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Spin Flagellum, Spin

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This month in Current Biology Vol 18 No 16, Howard C. Berg writes a “Quick guide” to the Bacterial Flagellar motor. In it he outlines what is currently known of these amazing structures.

“The flagellar motor is a remarkably small rotary electric motor that includes a stator, drive shaft, bushings, mounting plate, and a switch complex. The motors are powered by protons or sodium ions, that flow through channels from the outside to the inside of the cell. Depending upon the configuration, the rod, hook, and filament are driven clock wise or counter clock wise. Other components include a rod cap, discarded upon rod completion, hook cap, discarded upon hook completion, hook-length control protein, and a factor that blocks late-gene expression.”

As “nothing in biology makes sense except in the light of evolution”, Berg concludes with a few brief comments.

“Is the flagellar motor unique? Yes and no. As a device that powers flagellar rotation, yes. As a device composed of rings, rods, and external filaments, no. There is a homologous structure, called the needle structure, assembled by the same kind of transport apparatus, used by pathogenic species (such as Salmonella) to inject virulence factors into eukaryotic cells. Some argue that the flagellar rotary motor evolved from the needle structure, but it was probably the other way around, since flagellated bacteria existed long before their eukaryotic targets. Perhaps they evolved from a common ancestor. What was the rotary motor doing before the helical propeller was invented, if indeed that was the order of events? Serving as a secretory apparatus that acquired the ability to spin? Packaging polynucleic acids into virus heads? Food for thought.”

Recently Nature Reviews Microbiology volume 6 June 2008 p 455 has a review of the regulation of Flagellar construction, where the authors say “The bacterial flagellum, one of the most remarkable structures in nature: a complex self-assembling nanomachine” where “dozens of proteins, many of which have intrinsic self-assembly properties, need to come together in an ordered assembly process to complete these molecular nanomachines.”

These authors also need to remind us of the inescapable compelling logic of evolutionary biology:

“Finally, it seems that the bacterial flagellum is a structure of great complexity. In an attempt to understand why, it is not necessary to resort to intelligent designers, because surely a designer would have fashioned a simpler structure and gene regulation system. We only need to be reminded that evolution demands that changes occur on the existing structure — no starting from scratch. It is fair to say that we are at long last making a dent in our understanding of how this evolutionary process might have occurred for the reducibly complex bacterial flagellum and the beautiful result it has produced.”

The flagellum is obviously too complex to have been designed. It must have evolved. The logic is inescapable.

Comments
-----CGUGGreyArea: “Put it this way, if the evo biologists turn out to be right in that the evolutionary mechanism can account for the complexity of life as we see it then it does not follow that the entire universe was an accident - indeed it may still be possible to detect intelligent design at a different level, or even to detect some intention underlying the evolutionary mechanism.” I am not clear on this point or on how you are relating cosmology to biology. What does “design at a different level mean?” I don’t know how to interpret “intention underlying the evolutionary mechanism.” Does the “intention” influence the evolutionary process? If it does, then the program has been front loaded or guided in some way. That would mean it is not Darwinistic. If it does not influence the evolutionary process, then what is its point for being there?StephenB
September 12, 2008
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StephenB and DaveScot After some reflection... I also understand the point that this discussion is about flagellum, not definitions of science, and that this is not the forum for discussing unanswerable philosophical questions about creation. Totally fair enough but if I can beg a small indulgence I would just like to quickly clarify what I was trying to say (which is not really about TE) StephenB, you say "I get it that creationists make us look bad by claiming affinity with ID" Yes I agree but I would add that idiots like Dawkins also make biological evolution (the theory) look bad by trying to co-opt it into justifying their atheism when in reality it does not extend to providing a naturalistic explanation for the actual origin of life, or the universe. When I made the point about genetic algorithms I was trying to get across the idea that although the evolutionary mechanism its self does not (according to the theory) require intelligent intervention it also does not explicitly require the laws of nature that underpin it to have a naturalistic origin. Put it this way, if the evo biologists turn out to be right in that the evolutionary mechanism can account for the complexity of life as we see it then it does not follow that the entire universe was an accident - indeed it may still be possible to detect intelligent design at a different level, or even to detect some intention underlying the evolutionary mechanism. To sum up, when creationists claim ID supports their particular beliefs they are just as wrong as atheists claiming evolutionary theory to support theirs, or ID supporters claiming that evolutionary theory categorically excludes the possibility of any intelligence or 'plan'.GCUGreyArea
