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Author
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Topic: The Evolution of the Bacterial Flagellum
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Nel
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Member # 614
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posted 23. November 2003 15:09
I just read some of Nic's essay, Dembski's response and very little of this thread. I'm also trying to chase down all the references. I havn't finished reading it yet, but I thought I'd make some random remarks.
An area that Nicholas and I have already gone over in another thread caught my eye. This concerns the transport proteins Mot Tol and Exb, in which he writes:
quote:
(3) FliG was coopted simultaneously with MotAB, because it originated as a fragment of a TolA homolog that ancestrally interacted with a TolQ homolog. The third hypothesis is the simplest and most direct pathway; the only novel interaction would be the binding of the proto-FliG to FliF; binding to the proto-MotA would be inherited. This
is less demanding than postulating the re engineering of the interface between a TolQ homolog and its substrate (a feature of both hypotheses #1 and #2), and does not require postulating an independent cooption of FliG from an unknown source. The hypothesis also has the advantage of being testable via determination of the structures of TonB or TolA and investigation of their interactions with ExbBD and TolQR.
I think there are a limited number of designs for driving motion from a proton motive force or electrochemical gradient, and that the TolQR/MotAB molecular machines represent two different models based on one of these designs. Convergence cannot be ruled out as an explanation.
The major difference between the two systems is that Tol and Exb systems couple their energy in the extracellular environment while Mot couples energy to FliG/F within the cytoplasm.
Hypothesis 1 and 2 above suffers from lack of detail and seem, as Nic himself states, a bit complex. Hypothesis 3 has a bit more meat on it but contains these glaring difficulties: First, there is no similarity between the N terminal of TolQ and of MotA. Second, there is no cytoplasmic N terminal region of TolA to be converted into FliG.
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The linkage between the filament and motor is very complex, mediated by about ten proteins, and the filament subunits are secreted through the base of the flagellum via a type III export pathway, rather than via a type II pathway as might be expected for a protein derived from an outer membrane pore; type III virulence systems do utilize an outer membrane secretin secreted by the type II pathway, and the flagella P- and L-ring proteins FlgI and FlgH are similarly secreted via the type II pathway (Macnab, 2003).
Unless I'm mistaken, the outer ring of the flagellum is formed by proteins, that are
secreted via the normal signal-sequence dependent pathway, which just happens to be the first step in the type II secretion pathway, but is used for much broader purposes.
I'll probably keep adding my thoughts to this thread as I continue to read it.
[ 24. February 2006, 02:22: Message edited by: Nel ]
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Mike Gene
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posted 05. December 2003 00:46
Pim: And? Why would one expect science to be able to infer design without any independent knowledge?
I never said we should expect science to be able to infer design without independent knowledge of the designers. I’m simply considering the implications that follow if the critic’s position is valid. If they are correct, this is another limitation of science.
Again this is not a failure of science as much as a failure of the method used to infer design.
I never said it was a “failure” of science.
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Mike Gene
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posted 05. December 2003 00:54
Rex: The design theorist doesn't learn anything unless design could be inconsistent with (or an unlikely cause for) potential data.
Agreed. But making similarity/dissimilarity the fulcrum doesn’t make much sense. As I explained:
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Yet homology is “proved” without consideration of design (for, if most of the critics of design are right, science cannot detect it). Yet if we consider the possibility of design as an explanation, it’s hard to see how similarities amidst complexity rule out design. The logic of this would involve the notion that any designer would never reuse a design in any other form or any other context. The method used to detect homology in a non-teleological matrix would force us to assume that any designer is constrained to use completely unique designs in every instance.
So you really need competing hypotheses right away, or you learn nothing. Competing design hypotheses are fine.
That depends on what you think the competing hypothesis is supposed to be. Consider any police investigation. If Jones is the murder suspect, it doesn’t mean we can’t investigate the suspect unless we also come up with another competing suspect. The only hypothesis that needs to compete against Jones being the suspect is the hypothesis that Jones is not the suspect. If we turn to origins, it should be clear that the non-teleological explanations have never really competed against teleological explanations.
But ancient systems have so scant a record of their history that I wonder whether much progress can be made there, either.
Yet the ancient systems are the most important and most interesting. And if one proposes the hypothesis that life itself was designed, then these ancient systems are the most likely to have been designed.
