalsifiable.

    It might be useful for you to discuss this sort of activity with theologians or philosophers. But this scientist fails to see any future in it.

    And I suspect that smokey, if he can recover from the apoplexy induced by your smokescreens, will have a lot to say about this statement - However, we can make hypotheses about what the designer was trying to accomplish, and then see if the data fits it.

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  81. OK, I think I've made it clear that I think Art's argument and Smokey's argument count against the rational design of the Genetic Code. However, Mike Gene offered evidence that seemed to support the rational design of the Genetic Code. How do we resolve this apparent conflict?

    One way is from the non-teleological view: The Genetic Code is the result of a lengthy process of Darwinian evolution. Given many trials, Darwinian evolution can result phenomena that looks like it was rationally designed. But there may still be details that point to non-rational, non-intelligent design. Thus, the Genetic Code may look like it was rationally designed for faithful reproduction and transmission of information in the DNA, but really this is only because Darwinian evolution "tinkered" with it over many millions of years. And the fact that it still has 3 stop codons, and a start codon that looks irrational is evidence that there wasn't an intelligent, rational designer.

    Mike's reply (in his book) is that there is no evidence of precursors to the Genetic Code. There are no little niches where prototype Genetic Codes are still in use among bacteria. By and large, the Code is universal. The only exceptions are in some mitochondria, where there are some minor differences in the code. But most biologists agree that these are the result of degenerative evolution to the universal code, not precursors to it.

    This doesn't prove that the Code didn't evolve; just that there is little or no evidence that it did.

    The non-teleological view also has a second explanation: the frozen accident. There was no evolution of the Code. It was came into existence rather suddenly, and since organisms were using it already, it was too difficult to evolve a different code. This would explain apparent irrationality in the Code, such as 3 stop codons are a start codon that codes for an amino acid. But it would have difficulty explaining Mike's evidence for the extreme faithfulness of the Code.

    Meanwhile, teleologists can try to explain the apparent conflict of the data, also. They can try to come up with experiments that might explain why 3 stop codons really isn't irrational design, and why a start codon that codes for an amino acid also isn't an irrational design. And that is what I had been trying to do earlier: offer ways that a teleological scientist might go about searching for a teleological explanation for apparent irrationality in the Code.

    Now if our teleologist is not successful, it seems to me that strengthens Art's and Smokey's arguments, and weakens the ID hypothesis for the Genetic Code. But if our teleologist is successful, then we at least may have a way of strengthening the view that the Code was rationally designed. Whether or not it will convince non-teleologists that it was intelligently, rationally designed is a different question. My guess is that it would take a great deal of data, not only in regards to the Genetic Code, but also in regards to other features of life that teleologists claim were intelligently, rationally designed.

    And even then it may not convince non-teleologists. They may ultimately need independent evidence of the existence of a designer. And that, I'm afraid to say, teleologists are not able to provide. At least, not yet.

    But I think I have shown that we do have a way of conducting research that may eliminate objections to ID, or may strengthen objections to ID.

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  82. Bilbo

    In my view, the only thing that has been "made clear" is that you are still emitting smoke. That may be tough to see from where you are sitting, inside the smoke and all, but a little distance makes it abundantly clear to the rest of us.

    Furthermore you continue to ignore reality - But I think I have shown that we do have a way of conducting research that may eliminate objections to ID, or may strengthen objections to ID.

    That statement is remarkable. The entire point of my comments, which remain unrebutted by your clouds of smoke, is that you have absolutely no way of conducting research. You have no objective criteria for detecting design, you can't generate a testable hypothesis, and you have the escape-hatch of "Whoops! Maybe that's not what the designer was thinking after all."

    Talk is cheap. Talk that allows you to pretend to be discussing science, but is really only designed to make you feel better about your religious beliefs, is even cheaper. None of it is science.

    Wake me when you have done something besides talk about how your teleologist scientist buddies are gonna do something, someday, for sure, just you wait and see.

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  83. Dave wrote: "That statement is remarkable. The entire point of my comments, which remain unrebutted by your clouds of smoke, is that you have absolutely no way of conducting research. You have no objective criteria for detecting design, you can't generate a testable hypothesis, and you have the escape-hatch of "Whoops! Maybe that's not what the designer was thinking after all.""