September 12, 2008
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By the way, Timeuas fell into that same trap, following up on JK’s and TD’s theological references. That is why I think you should give him a reprieve. He is a neo-Platonist and doesn’t normally approach things that way.StephenB
September 12, 2008
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Dave: I get your point, here. This thread is primarily about the flagellum and measurement, and only secondarily about definitions of science, although the latter point is relevant. Also, I get it that creationists make us look bad by claiming affinity with ID while flooding cyberspace with extraneous theological references, and we don’t want anything like that on this site. That is why I enthusiastically contend that ID is real science and vociferously challenge those who deny that fact. On the other hand, when someone implies that ID isn’t science because [expletive deleted] is a different kind of designer, I can hardly meet that objection without making references to [expletive deleted].StephenB
September 12, 2008
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"a genetic algorithm requires intelligence’s involvement in order to function. " Yes, I was making a point about theistic evolution, but I'll stop now because I don't want to get banned.GCUGreyArea
September 12, 2008
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Hey guys, can you please cool it with all the God talk and bible quotes? I understand the TE invasion got your hackles up, mine too, but I gave the worst offenders the boot. Let's get the conversation back on things that can be weighed and measured. Unless you can put the God of Abraham on a scale and tell me how much He weighs take it offline or move it to another forum. Thanks.DaveScot
September 11, 2008
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StephenB, Fair enough. I actually agree with Romans 1, believe it or not. And I believe the design in the universe is abundant and evident. I simply do not believe that it is the kind which can be specifically tested for and falsifiable. Nevertheless, my pleasure, and thank you for the exchange.nullasalus
September 11, 2008
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nullasalus: Yes, I agree. It is time to wind down and reflect. You last point is a meaningful one, and it does frame the issue nicely. Is God a different kind of designer? It's a thoughtful question, and one rapid fire answer occurs to me: He seems to have created in a way that he intended to leave clues about his existence, just as is says in Romans 1: and just as all the great scientists of the past believed. We have been talking exclusively about science, but from a theological perspective, I would say this: If God's revelation in Scripture is not consistent with God's revelation in nature, then we don't really live in a rational universe. Thanks for keeping your sense of humor through the sprited exchanges.StephenB
September 11, 2008
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-----“so the flagellum could have evolved in exactly the way that EvoBiologists think it did, except that if the universe was designed for evolution to work then the theory of evolution is wrong, even though it works in exactly the way they describe… The question is this: Was the evolutionary pathway to complexity thought out or was it not? EvoBiologists say that it was not thought out---it just happened. Intelligent design says that it was thought out. It cannot be both thought out and not thought out (unless you are a TE and believe that a thing can be true and false at the same time.) . One side must be right; one side must be wrong. -----I wasn’t aware that the theory of evolution is an attempt to provide a naturalistic explanation for the origin of the universe. It isn’t. But the questions always seem to come up anyway. -----“Darwinian mechanisms do not ‘by definition’ have nothing to do with an intelligent agent because the theory does not provide an explanation for how those mechanisms came to exist - if the universe was designed for evolution then Darwin was basically right, the mechanisms he proposed work.” Darwinian mechanisms have no room for an intelligent agent, because the process is said to operate solely by law and chance, meaning that no purpose, direction, or design can be considered. That is what all the fuss is about: ID--says-design is real, Darwin---says design is an illusion. ID says that an intelligent agent is the MOST LIKELY cause; Darwinism says that unaided naturalistic forces are DEFINITELY the cause. (Darwinists do not allow for the possibility that they could be wrong, which is actually one of their least offensive qualities)StephenB
September 11, 2008
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StephenB, I think we're winding down here now. We both agree important and real truths can be explored without resort to science. Therefore, we at least agree that there are some spheres - some important ones - where science cannot delve into. The problem for me is that God is unlike any other designer. A given design may be the work of God, but science cannot prove or disprove that (And I believe even ID proponents agree that speculating about identity is beyond the scope of ID.) When you say "Snowflakes and moon craters, for example, appear to be designed, but are not. (Something science tells us, by the way).", I have to disagree. Instead, at best, we can rule out any designer for snowflakes and moon craters except for God, or frankly the God-equivalent. Oddly, I think I may be in the more orthodox ID position here - I could be wrong, though I do wonder if Behe and Dembski believe that, if a given thing is not IC, it is not designed by God. Or better yet, if a given IC structure is shown not to be IC, that it demonstrates the given thing was absolutely not designed. The more reasonable conclusion seems to be 'It's not demonstrating the threshold of design indicators necessary for us to scientifically infer design, but there may be non-scientific considerations.' In fact, I could possibly get behind such a view, with such a stipulation.nullasalus