Imagine I’m looking for a lost key. I have suggestive evidence to think the document is buried somewhere in my messy garage. Since my garage is such a mess, it would seem almost impossible that I would find it there. Should I nevertheless begin looking there? Or maybe I should check out the local K-Mart since everything there is so neatly arranged?
Of course I agree that design is not inconsistent with the formation of life, given a sufficiently intelligent and knowledgeable designer. Now what?
I’ve started down that road as outlined in the 29 essays on my web page. I hope to add a few more as the holidays draw closer.
[ 05. December 2003, 01:02: Message edited by: Mike Gene ]
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Pim van Meurs
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posted 05. December 2003 13:20
Mike: If we turn to origins, it should be clear that the non-teleological explanations have never really competed against teleological explanations.
What about selection which is quite teleological (See Ruse's latest book on this for instance).
Mike: And if one proposes the hypothesis that life itself was designed, then these ancient systems are the most likely to have been designed.
Again, the issue is not the design of these systems but the nature of the designer. Most would accept the 'design' in nature, the issue is was it 'intelligent' or non-intelligent design. With that in mind evolutionary theory has its mechanisms (read designers). Perhaps it is time to compare them with ID designer(s)?
Mike: I never said we should expect science to be able to infer design without independent knowledge of the designers. I’m simply considering the implications that follow if the critic’s position is valid. If they are correct, this is another limitation of science.
Again, it is not a limitation of science but a limitation of the ID approach. It is important to recognize where the failure resides.
[ 05. December 2003, 13:29: Message edited by: Pim van Meurs ]
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Mike Gene
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posted 05. December 2003 19:26
Pim: What about selection which is quite teleological (See Ruse's latest book on this for instance).
The culling of variations, such that they “match” the environmental challenges, can give the appearance of teleology (making it ‘teleologcoid’, borrowing from Dawkins). Yet the “end” here is simply anything that improves fitness in any way. It’s a blind watchmaker with little demand.
Again, the issue is not the design of these systems but the nature of the designer.
Most would accept the 'design' in nature, the issue is was it 'intelligent' or non-intelligent design.
Do you have any survey or polling data that demonstrate “most accept the ‘design’ in nature”? And among those who do, do they accept design in its literal sense or a metaphorical sense? I would say you have no such data and most who accept the ‘design’ do so purely in a metaphorical sense.
There have long been two forms of criticism against a design inference. First, there is the path of Hume, whereby one denies the appearance of design. Secondly, there is the path of Darwin, where one grants the appearance of design, but asserts it is only an illusion (Dawkins calls it ‘designoid’). Thus, we really have two types of ID critics (who rarely argue with each other), where for some, the issue is indeed the design of these systems. If that’s not an issue for you, this doesn’t mean it is not an issue for everyone. This means you should rephrase your claim as follows: “For me, the issue is not the design of these systems….” And without polling or survey data, you should refrain from asserting what “most” would accept. I think it is important that people take personal responsibility for their own claims and not try to smear them into some authority group.
With that in mind evolutionary theory has its mechanisms (read designers). Perhaps it is time to compare them with ID designer(s)?
This depends on the expression of ID. If we are talking about intelligent intervention, where mentation imposes form on physical reality, it is clear, from a mechanistic viewpoint, that natural causes have an epistemic advantage. Put simply, it’s easier to track them. Being regularities, they are amenable to direct study and more readily incorporated into explanations. And being regularities, they also play roles. Intelligent intervention is a form of causation that need not express itself as a regularity (I do not envision it as such). Uncovering the “mechanisms” behind such activity is asking for the recipes, protocols, blueprints, etc., things that are not part of the reality we can observe. And that poses a very real epistemic problem as I outlined here.
On the other hand, an ID designer might very well design life to exploit evolutionary mechanisms. In fact, certain evolutionary mechanisms themselves may be designed.
I’ve been exploring things from this angle.
Now, if you insist on “comparing” “evolutionary mechanisms” with some expression of ID, feel free to outline the actual mechanisms that were behind the origin of the bacterial flagellum and the evidence that indicates they were indeed the cause behind the flagellum. We can go from there.
Pim: Again, it is not a limitation of science but a limitation of the ID approach. It is important to recognize where the failure resides.
You need to explain your reasoning. In the meantime, I’ll (again) explain mine.
