tag:blogger.com,1999:blog-1090883723146476626.post7219235619310030225..comments2023-11-03T06:35:51.218-06:00Comments on Evolution Engineered: ID Research ThemesJJS P.Eng.http://www.blogger.com/profile/05029579563816207022noreply@blogger.comBlogger95125tag:blogger.com,1999:blog-1090883723146476626.post-79746246775657780812011-05-25T03:53:09.563-06:002011-05-25T03:53:09.563-06:00your assumptions and designers layout differ from ...your assumptions and designers layout differ from this concept. So both coincide only we product new layout for this site.Best Website Hostinghttp://www.best-hostings.innoreply@blogger.comtag:blogger.com,1999:blog-1090883723146476626.post-4047177783768180182008-09-19T14:52:00.000-06:002008-09-19T14:52:00.000-06:00Bilbo wrote (upthread): Because we are dealing wit...Bilbo wrote (upthread): <I>Because we are dealing with minds, which aren't very predictable. </I><BR/><BR/>Imagine that.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-1090883723146476626.post-4867588010136816102008-09-19T14:25:00.000-06:002008-09-19T14:25:00.000-06:00Dave: "Your assumption that the designer is "like ...Dave: <B>"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"."</B><BR/><BR/>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. <BR/><BR/>I'll wake you up in case we find anything interesting about the stop and start codons.Bilbohttps://www.blogger.com/profile/06231440026059820600noreply@blogger.comtag:blogger.com,1999:blog-1090883723146476626.post-20956629666937589502008-09-18T13:05:00.000-06:002008-09-18T13:05:00.000-06:00Bilbo - But I think we've both made good points. I...Bilbo - <I>But I think we've both made good points. Is this a good place to end our present discussion?</I><BR/><BR/>I'll agree with the second sentence. But not the first. You have made a lot of points...<BR/><BR/>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".<BR/><BR/>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.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-1090883723146476626.post-68968861088908694442008-09-18T11:56:00.000-06:002008-09-18T11:56:00.000-06:00Dave wrote: " But you can't study design, or mo...Dave wrote: <B>" 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.</B><BR/><BR/>I'm quite willing to investigate WHO, WHEN, WHERE, and HOW. I'm just not sure how to carry out that investigation. For example: <BR/><BR/>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? <BR/><BR/>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? <BR/><BR/>As to WHEN, it seems to be about 3.5 billion years ago. <BR/><BR/>As to WHERE, somewhere on Earth. <BR/><BR/>Of course, if Hoyle is right, then both those WHENs and WHEREs are mistaken. <BR/><BR/>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). <BR/><BR/>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. <BR/><BR/> <B>"And neither you, nor your hypothetical teleologist scientist buddies, can navigate past that."</B><BR/><BR/>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? <BR/><BR/> <B>"No hypotheses, no criteria for recognizing good design, no experiments have been forthcoming."</B><BR/><BR/>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. <BR/><BR/> <B>"Another comment, sorry."</B><BR/><BR/>No need to apologize. At least you're not calling me a "rube" anymore. <BR/><BR/> <B>"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.<BR/><BR/> Please answer just one question. If you don't know WHO, how do you define "rational", and what would be evidence of "rational design"?"</B><BR/><BR/>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? <BR/><BR/>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. <BR/><BR/> <B>"Are you starting to understand why WHO (or HOW) is an essential step toward detecting design?"</B><BR/><BR/>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. <BR/><BR/>But I think we've both made good points. Is this a good place to end our present discussion?Bilbohttps://www.blogger.com/profile/06231440026059820600noreply@blogger.comtag:blogger.com,1999:blog-1090883723146476626.post-72740168516944684102008-09-17T16:26:00.000-06:002008-09-17T16:26:00.000-06:00BilboAnother comment, sorry.You are going in circl...Bilbo<BR/><BR/>Another comment, sorry.<BR/><BR/>You are going in circles. You wrote, re your Stonehenge scenario: <I>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.</I><BR/><BR/>Please answer just one question. <B>If you don't know WHO, how do you define "rational", and what would be evidence of "rational design"?</B><BR/><BR/>Are you starting to understand why WHO (or HOW) is an essential step toward detecting design?Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-1090883723146476626.post-53939986690678047152008-09-17T15:16:00.000-06:002008-09-17T15:16:00.000-06:00BilboThanks for confirming that you have no earthl...Bilbo<BR/><BR/>Thanks for confirming that you have no earthly clue about how to proceed with actual hypotheses or experiments.<BR/><BR/>As for the rest of your comment, my rebuttal comes down to this.<BR/><BR/>Yes, you can always <B>suspect</B> design. SETI, Stonehenge, Neanderthal flutes, flagella, cells, watches on the blasted moor all might be designed. Or not.<BR/><BR/>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.<BR/><BR/>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.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-1090883723146476626.post-12393567098186892172008-09-17T12:36:00.000-06:002008-09-17T12:36:00.000-06:00Dave wrote: "You really don't get it, do you? Or, ...Dave wrote: <B>"You really don't get it, do you? Or, more likely, you don't want to get it.