    Dave, if you think about it, this is how investigation of supposedly designed objects is done. For example, look at the investigation of Stonehenge: There has been speculation that it was some sort of temple; some sort of celestial observatory; and now that it is some sort of cemetery. With each hypothesis, archaeologists have some supporting evidence, and use that to support looking for further evidence to support their hypothesis. Of course, in the case of Stonehenge, we know for sure that it was intelligently designed, so we don't have naysayers screaming, "Ha! You have no way objective way of determing why it was designed!" Instead, the archaeologists are allowed to proceed, looking for evidence that will either support or weaken their hypothesis.

    In the case of living organisms, there is much more doubt about whether certain features were designed, so we have all sorts of naysayers screaming that research can't be done.

    But surely this is mistaken. If Art's objection -- that 3 stop codons is irrational, and Smokey's objection -- that our start codon is irrational, are good objections, then research that would show that 3 codons are a rational design, or that our start codon is a rational design, and that they are consistent with our other evidence -- proofreading systems and a very reliable Genetic Code -- would be good evidence for rational design. You can scream all you want about there not being an objective standard for rational design, but this isn't really true. A rational design will be one that is consistent with what we know about the phenomena in question, and sheds more light on why the phenomena was designed that way. An irrational design won't fit in with the other data, and will just create more of a mystery than we had before.

    So go back to sleep, Dave. You really have nothing to add to this dicussion anyway, other than your broken recording, "No objective criteria! No objective criteria!" We can get a parrot to do the same work.

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  84. Bilbo's parrot squawked: Dave, if you think about it, this is how investigation of supposedly designed objects is done. For example, look at the investigation of Stonehenge: There has been speculation that it was some sort of temple; some sort of celestial observatory; and now that it is some sort of cemetery.

    Nice goalpost move.

    In the case of Stonehenge we can speculate about WHY because we are pretty sure about WHO and WHEN and HOW. In the absence of the information about WHO built the thing and WHEN it was built and HOW it was built, science would be reduced to the state that ID currently finds itself in, ie., hand-waving and pretending to be sciency.

    Science can provide decent hypotheses about WHY if we are provided with a modicum of information about WHO, WHEN, WHERE, or HOW. ID provides exactly none of those, but merely speculates about the WHY. That is, from a scientific point of view, exactly backwards.

    Furthermore, to wade back into the pink mist surrounding your argument about stop codons, please support this assertion - But surely this is mistaken. If Art's objection -- that 3 stop codons is irrational, and Smokey's objection -- that our start codon is irrational, are good objections, then research that would show that 3 codons are a rational design, or that our start codon is a rational design... would be good evidence for rational design.

    What kind of research could be done to "show" that one or the other of these is a rational design? What kind of evidence would be produced? HOW, exactly, would you proceed to generate a testable hypothesis without any criteria for "rational design" or "good design"? HOW, exactly, would you get around the Smokey's objection that the realities of the start codon situation make the stop codon situation a bad design, and vice versa?

    HOW would you test any of these alleged hypotheses, please? What kinds of experiments would you do, and what would the "evidence" look like?

    I predict that your parrot will respond - I'm not a scientist, but surely teleologically-minded scientists can do this, somehow, someday.

    Which is not a useful response, as I hope you understand.

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  85. Bilbo

    The more I thought about your example of Stonehenge, the more I have to thank you for it. It allows us to see perfectly what is wrong with ID, in all of its incarnations.

    Imagine for a minute that you found Stonehenge, and that you had absolutely no idea WHO constructed it, or WHEN it was constructed, or HOW it was constructed. But you immediately wanted to speculate on WHY it was constructed, and, even worse, you wanted others to accept those speculations as serious, perhaps even scientific.

    This is exactly what you are doing with ID. With no information on the designer in hand, and no information about the tools or processes that he/she used, and no information about when this design was initiated (or even if it is still happening, a la Behe), you are leaping to speculations about WHY.

    I submit that you cannot speculate on WHY until you at least have some idea about WHO. In addition, information about WHEN and HOW would make these speculations a lot more sensible.