September 11, 2008
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-----nullasalus: "Really depends on the context.Perfect example: The Divje Babe flute. Is it a flute, or a chew toy? There’s disagreement. Is either claim scientific? I’m not sure, even though science may be used to investigate the matter. Though it doesn’t need to be science for speculation to be insightful and warranted." Sorry, but the difference between a flute and a toy is irrelevant. ID has no methodology to make those kinds of distinctions. Science can detect the presence of an intelligent agent in both cases. I don't think you understand intelligent design at all, which may be why you question the science. In any case, the question was this: "Can archeology detect design in an ancient hunter's spear? The question you answered (which wasn't asked), was "can science detect design every time." They are two radically different questions. While the answer to the second question is "no," the answer to the first question is obviously, "yes." By questioning the obvious fact that archeology can detect design, which it clearly can, you are, in effect, saying that it is not a science.StephenB
September 11, 2008
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Though it doesn’t need to be science for speculation to be insightful and warranted. That's right. We can detect design or figure out many things without science. On the other hand, science can tell us, among other things, about the probabilities involved. Example: The more words I write in this paragraph, the less the chance that the seemingly purposeful arrangement of letters occurred by chance. If you saw them written on the planet Mars, you would infer (without science) that they were formed with purpose, but you could also measure the likelihood that they were not (through science). As the functionally specified complex information grows in quantity, the probability that it was designed increases proportionally. Science can measure that probability-- it can also detect the “effects” (not the “mechanism” or “process”) of design by the texture of the patterns, which, as it turns out, is always the same (FSCI). Again, if you see the letters, “SOS” written on the sand, you may suspect that the “message” was designed, but you also know that it may well not have been designed. In other words, the appearance of design can be misleading. There is a reasonable chance that natural forces could have carved it out; coincidences like that happen every day. Snowflakes and moon craters, for example, appear to be designed, but are not. (Something science tells us, by the way). Since there is very little complexity in the sequence “SOS,” or very little information, science can tell us that a design inference is not really warranted. As you have suggested many times, you don’t need science to draw the conclusion. On the other hand, science can also lead us to this same kind of conclusion and can also justify that conclusion by analyzing the evidence. Science can either confirm or disconfirm our intuitions about design.StephenB
September 11, 2008
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StephenB, "Do you believe that the science of archeology can detect design in an ancient hunter’s spear or from the writings on a caveman’s wall? Do you believe that science can be used to decipher hieroglyphic writing?" Really depends on the context. Perfect example: The Divje Babe flute. Is it a flute, or a chew toy? There's disagreement. Is either claim scientific? I'm not sure, even though science may be used to investigate the matter. Though it doesn't need to be science for speculation to be insightful and warranted.nullasalus
September 11, 2008
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"...Darwinian mechanisms which, by definition, have nothing to do with an intelligent agent?" Fair point, so the flagellum could have evolved in exactly the way that EvoBiologists think it did, except that if the universe was designed for evolution to work then the theory of evolution is wrong, even though it works in exactly the way they describe... I wasn't aware that the theory of evolution is an attempt to provide a naturalistic explanation for the origin of the universe. Darwinian mechanisms do not 'by definition' have nothing to do with an intelligent agent because the theory does not provide an explanation for how those mechanisms came to exist - if the universe was designed for evolution then Darwin was basically right, the mechanisms he proposed work.GCUGreyArea
September 11, 2008