<BR/><BR/>You understand how to study Stonehenge, but you are doing exactly the opposite thing with ID. Look at this simplifed flow diagram.<BR/><BR/>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. <BR/><BR/>Applying that same logic, the discoverer of Stonehenge would have been laughed out of the archaeology business."</B><BR/><BR/>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. <BR/><BR/>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). <BR/><BR/>Nevertheless, there seems to be enough evidence to at least <I>suspect</I> 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. <BR/><BR/>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 <I>do</I> 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. <BR/><BR/>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.<BR/><BR/>As to Rationality, I think a good place to start is with objections to the rationality of the supposed design of the cells. <BR/><BR/>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. <BR/><BR/>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. <BR/><BR/>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.Bilbohttps://www.blogger.com/profile/06231440026059820600noreply@blogger.comtag:blogger.com,1999:blog-1090883723146476626.post-8156404310259374552008-09-16T13:58:00.000-06:002008-09-16T13:58:00.000-06:00Bilbo wrote: But I don't want to "immeditately" sp...Bilbo wrote: <I>But I don't want to "immeditately" speculate on "WHY" Stonehenge was constructed.</I><BR/><BR/>You really don't get it, do you? Or, more likely, you don't want to get it.<BR/><BR/>You understand how to study Stonehenge, but you are doing exactly the opposite thing with ID. Look at this simplifed flow diagram.<BR/><BR/>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. <BR/><BR/>Applying that same logic, the discoverer of Stonehenge would have been laughed out of the archaeology business. <BR/><BR/>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. <BR/><BR/>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? <BR/><BR/>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?<BR/><BR/>And I did note that you ignored an important section of my comment. Here 'tis again. <BR/><BR/>-------<BR/>Furthermore, to wade back into the pink mist surrounding your argument about stop codons, please support this assertion - <I>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</I>.<BR/><BR/>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?<BR/><BR/>HOW would you test any of these alleged hypotheses, please? What kinds of experiments would you do, and what would the "evidence" look like?<BR/>-----------<BR/><BR/>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.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-1090883723146476626.post-19436364390136499942008-09-16T11:55:00.000-06:002008-09-16T11:55:00.000-06:00Dave wrote: "Imagine for a minute that you found S...Dave wrote: <B>"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."</B><BR/><BR/>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. <BR/><BR/>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. <BR/><BR/>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. <BR/><BR/>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. <BR/><BR/> 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. <BR/><BR/>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.Bilbohttps://www.blogger.com/profile/06231440026059820600noreply@blogger.comtag:blogger.com,1999:blog-1090883723146476626.post-7859528292541226132008-09-16T05:39:00.000-06:002008-09-16T05:39:00.000-06:00BilboThe more I thought about your example of Ston...Bilbo<BR/><BR/>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.<BR/><BR/>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.<BR/><BR/>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. <BR/><BR/>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. <BR/><BR/>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.<BR/><BR/>Thanks for that example. It was extremely helpful in crystallizing my thinking about exactly why ID is not a scientifically useful enterprise.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-1090883723146476626.post-69237870921935764022008-09-15T12:18:00.000-06:002008-09-15T12:18:00.000-06:00Bilbo's parrot squawked: Dave, if you think about ...Bilbo's parrot squawked: <I>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. </I><BR/><BR/>Nice goalpost move. <BR/><BR/>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.<BR/><BR/>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.<BR/><BR/>Furthermore, to wade back into the pink mist surrounding your argument about stop codons, please support this assertion - <I>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.</I><BR/><BR/>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?<BR/><BR/>HOW would you test any of these alleged hypotheses, please? What kinds of experiments would you do, and what would the "evidence" look like?<BR/><BR/>I predict that your parrot will respond - I'm not a scientist, but surely teleologically-minded scientists can do this, somehow, someday. <BR/><BR/>Which is not a useful response, as I hope you understand.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-1090883723146476626.post-47686486363123751172008-09-15T11:31:00.000-06:002008-09-15T11:31:00.000-06:00Dave wrote: "That statement is remarkable. The ent...Dave wrote: <B>"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.""