    We all know that you have your own ideas about WHO, and those ideas are based in a Bronze Age myth. We all know that you cannot talk about WHO in public education, because not everyone accepts your myth as their religion. And I suspect that we all know (even you, because you seem like a bright enough guy) that it is fundamentally impossible, and completely unscientific, to talk about WHY when you can't figure out (or talk about) WHO or WHEN or HOW.

    Thanks for that example. It was extremely helpful in crystallizing my thinking about exactly why ID is not a scientifically useful enterprise.

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  86. Dave wrote: "Imagine for a minute that you found Stonehenge, and that you had absolutely no idea WHO constructed it, or WHEN it was constructed, or HOW it was constructed. But you immediately wanted to speculate on WHY it was constructed, and, even worse, you wanted others to accept those speculations as serious, perhaps even scientific."

    But I don't want to "immeditately" speculate on "WHY" Stonehenge was constructed. It would sure be helpful if I knew when Stonehenge came into existence, and if I knew that there were beings that had the ability to construct it at the time. If, for example, I found out that Stonehenge came into existence long before there were human beings, I would doubt its intelligent design. However, if I then found the quarry that it came from (in France, I think), and noticed things like chisel marks, symmetry, regular geometric shapes -- the sort of things analogous to how we design things; and if I couldn't find that kind of rock in England, and couldn't come up with a reasonable, natural (non-intelligent) explanation for how Stonehenge came to be, then I would suspect intelligent design, even though I didn't know "WHO" did it. Now how do I strengthen or weaken my suspicions? One way would be to figure out "WHY" Stonehenge was designed. And since I didn't know WHO might have done it, I would need to rely on why we humans design things. I would need to rely on our conception of rationality.

    Now lets apply this same methodology to the origin of life. It happened WAY before there human beings around (about 3.5 billion years ago). So it is reasonable to doubt that it was intelligently designed. However, if we are unable to come up with a natural (non-intelligent) explanation of how it came to be; if it resembled how we design things -- codes, coordinated action between complex machinery; I would begin to suspect intelligent design (ID). I would understand why others might not suspect ID, and I wouldn't doubt their rationality for doubting it. But meanwhile, I would suspect ID. Now how do I strengthen or weaken my suspicions? One way would be to try to understand WHY certain features were designed. The Genetic Code, proofreading, and all the machinery needed to get from the DNA to proteins suggests that the purpose of all those particular features was to make proteins.

    But then there are good, reasonable objections, such as Art's and Smokey's. Now one way to make progress is to try to investigate and see if we can come up with answers to those objections. Maybe we can. Maybe we can't. If we can, I think it strengthens our suspicions. If we can't, I think it weakens them.

    As to why we IDists don't talk about the WHO: Mainly, because there is inadequate evidence for the WHO. Yes, I believe that Bronze age myth, that Yahweh created the universe. So it seems likely to me that if life had a designer, Yahweh was probably the one. But I don't see anyway of offering empirical evidence for that. If I did, I would. So for me, the WHO remains a WHO.

    Sir Fred Hoyle also thought that the first cells were intelligently designed, by the way. But he didn't believe in Yahweh. It's not clear, but it seems he thought they might have been created by a pre-existing ancient civilization in some other part of the universe (which he thought was eternal). How do I prove that Hoyle was mistaken? I'm not sure I can. But he had the same suspicions about ID that I have.

    Can those suspicions about ID ever reach the point where they will be accepted as reasonable beliefs by the scientific community? Not sure. On the one hand, not having empirical evidence of a WHO is a big hurdle. On the other, as our own bio-nanotechnology advances, we may come to see and understand living cells as instantiations of that kind of technology. Like finding a 3.5 billion year old pocket watch. We wouldn't know WHO designed it, but we would know it was designed.

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  87. Bilbo wrote: But I don't want to "immeditately" speculate on "WHY" Stonehenge was constructed.

    You really don't get it, do you? Or, more likely, you don't want to get it.

    You understand how to study Stonehenge, but you are doing exactly the opposite thing with ID. Look at this simplifed flow diagram.

    You see objects (cells). You have no idea WHO made them, WHEN they were made, HOW they were made, etc. But you immediately want to talk about WHY they were made.