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StephenB, "It is not logically possible that a Darwinian pathway to evolution could be designed, because a Darwinian evolutionary pathway by definition is one that was not associated with an intelligent agency." And I say, again, that insofar as 'Darwinian evolution' rules on the involvement of agency at that level, it is outside of science. Let's assume the darwinist case for something, unwarranted as it may be. Let's say Celltype-B. We know that Celltype-B evolved from Celltype-A from darwinian mechanisms - in this case, just mutations and natural selection (Let's ignore neutral drift, etc for this case). We know with certainty this is what happened. Was Celltype-B therefore not designed? Many darwinists will say 'Absolutely not. NS+M was sufficient for Celltype-B to come about.' My response is: You cannot rule out front loading. You cannot rule out design of the very laws that allow NS+M to provide the result we know we see. If you assert mutation is random, at best you can assert "for all practical purposes random" which is tantamount to saying you are in the dark about what went on behind the involved mutations. It's a statement of ignorance, and it has to remain so when you examine the mechanics deep enough, because you get to a question of, ultimately, determinism and indeterminism. Pleading the overall pattern fits a stochastic result doesn't help because a single guided result in the pattern would poison the well. At best you can get to 'Well, we don't need to make an appeal to design. What happened happened, and the general development happens with enough regularity for us to rely on practically.' And that's true, for both design and a lack of design. Assume the universe just happened to spit out all the right laws and properties to give what we see without forethought. Assume that there's fundamental ex nihilo randomness and indeterminacy at work in the world. Assume you're seeing the work of a powerful deity who orchestrated all the laws and properties in advance. Assume the deity works constantly and subtly. Assume chance explains everything. You can reconcile all the views with the results. And therefore, you need not appeal to any of them for what you see - and the questions therefore are extraneous to the science.nullasalus
September 11, 2008
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"Do you believe that the science of archeology can detect design in an ancient hunter’s spear" We know human beings exist and that they manipulate the environment in ways that, so far, appear to be unlike anything else, so it is quite reasonable to use what we know about humans to detect their influence on objects we find. It doesn't always work though, people still worship vaguely human looking stains or other naturally occurring simulacrum thinking they are intentional creations.GCUGreyArea
September 11, 2008
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-----"Put another way - If the universe was designed by an intelligent agent such that life might (or would) evolve, then it is not really an intelligent agent." If the universe was designed by an intelligent agent such that life would evolve, then it is obviously an intelligent agent. What does that have to do with Darwinian mechanisms which, by definition, have nothing to do with an intelligent agent?StephenB
September 11, 2008
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Nalluasalus: “Science is not capable of ruling on design of this nature. Do you believe that the science of archeology can detect design in an ancient hunter's spear or from the writings on a caveman's wall? Do you believe that science can be used to decipher hieroglyphic writing?StephenB
September 11, 2008
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"It is not logically possible that a Darwinian pathway to evolution could be designed, because a Darwinian evolutionary pathway by definition is one that was not associated with an intelligent agency." Are you calling me stupid! When I 'design' something using a genetic algorithm then according to you I am not an intelligent agent. There's a reason you're getting ignored...a genetic algorithm requires intelligence's involvement in order to function. Darwinian evolution is supposedly independent of intelligence. You yourself admitted in the past that genetic algorithm are limited and thus could not directly equate to biology in order for Darwinian evolution to work. You seem to believe there is some "unknown factor" which allows biology to exceed the limitations of GAs. - Admin Put another way - If the universe was designed by an intelligent agent such that life might (or would) evolve, then it is not really an intelligent agent.GCUGreyArea
September 11, 2008
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Nalluasalus: “Science is not capable of ruling on design of this nature. Are you honestly, truly taking what amounts to a New Atheist scientism view here? ‘If science cannot demonstrate it, it did not happen, and is therefore false.’? If so, I vehemently disagree with you.” No. I believe that more can be learned through non-scientific means than through science, and I certainly don’t subscribe to New Atheist scientism, inasmuch as I am an ID theist. That is not the issue. The point is that science is not needed to determine is something is logically impossible. You stated,-“But the bacterial flagellum could still be the result of design even if such a pathway could be found.” It is not logically possible that a Darwinian pathway to evolution could be designed, because a Darwinian evolutionary pathway by definition is one that was not associated with an intelligent agency. If a Darwinian pathway to an organism was found, then that organism could not have been designed. That is why finding one would falsify claims about “irreducible complexity” I press the issue not to be irksome, which I fear is happening, but because this is what all the fuss is about.StephenB
September 11, 2008
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Short on time so I'll only respond to this:
In other words, when credible evolutionary models exist, they’re likely to be true, and when we don’t understand how things happened, that’s a sign of design.