</B><BR/><BR/>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. <BR/><BR/>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. <BR/><BR/>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. <BR/><BR/>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.Bilbohttps://www.blogger.com/profile/06231440026059820600noreply@blogger.comtag:blogger.com,1999:blog-1090883723146476626.post-88679766160547401912008-09-14T14:09:00.000-06:002008-09-14T14:09:00.000-06:00BilboIn my view, the only thing that has been "mad...Bilbo<BR/><BR/>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.<BR/><BR/>Furthermore you continue to ignore reality - <I>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.</I><BR/><BR/>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."<BR/><BR/>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. <BR/><BR/>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.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-1090883723146476626.post-16636273124226702392008-09-14T11:52:00.000-06:002008-09-14T11:52:00.000-06:00OK, I think I've made it clear that I think Art's ...OK, I think I've made it clear that I think Art's argument and Smokey's argument count <I>against</I> the rational design of the Genetic Code. However, Mike Gene offered evidence that seemed to <I>support</I> the rational design of the Genetic Code. How do we resolve this apparent conflict? <BR/><BR/>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 <I>looks like</I> 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. <BR/><BR/>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. <BR/><BR/>This doesn't <I>prove</I> that the Code didn't evolve; just that there is little or no evidence that it did. <BR/><BR/>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. <BR/><BR/>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.<BR/><BR/>Now if our teleologist is <I>not</I> 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 <I>is</I> 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. <BR/><BR/>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. <BR/><BR/>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.Bilbohttps://www.blogger.com/profile/06231440026059820600noreply@blogger.comtag:blogger.com,1999:blog-1090883723146476626.post-67185318541312770602008-09-14T07:31:00.000-06:002008-09-14T07:31:00.000-06:00BilboI don't need to comment further. This stateme...Bilbo<BR/><BR/>I don't need to comment further. This statement of yours - <BR/><BR/><I>Perhaps the designer was trying to design a Genetic Code that would be very unfaithful, but failed.</I><BR/><BR/>sums up the futility of this discussion. <BR/><BR/>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.<BR/><BR/>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.<BR/><BR/>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 - <I>However, we can make hypotheses about what the designer was trying to accomplish, and then see if the data fits it. </I>Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-1090883723146476626.post-62308412538309704142008-09-13T13:21:00.000-06:002008-09-13T13:21:00.000-06:00Dave: "Looks to me like you are saying that the si...Dave: <B>"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."</B><BR/><BR/>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 <I>do</I> have has <I>3</I> 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? <BR/><BR/>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 <I>does</I> 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. <BR/><BR/>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. <BR/><BR/>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. <BR/><BR/>Now let's get back to <B>your</B> objection: I have no objective criteria for good design. In part that's true. I don't have an explicit <I>general</I> 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 <I>trying</I> 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. <BR/><BR/>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. <BR/><BR/>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.<BR/><BR/>Before I proceed further, I'll give you a chance to comment.Bilbohttps://www.blogger.com/profile/06231440026059820600noreply@blogger.comtag:blogger.com,1999:blog-1090883723146476626.post-82562543049249142372008-09-12T12:50:00.000-06:002008-09-12T12:50:00.000-06:00BilboThat's baloney. It doesn't jibe with this:Now...Bilbo<BR/><BR/>That's baloney. It doesn't jibe with this:<BR/><BR/><I>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.</I><BR/><BR/>or this:<BR/><BR/><I>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.</I><BR/><BR/>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. <BR/><BR/>But <B>again</B>, that's enough of this smokescreen. It merely brings me back to the point that you have consistently ignored throughout all your comments. <B>You don't have any criteria for recognizing "good design".</B> 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.<BR/><BR/>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.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-1090883723146476626.post-38212304155358057402008-09-12T10:37:00.000-06:002008-09-12T10:37:00.000-06:00Dave wrote: "It is not much of a prediction to say...Dave wrote: <B>"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.<BR/><BR/>If that is the best ID hypothesis you can launch, it is the Titanic."