    Applying that same logic, the discoverer of Stonehenge would have been laughed out of the archaeology business.

    You simply can't do it the way you want to do it. Information about WHO and HOW, at the very least, is needed to speculate about WHY.

    The example of the Neanderthal flute is perfect here. If you discovered it, would you ask WHY? Or would you want to know WHO (bear or human) before you speculated on that? Would you want to know HOW (drill or toothy chewing) before you speculated on that? Be honest with yourself. What makes more sense?

    You seem to understand reality when it comes to investigating Stonehenge. You figured out that knowing WHEN and WHO should logically come first. Why do you refuse to apply this approach to ID?

    And I did note that you ignored an important section of my comment. Here 'tis again.

    -------
    Furthermore, to wade back into the pink mist surrounding your argument about stop codons, please support this assertion - But surely this is mistaken. If Art's objection -- that 3 stop codons is irrational, and Smokey's objection -- that our start codon is irrational, are good objections, then research that would show that 3 codons are a rational design, or that our start codon is a rational design... would be good evidence for rational design.

    What kind of research could be done to "show" that one or the other of these is a rational design? What kind of evidence would be produced? HOW, exactly, would you proceed to generate a testable hypothesis without any criteria for "rational design" or "good design"? HOW, exactly, would you get around the Smokey's objection that the realities of the start codon situation make the stop codon situation a bad design, and vice versa?

    HOW would you test any of these alleged hypotheses, please? What kinds of experiments would you do, and what would the "evidence" look like?
    -----------

    Until you answer these questions in some detail, I'll stand by my argument that you can't do science the way you want to do it. You can't make any hypothesis about good or bad design (WHY) unless you know a lot more about WHO and HOW and WHEN and WHERE.

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  88. Dave wrote: "You really don't get it, do you? Or, more likely, you don't want to get it.

    You understand how to study Stonehenge, but you are doing exactly the opposite thing with ID. Look at this simplifed flow diagram.

    You see objects (cells). You have no idea WHO made them, WHEN they were made, HOW they were made, etc. But you immediately want to talk about WHY they were made.

    Applying that same logic, the discoverer of Stonehenge would have been laughed out of the archaeology business."


    I disagree. I used the hypothetical situation of discovering that Stonehenge existed before there were human beings. Would we immediately dismiss it as being intelligently designed? Or would the fact that it has strong analogies with how we design things make us suspect design. I think the latter. But then we are left wondering, "Who did it? And how? Did they come here in a spaceship and design it and leave? Did God design it? Was there another intelligent species on Earth before human beings (or other hominids)that had the capability to design it?" If we can't come up with answers to those questions, does that mean that suspecting Stonehenge was designed is unreasonable? I don't think so. But where do we go from there? One way is to try to "make sense" of Stonehenge -- showing that it exhibits marks of rational design. By doing so, we would strengthen our suspicions that it was designed.

    There are similar problems with the origin of life. How did they design it? Other than saying, "By using bio-nanotechnology," it would be difficult to say. Did they have labratories, like we do? Were those labratories on Earth? Did they send the first cells here in a spaceship (directed panspermia), as Francis Crick suggested might have happened? Did they eject the cells into space, which then eventually either drifted down onto Earth, or were absorbed into a comet and crashed here (undirected panspermia), as Fred Hoyle suggested? Or did God create the first cells here on Earth? Or some other alternative? We might not be able to come up with an answer to that (although I recently read that they have found fossils of cyanobacteria in all the remnants of comets on Earth. That alone should make Hoyle jump out of his grave and dance a jig).

    Nevertheless, there seems to be enough evidence to at least suspect design. We have no idea how cells could have come into being without intelligent design. All pathways explored so far look hopelessly implausible. And cells have strong analogies to how we design things -- codes and coordinated action between complex machines to achieve various purposes.

    So how do we strengthen or weaken our suspicions? One way would be to find a plausible pathway for abiogenesis. Origin of life researchers are trying to do just that. And I don't think it's time for them to give up. But must we wait until they do give up until we explore the alternative of ID? I would say no. When Hoyle writes seriously about panspermia, and Crick writes seriously about directed panspermia, and Leslie Orgel (one of the leading origin of life researcher) writes that coming up witht the first RNA molecule would have been tantamount to a miracle, then I think it's reasonable -- for those who want to -- to explore ID.