ID is not "we don't know". The positive case for ID is discussed in the books Dave mentioned as well as on Bill's site www.designinference.comPatrick
September 11, 2008
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StephenB, "You seem to have forgotten the reason I brought it up in the first place." "No, in fact, it could not. There are only two options: evolution associated with intelligent agency (designed) and evolution unassociated with intelligent agency (not designed). A Darwinian pathway to complexity is totally incompatible with design because it is unassociated with intelligent agency." And you're forgetting my response: Science is not capable of ruling on design of this nature. Are you honestly, truly taking what amounts to a New Atheist scientism view here? 'If science cannot demonstrate it, it did not happen, and is therefore false.'? If so, I vehemently disagree with you. So yes, there are only two options: Designed evolution, and not designed. And I say that whether evolution is design or not designed, especially when God is in the picture, is a question that science is incapable of answering in either direction. "Your view on science is the main point at issue. How one defines science determines whether one accepts ID as science. So, I will ask the relevant question again: If the Red Sea parted, could science legitimately try to investigate the matter?" I believe this was already asked of me, and I gave an answer. I'll try to give another: It depends on the context. A claim that the Red Sea parted in conditions not ideal to observation (once, thousands of years ago, lacking in scientific detail)? Likely not, or not in any decisive way. In better conditions? Well, then it depends on the conditions. Could science propose mechanisms for parting the Red Sea in general? Sure, though that's getting into questions of technology as well. Still: "If science cannot demonstrate it, it did not happen." Is this your view?nullasalus
September 11, 2008
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Patrick, Thank you for your extended answer. I greatly appreciate the effort, now I begin to understand the ID ideas better. I did not understand that ID accepts evolution as an important force, and that instances of design may be rare. In other words, when credible evolutionary models exist, they’re likely to be true, and when we don’t understand how things happened, that’s a sign of design. The only problem is that the examples you provide have, according to evolutionary theory, highly sensible explanations that are supported by evidence. The difficulties in phylogenetic analysis that you highlight are indeed very real; either inabilities to at all find reasonably supported evolutionary hypotheses, or the misleading problem that strong support can be obtained for incorrect hypothesis when large datasets are used. The limitations of our methods do not prove that trees don’t exist, however. I’ll explain the problems: 1. Phylogenetic inference commonly uses of Markov rate matrices and make assumptions on, for example, time-reversibility, which are not always realistic. Different lineages can also experience different evolutionary rates (heterotachy). These issues can be problematic, especially at deeper phylogenetic levels where the phylogenetic signal is weak because of saturation effects. Biases can significantly influence the end result or you might not get any reliable result at all. 2. Lateral gene flow will naturally influence phylogenetic relationships, simply because different genes will have different evolutionary histories. 3. A phenomenon called lineage sorting can also result odd phylogenies for individual genes. This occurs when genes have been duplicated earlier in history and copies are differentially inherited in different lineages. Lineage sorting is a very real evolutionary process with tons of evidence to back it up. http://people.bu.edu/msoren/Maddison.pdf I would also be extremely surprised if lineage sorting could not explain all the oddities of the platypus. In fact, in figure 4 of the genome paper for this animal they provide an inheritance scheme for beta-defensin peptides which illustrate the effects of lineage sorting. http://www.nature.com/nature/journal/v453/n7192/pdf/nature06936.pdfparlar
September 11, 2008
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-----nullasalus: “And the Darwinists step outside of science the moment they “rule it out in principle”, because they’ve now gotten into the wonderful and unfalsifiable world of philosophical and theological speculation. So I’d reject the classification of evolution as ‘completely autonomous and unassociated with intelligent agency’ as a scientific statement, and I stand by the view that whether or not the bacterial flagellum is IC, the question of design v no-design cannot be settled by science. I will admit that whether the bacterial flagellum is IC is a question which itself may be scientific, but those two declarations are distinct.” You seem to have forgotten the reason I brought it up in the first place. You stated as follows: --- -“But the bacterial flagellum could still be the result of design even if such a pathway could be found.” No, in fact, it could not. There are only two options: evolution associated with intelligent agency (designed) and evolution unassociated with intelligent agency (not designed). A Darwinian pathway to complexity is totally incompatible with design because it is unassociated with intelligent agency. -----"I’d be more interested in defending my view on science another time, but I’m glad at least we can agree I avoid double standards." Your view on science is the main point at issue. How one defines science determines whether one accepts ID as science. So, I will ask the relevant question again: If the Red Sea parted, could science legitimately try to investigate the matter?StephenB
September 11, 2008