</B><BR/><BR/>Apparently I'm a miserable communicator, Dave. Let's move back a little in history. In his book, <I>The Design Matrix</I>, 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. <BR/><BR/>Art responded by trying to show that there is evidence that the Genetic Code is <B>not</B> 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. <BR/><BR/>That looks like a good argument to me -- for <B>YOUR</B> side, Dave. Do you get it? I was bringing up Art's point <B>NOT</B> because it <I>supported</I> ID, but because it <I>challenged</I> ID. <BR/><BR/>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.Bilbohttps://www.blogger.com/profile/06231440026059820600noreply@blogger.comtag:blogger.com,1999:blog-1090883723146476626.post-61395975951989397512008-09-11T14:57:00.000-06:002008-09-11T14:57:00.000-06:00Smokey, please re-post sans insults (see here for ...Smokey, please re-post sans insults (see <A HREF="http://evolutionengineered.blogspot.com/2008/09/redundancy-mark-of-design.html?showComment=1221146340000#c6911890313304238162" REL="nofollow">here</A> for new moderation policy).JJS P.Eng.https://www.blogger.com/profile/05029579563816207022noreply@blogger.comtag:blogger.com,1999:blog-1090883723146476626.post-25136552153322815362008-09-11T14:28:00.000-06:002008-09-11T14:28:00.000-06:00Bilbo - Let's assume, for the sake of argument tha...Bilbo - <I>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.</I><BR/><BR/>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. <BR/><BR/>If that is the best ID hypothesis you can launch, it is the Titanic.<BR/><BR/>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.<BR/><BR/>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.<BR/><BR/>As for the rest of your latest comment, it still fails to acknowledge what we all can see with our own eyes. <B>You have no criteria for a good design</B>. That is not something you generate <I>after</I> starting an experiment. It is an integral part of your hypothesis, and must come prior to the experiment.<BR/><BR/>Then Bilbo wrote: <I>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><BR/><BR/>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 <B>know</B> that life is not designed. <BR/><BR/>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 <B>understand what they are talking about</B> 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.<BR/><BR/>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.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-1090883723146476626.post-87477668177077453312008-09-11T11:48:00.000-06:002008-09-11T11:48:00.000-06:00Dave, Let's assume, for the sake of argument that ...Dave, <BR/><BR/>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. <BR/><BR/>You write: <B>"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."</B><BR/><BR/>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. <BR/><BR/>However, could we wait until <I>after</I> 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? <BR/><BR/>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 <B>knows</B> 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. <BR/><BR/>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.Bilbohttps://www.blogger.com/profile/06231440026059820600noreply@blogger.comtag:blogger.com,1999:blog-1090883723146476626.post-4894820145062631322008-09-10T12:50:00.000-06:002008-09-10T12:50:00.000-06:00BilboI'm sorry to offend you, but that explanation...Bilbo<BR/><BR/>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"<BR/><BR/><I>If it turns out that 3 stop codons results in more nonsense DNA,</I><BR/><BR/>I requested this explanation in my previous comment. You didn't provide it. Your alleged explanation, <I>it would be much more rational to have only one stop codon, since it would reduce the chances of nonsense mutations</I> 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?<BR/><BR/>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.<BR/><BR/>That's the whole point of this discussion, and focusing on the insults is avoiding that question. <B>You and Mike/Julie have no criteria for "good design"</B>. 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.<BR/><BR/>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.<BR/><BR/>Sorry.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-1090883723146476626.post-39350148516496772642008-09-10T11:45:00.000-06:002008-09-10T11:45:00.000-06:00Dave, I perfectly understood Art's point, that pre...Dave, <BR/><BR/>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. <BR/><BR/>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. <BR/><BR/>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 <I>in vitro</I> 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. <BR/><BR/>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. <BR/><BR/>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.Bilbohttps://www.blogger.com/profile/06231440026059820600noreply@blogger.comtag:blogger.com,1999:blog-1090883723146476626.post-18216486799505295512008-09-09T20:35:00.000-06:002008-09-09T20:35:00.000-06:00Bilbo hoped: Whether I erred in calling nonsense m...Bilbo hoped: <I>Whether I erred in calling nonsense mutations, "nonsense DNA", isn't clear from the article, and is irrelevant to the point.</I><BR/><BR/>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. <BR/><BR/>No, it is not irrelevant; an error in the basic facts surrounding what you think you are discussing is very relevant.<BR/><BR/>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. <BR/><BR/>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?<BR/><BR/>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).<BR/><BR/>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.<BR/><BR/>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.<BR/><BR/>Can you be that honest with yourself? Please? <BR/><BR/>If not, smokey's description of you as a hypocrite rings pretty true with me.Anonymousnoreply@blogger.com