    Well, if we don't know Who or How (though we seem to know When), what's left? It seems to me that exploring whether or not there is Rationality or Foresight in the supposed design is a good place to start. Mike Gene is exploring the idea of Front-Loaded evolution -- that the first cells were loaded with the information necessary to evolve into at least multicellular organisms. I think that would come under Foresight.

    As to Rationality, I think a good place to start is with objections to the rationality of the supposed design of the cells.

    Let's start with Art's objection: That 3 stop codons is irrational, because there are more chances of nonsense mutations. I've suggested computer simulations, where we have just 1 stop codon, instead of 3. What would happen? For example, would the 1 stop codon tend to be lost through mutations, resulting in amino acid sequences that are too long, and functionless? In other words, does having 3 stop codons provide some sort of necessary redundancy? Frankly, I don't know. I think it would be interesting to find out. Or maybe there are other, unforeseen effects. If I knew more about molecular biology, I might know better what to look for, and what experiments to design. But at least I've given one example. But let's say that whatever experiments we design, it shows that 1 stop codon would have been better than 3. Then we've weakened the ID hypothesis.

    Next, let's think about Smokey's objection: Why a start codon that codes for a particular amino acid? Clearly knowing more about molecular biology would help. For example, does the Ribosome need an amino acid in order to start the process of protein formation? Is it a simple system, where no amino acids means stop, and one amino acid means go? But why couldn't just any amino acid start the process? Why methionine (or sometimes valine)? Do we know the answers to those questions? Here, understanding the process might help us understand why it might have been designed this way. And I'm not sure what kind of experiment might help, right now. Maybe after I get my degree in molecular biology (by the time I'm 90). On the other hand, perhaps whatever experiments we come up with will just show that our start codon is irrational. And that would weaken the ID hypothesis.

    So again, I don't "immediately" start with WHY? I think there is already enough data to justify a suspicion of design. I'm just trying to think of ways to strengthen or weaken that suspicion.

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  89. Bilbo

    Thanks for confirming that you have no earthly clue about how to proceed with actual hypotheses or experiments.

    As for the rest of your comment, my rebuttal comes down to this.

    Yes, you can always suspect design. SETI, Stonehenge, Neanderthal flutes, flagella, cells, watches on the blasted moor all might be designed. Or not.

    But you can't study design, or move toward any evidence of it, unless you are willing to investigate WHO and WHEN and WHERE and HOW. Even your latest smokescreen, "rationality", depends on WHO, and to a lesser extent, HOW.

    And neither you, nor your hypothetical teleologist scientist buddies, can navigate past that. No hypotheses, no criteria for recognizing good design, no experiments have been forthcoming.

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  90. Bilbo

    Another comment, sorry.

    You are going in circles. You wrote, re your Stonehenge scenario: One way is to try to "make sense" of Stonehenge -- showing that it exhibits marks of rational design. By doing so, we would strengthen our suspicions that it was designed.

    Please answer just one question. If you don't know WHO, how do you define "rational", and what would be evidence of "rational design"?

    Are you starting to understand why WHO (or HOW) is an essential step toward detecting design?

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  91. Dave wrote: " But you can't study design, or move toward any evidence of it, unless you are willing to investigate WHO and WHEN and WHERE and HOW. Even your latest smokescreen, "rationality", depends on WHO, and to a lesser extent, HOW.

    I'm quite willing to investigate WHO, WHEN, WHERE, and HOW. I'm just not sure how to carry out that investigation. For example:

    WHO: If Stonehenge was designed before there were hominids, how do determine WHO did it? If we found a fossilized spaceship, it might help. But if we don't, does that rule out aliens? And how exactly do we rule in or out supernatural beings? And we can look for fossils of other pre-historic creatures that might have been able to design Stonehenge (intelligent dinosaurs?), but if we don't find any, does that mean they didn't exist, or just that we don't have fossils of them?

    Likewise, we can look for clues of WHO might have designed the first cells, but if we don't find any, how do we proceed with the investigation? Does lack of clues mean that we've ruled out all WHOs?

    As to WHEN, it seems to be about 3.5 billion years ago.