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StephenB, "Let’s remember, though, that your standard for science is arbitrary." If that's your view, so be it. I'd be more interested in defending my view on science another time, but I'm glad at least we can agree I avoid double standards. "No, not really. If the evolutionary process is completely autonomous and unassociated with an intelligent agency, which is what Matzke and the other Darwinists are proposing, then it cannot be designed. The whole point of their enterprise is to find a logical alternative to design and characterize its conception as an “illusion.” Of course, it is possible that an intelligent agency could design evolutionary pathways, but that would be intelligent design, the very thing that Darwinists have ruled out in principle." And the Darwinists step outside of science the moment they "rule it out in principle", because they've now gotten into the wonderful and unfalsifiable world of philosophical and theological speculation. So I'd reject the classification of evolution as 'completely autonomous and unassociated with intelligent agency' as a scientific statement, and I stand by the view that whether or not the bacterial flagellum is IC, the question of design v no-design cannot be settled by science. I will admit that whether the bacterial flagellum is IC is a question which itself may be scientific, but those two declarations are distinct. "If you falsify irreducible complexity, you falsify the design hypothesis." You falsify the design hypothesis with regards to a specific view and claim of design on the table. You do not falsify design/no-design as a live and (in the former's case) very powerful argument philosophically. This is stepping into an area of science-abuse that I abhor - 'If earth isn't 6000 years old, there is no God!' and 'If evolution is true, there is no God!' type challenges and lines in the sand that I see no reason to accept, and every reason to reject.nullasalus
September 11, 2008
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-----nullasalus: “No, it’s back to falsifiability - and I don’t think design of the type ID explores can be subject to falsification (Remember, I’m not saying this about every idea an ID proponent advocates). And again, no, this holds true both for ‘design’ and ‘lack of design’ - I’m just as critical of the latter, moreso because I think it’s the established viewpoint, and those who hold said viewpoint while criticizing ID are hypocrites.” OK---no double standard. Fair enough. Let’s remember, though, that your standard for science is arbitrary. In effect, you are accepting a faddish and constricted definition, which you “more or less” subscribe to. That is an awful lot of equivocation. At the same time, you totally ignore my definition as if it doesn’t deserve a second look, even though it contains a lot more tradition, a lot more public support, a lot more information, and a lot more explanation than yours. Under the circumstances, I don' think that you don’t have a very solid basis for challenging ID’s scientific status. ----“But the bacterial flagellum could still be the result of design even if such a pathway could be found.” No, not really. If the evolutionary process is completely autonomous and unassociated with an intelligent agency, which is what Matzke and the other Darwinists are proposing, then it cannot be designed. The whole point of their enterprise is to find a logical alternative to design and characterize its conception as an “illusion.” Of course, it is possible that an intelligent agency could design evolutionary pathways, but that would be intelligent design, the very thing that Darwinists have ruled out in principle. -----“So in this case, I would hesitantly agree that ‘the bacterial flagellum is irreducibly complex’ is a falsifiable statement.”While ‘the bacterial flagellum was/was not designed’ is not. If you falsify irreducible complexity, you falsify the design hypothesis. Put another way, if it is irreducibly complex, then it is reasonble to conclude that it was probably designed, since it is our experience that all things known to be irreducibly complex are also known to be designed.StephenB
September 10, 2008
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StephenB, "So, you can’t logically say that science doesn’t meet your standard unless you disclose that standard. Or, are you saying that “falsifiability” is your sole standard?" More or less. If someone has an idea that explains what we see in the world, but there's no way to falsify it, that's not the stuff of science by my view. "Are you saying that all logical inferences are philosophical and no logical inferences are scientific? Or, are you saying that a design inference can be scientific UNLESS it leads to “design?” How would you justify either assertion?" No, it's back to falsifiability - and I don't think design of the type ID explores can be subject to falsification (Remember, I'm not saying this about every idea an ID proponent advocates). And again, no, this holds true both for 'design' and 'lack of design' - I'm just as critical of the latter, moreso because I think it's the established viewpoint, and those who hold said viewpoint while criticizing ID are hypocrites. "If, for example, Nick Matzke keeps plugging away and finds his evolutionary pathway to complexity, then “irreducible complexity” has been falsified. Such a discovery would confirm the fact that the bacterial flagellum is not irreducibly complex." But the bacterial flagellum could still be the result of design even if such a pathway could be found. (And I notice that many ID opponents claim that such pathways HAVE been found. I'm not in the position to judge the arguments of either side, so I take a hands-off approach to this.) So in this case, I would hesitantly agree that 'the bacterial flagellum is irreducibly complex' is a falsifiable statement. While 'the bacterial flagellum was/was not designed' is not.nullasalus
September 10, 2008
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-----nullasalus: “Maybe we’re talking past each other. I’m not arguing that nothing an ID proponent (or an ID opponent) can propose as an experiment is scientific by my standard. “ Perhaps, but we must establish what it is that you are calling a standard. To say that ID is or is not science is to say that it does not conform to whatever standard or definition of science we are talking about. So, you can’t logically say that science doesn’t meet your standard unless you disclose that standard. Or, are you saying that “falsifiability” is your sole standard? -----“Propose something which can be falsified, engage in research/testing, and I’ll say you’re doing science. Say you infer design based on what you’re seeing, and I may even agree with what you infer. But when you start talking about inferring design or a lack of design, that is when you’re no longer doing science by my view.” Are you saying that all logical inferences are philosophical and no logical inferences are scientific? Or, are you saying that a design inference can be scientific UNLESS it leads to “design?” How would you justify either assertion? Actually, my favorite comment on this subject comes from Dave Scot, who once asked a question something like this: If the Red Sea parted down the middle, could science legitimately TRY investigate the matter? I say yes. If you are going to say no, which I assume is the case, then your answer needs to be grounded in something, namely your definition of science and the scientific method. -----“So let me ask this: “The bacterial flagellum could/could not have come to be without design.” Is this, to you, a falsifiable statement? In this case, I think that you are imposing a philosophical formulation (“come to be”) on a scientific construct (falsifiability). Only a scientific construct can be scientifically falsified. On the other hand, the statement can be philosophically falsified by simply pointing out that something cannot come from nothing. The scientifically falsifiable statement is that the bacterial flagellum is “irreducibly complex.” That is why Behe devised the term---it has the requisite scientific dimensions. If, for example, Nick Matzke keeps plugging away and finds his evolutionary pathway to complexity, then “irreducible complexity” has been falsified. Such a discovery would confirm the fact that the bacterial flagellum is not irreducibly complex. Even so, I don’t accept falsifiability as a standard of science. I submit that science is exactly what I said it is: science: a branch of knowledge conducted on objective principles involving the systematized observation of and experiment with phenomena, esp. concerned with the material and functions of the physical universe. scientific method: principles and procedures for the systematic pursuit of knowledge [”the body of truth, information and principles acquired by mankind”] involving the recognition and formulation of a problem, the collection of data through observation and experiment, and the formulation and testing of hypotheses. Because I have offered my standard, I can reasonably claim that ID conforms to it.StephenB
September 10, 2008
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DaveScot, Thanks for the reply and the kind words. For me, the issue is not a stark choice between design or statistical mechanics - even if the latter can explain what is seen, you're still left with questions of why systems function in the way that they do to provide those statistics, how systems can be designed in ways to make certain patterns more/less likely, etc. On the flipside, even if we do observe biological structures that defy appeal to statistical mechanics, you already know the typical responses - "Well, we just got extremely lucky! Maybe there are multiple universes even." or "Clearly we're just missing something, and science will up and die if we think otherwise." This gets worse since the fight isn't really over pure science besides, or even what kind of research is done - it's also about wanting people to reject certain possibilities out of hand because they're too congruent with worldviews that are unacceptable. StephenB, "If, indeed, falsifiability is your standard, it would seem that you would acknowledge that ID is science, since ID is obviously falsifiable. Yet, you do not accept ID as science, so evidently you have some other standard." Maybe you missed my saying this: Hey, even particular ID claims may be falsifiable - Behe’s comes to mind, though I’m in no way prepared to judge his scientific claims. But let's say Behe's claims are accurate. There really does seem to be an edge to evolution, and claims are made which could be falsified by research (Say speculation about mutation rates and possibility are made and tested.) As DaveScot said, what evolution cannot explain are (at least by and large) past events. Saying 'this event/structure could not have come about through known mechanisms of evolution according to what we know' does not mean you've proven design, anymore than 'this could have come about through evolution' proves a lack of design. You can argue that you've at least inferred it - I'd agree. But the question of design or a lack of design in nature still goes beyond science. Maybe we're talking past each other. I'm not arguing that nothing an ID proponent (or an ID opponent) can propose as an experiment is scientific by my standard. Propose something which can be falsified, engage in research/testing, and I'll say you're doing science. Say you infer design based on what you're seeing, and I may even agree with what you infer. But when you start talking about inferring design or a lack of design, that is when you're no longer doing science by my view. So let me ask this: "The bacterial flagellum could/could not have come to be without design." Is this, to you, a falsifiable statement? To me it isn't - even if you show a definite and past-plausible evolutionary or material mechanism that could have conceivably resulted in the bacterial flagellum, you still have the design of the overall system, the historical pattern, etc to contend with. Design speculation never goes away, and in fact may become even stronger depending on the conditions required to enable those mechanisms. And even if you show that no known evolutionary or material mechanism could have resulted in what we see, despite considerable research, the claim always will linger - we missed something, it was just luck, or in the most extreme case, 'maybe it was designed, but not by who you think'.nullasalus
September 10, 2008
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parlar, Personally I don't have the time to respond at length...never mind that your objections are very common and have been discussed before at length. As such most of my response is copy and paste.