    As to WHERE, somewhere on Earth.

    Of course, if Hoyle is right, then both those WHENs and WHEREs are mistaken.

    As to HOW, bio-nanontechnology. This is a new technology to us. But we already know how to design nucleic acids and proteins. In a hundred years or so we may be able to design complete living cells (unless there's some magic, vitalistic element to them).

    In fact, it is the fact that we are beginning to understand the HOW that is lending support to the ID hypothesis. In Behe's words, the cell is no longer a black box. We are seeing that it is a highly organised, intricate, complex entity, that looks very much like it required intelligent design.

    "And neither you, nor your hypothetical teleologist scientist buddies, can navigate past that."

    You're right, we can't navigate past not having a WHO. That's why doubting ID may always be a reasonable choice. But does not having a WHO mean that it is unreasonable to proceed with ID hypotheses? I would say no. We would proceed with an ID hypothesis for a pre-hominid Stonehenge. We would proceed with an ID hypothesis for a 3.5 billion year old pocket watch. Why not for living cells?

    "No hypotheses, no criteria for recognizing good design, no experiments have been forthcoming."

    Well...there's Mike Gene's hypothesis: The first living cells were intelligently designed by human-like minds, and front-loaded to exploit Darwinian Evolution to result in at least multicellularity. Recognizing good design? Design that would be consistent with that hypothesis. Experiments? Mike outlined some. I suggested another.

    "Another comment, sorry."

    No need to apologize. At least you're not calling me a "rube" anymore.

    "You are going in circles. You wrote, re your Stonehenge scenario: One way is to try to "make sense" of Stonehenge -- showing that it exhibits marks of rational design. By doing so, we would strengthen our suspicions that it was designed.

    Please answer just one question. If you don't know WHO, how do you define "rational", and what would be evidence of "rational design"?"


    In terms of what we understand to be rational. Let's suppose, for example, that Stonehenge lined up with all sorts of significant celestial events -- summer and winter solstices, solar and lunar eclipses, etc. From our point of view, this would make sense, and would strengthen our suspicions that Stonehenge was designed. Now it could be that this all was just an amazing coincidence, and even if there was a designer of Stonehenge, this had nothing to do with the original purpose. We can never rule this out. But if there were a tremendous number of "lining ups" with celestial events, we would rule out coincidence, wouldn't we?

    Likewise with the cell: we already have a number of factors that point to the cell being designed to faithfully reproducing proteins. If we find out that 3 stop codons help in some way, I think this lends additional support.

    "Are you starting to understand why WHO (or HOW) is an essential step toward detecting design?"

    I agree that knowing WHO would help a heck of a lot. And that not knowing WHO raises all sorts of problems, perhaps including not ever knowing for sure that ID is true. Is it essential? I think we can proceed with the assumption that the WHO is like us, and see if it helps us understand more of what is going on.

    But I think we've both made good points. Is this a good place to end our present discussion?

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  92. Bilbo - But I think we've both made good points. Is this a good place to end our present discussion?

    I'll agree with the second sentence. But not the first. You have made a lot of points...

    Your assumption that the designer is "like us" is negated by the fact that if it was "like us", the designs we find would be a lot better. But when this is pointed out to you (e.g. in the example of the stop codons and start codon), you get to retreat into the "maybe we just don't understand the whims of the designer".

    Either make that assumption and test it, or quit hiding behind the possibility of the supernatural designer who isn't like us at all. You can't have it both ways, no matter how desperately you desire it.

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  93. Dave: "Your assumption that the designer is "like us" is negated by the fact that if it was "like us", the designs we find would be a lot better. But when this is pointed out to you (e.g. in the example of the stop codons and start codon), you get to retreat into the "maybe we just don't understand the whims of the designer"."

    But that's not even close to what I said. If there are other people reading this thread, I'll trust that they understand what I said better than you have. But at least we agree to end it here.

    I'll wake you up in case we find anything interesting about the stop and start codons.

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  94. Bilbo wrote (upthread): Because we are dealing with minds, which aren't very predictable.

    Imagine that.

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  95. your assumptions and designers layout differ from this concept. So both coincide only we product new layout for this site.

    ReplyDelete