spreading of antibiotic resistance
Micro-evolution. No "special ID explanation" required. Why, do you hold the misconception that ID proponents consider everything in evolutionary biology to be false? Behe had this to say:
Intelligent design is a good explanation for a number of biochemical systems, but I should insert a word of caution. Intelligent design theory has to be seen in context: it does not try to explain everything. We live in a complex world where lots of different things can happen. When deciding how various rocks came to be shaped the way they are a geologist might consider a whole range of factors: rain, wind, the movement of glaciers, the activity of moss and lichens, volcanic action, nuclear explosions, asteroid impact, or the hand of a sculptor. The shape of one rock might have been determined primarily by one mechanism, the shape of another rock by another mechanism. Similarly, evolutionary biologists have recognized that a number of factors might have affected the development of life: common descent, natural selection, migration, population size, founder effects (effects that may be due to the limited number of organisms that begin a new species), genetic drift (spread of “neutral,” nonselective mutations), gene flow (the incorporation of genes into a population from a separate population), linkage (occurrence of two genes on the same chromosome), and much more. The fact that some biochemical systems were designed by an intelligent agent does not mean that any of the other factors are not operative, common, or important.
and
I think a lot of folks get confused because they think that all events have to be assigned en masse to either the category of chance or to that of design. I disagree. We live in a universe containing both real chance and real design. Chance events do happen (and can be useful historical markers of common descent), but they don’t explain the background elegance and functional complexity of nature. That required design.
you say:
or the existence of DNA homology.
ID proponents typically interpret homology as compatible with universal common descent, common descent from multiple LUCAs, or Designer Information Reuse (which is itself compatible with multiple scenarios). http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371%2Fjournal.pbio.0040352&ct=1 Read this article where they’re seeing multiple bushes, not a tree. They even discuss the biases used to resolve this bad picture for Darwinists like long-branch attraction: “Thus, a priori expectations of obtaining fully resolved topologies combined with the use of large amounts of data (which generate high support values) can make trees out of bushes." And it keeps getting worse: “recent analyses of some key clades in life's history have produced bushes and not resolved trees.” “The patterns observed in these clades are both important signals of biological history and symptoms of fundamental challenges that must be confronted.” “Wolf and colleagues omitted 35% of single genes from their data matrix, because those genes produced phylogenies at odds with conventional wisdom” “The evidence presented here suggests that large amounts of conventional characters will not always suffice, even if analyzed by state-of-the-art methodology.” They even discuss the “high frequency of independently evolved characters” aka convergent evolution. I think it would help the conversation to differentiate between Darwinian Common Descent and Common Descent compatible with ID hypotheses (which is fine with the above picture of bushes and not a consistent TOL). For example, you wouldn’t expect to find the same information being used in divergent lines from a Darwinian viewpoint if they’re geographically isolated or if the divergence supposedly took place a very large amount of time before. Instead of resolving a tree we're getting bushes since we cannot find the gradual informational links that would be expected of Darwinian Common Descent. Continuing the theme of "islands of functional information", these bushes could also be called "archipelagos of functional information" which must be bridged by informational leaps. Designed mechanisms could bridge (or traverse) these informational leap, thus producing Designed Common Descent. Another thing that ID proponents predicted is homologous information where none would be expected if Darwinian mechanisms were responsible for macro-evolution. Like the platypus, for example, whose genome is a patchwork of mammal, reptile, and bird. Chromosomal sex determination in the platypus was also discovered to be a combination of mammal and bird systems. Yet TO says: “birds are thought to have evolved from dinosaurs in the Jurassic about 150 million years ago, and that mammals are thought to have evolved from a reptile-like group of animals called the therapsids in the Triassic about 220 million years ago. No competent evolutionist has ever claimed that platypuses are a link between birds and mammals.” In the past I've mused what might happen if the genomes for animals not considered to be related were compared. My predication would be that we’d find evidence for front-loading, other scenarios, and information re-use in general. I personally want to see a comparison of North American flying squirrels and Australian sugar gliders. Often the the convergent evolution storytelling card is played…you’d think Darwinist would have run out of cards in that deck by now. Universal common descent from a single LUCA may be true itself but the historical narratives we have now may not be true themselves. Some ideas like land mammals to whales may have never existed (or persisted to this day) if the bearded buddha had never posited his bear story. If front-loading and universal common descent are both true then why couldn’t the whale have evolved entirely in the ocean and received the mammal-like features from internal information? I have my personal preferences but I also have no problems with multiple LUCAs and other narratives. Directed panspermia (front-loading with no further design interaction), intelligent evolution, progressive creation, separate creation (possibly combined with more limited front-loading), it doesn’t matter. As long as intelligence is involved as the data shows and the evidence is compatible with a scenario.Patrick
September 10, 2008
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