If it is true that science needs independent knowledge of the designers (their methods, motives, identity) etc. before we can infer design, then science cannot, by definition, infer design without such a base of independent knowledge.
Science is therefore limited to identifying only a subclass of designed things – those things whose designers can also be studied in the here and now. For example, since you subscribe to the idea that such a base of independent knowledge is a necessary prerequisite to infer design, you only detect the designs of the blind watchmaker (since you have a good feel for this ‘designer’). Yet is this merely a function of your ground rules? After all, this explains a significant admission on your part (on the ARN forum): when I asked you what science would look like if ID was true, you said, “I don’t know.”
What ID theorists contemplate are ways of scoring for design without the luxury of having a rigorous base of knowledge about the designer. That has always been the starting place. And it takes me back to my argument:
quote:
Do we require independent information about the designer (identity, motives, methods, etc.) in order to infer/detect design?
If the answer is no, then how does one go about inferring/detecting design without relying on such information?
If the answer is yes, this is a limitation of science. That is, without knowledge about the designers, science cannot infer/detect design.
Correct me if I am wrong, but you seem to be arguing that yes, science is completely dependent on knowledge about the designers in order to infer design, but no, this is not a limitation of science.
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Rex Kerr
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posted 06. December 2003 00:43
Mike draws an interesting analogy between scientific hypothesis testing and police work. However, there is a very important difference between the two, in that in science we are allowed to say (and indeed, it is very helpful in accelerating progress to say) "X is the most likely candidate" even when the evidence isn't airtight. Now, at some point, I think the responsible thing to do is to simply say "We don't know" when there is too much evidence against every hypothesis. So when evidence is very poor (or very outstanding), police-work and scientific judgments match. In the middle, science advances a more tentative theory while the justice system refuses to pass judgment.
But this is something of a tangent, because when I said "So you really need competing hypotheses right away, or you learn nothing." it was intended with the implicit acknowledgement that design can explain absolutely any data whatsoever. Everyone has to compete with the "everything is designed by the whimsy of an omnipotent being" hypothesis. Normally, science makes the assumption that such beings do not exist, which initially is no more than a speculation; but as such beings continue to be unnecessary, one can gain confidence that either such beings don't exist, or in terms of studies of the physical world, it is as if they didn't exist. My impression, however, was that design theory was formulated to avoid ruling out omnipotent (or nearly so) beings meddling with things.
So, again, I think you do need competing hypotheses right at the start.
Mike also said
quote:
The ancient systems are the most important and most interesting. And if one proposes the hypothesis that life itself was designed, then these ancient systems are the most likely to have been designed.
Fair enough. But the question remains: is it possible to distinguish design from evolution in these ancient systems even in principle, or is the data too scant? If the data is too scant for now, it doesn't matter that these systems are the most important, interesting, and likely to be designed: we still won't be able to answer the question. I fear the data is too scant.
This is why I advocate studying more recent systems. Not because they're the most interesting, but because they're the easiest to study. Unlike keys, where there is only one set, design could be in many places. If my garage is a complete mess, I will search in K-mart for a snap-lock hose fitting or a clothes hangar, because I can find it there.
Also, things we learn about the evolution or designed construction of recent systems may help us interpret what little data is left from ancient systems. We may gain additional insight into how protein complexes evolve and thus be able to formulate reasonable-probability hypotheses for, say, flagellum evolution; or we may discover signatures of design input, which we can then look for in the flagellum.
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Pim van Meurs
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posted 06. December 2003 01:59
Mike Gene: The culling of variations, such that they “match” the environmental challenges, can give the appearance of teleology (making it ‘teleologcoid’, borrowing from Dawkins). Yet the “end” here is simply anything that improves fitness in any way. It’s a blind watchmaker with little demand.
But this shows that the appearance of design or teleology can be well understood from a Darwinian perspective. Thus ID explanations, based so far on eliminations or moving the ID relevant incident to outside our direct observations seem to be at somewhat of a disadvantage here.
Mike Gene: Do you have any survey or polling data that demonstrate “most accept the ‘design’ in nature”? And among those who do, do they accept design in its literal sense or a metaphorical sense? I would say you have no such data and most who accept the ‘design’ do so purely in a metaphorical sense.
I cannot speak for ID proponents but I would argue that the issue is NOT the appearance of design in nature which you yourself claim can be due to Darwinian processes but the nature of the designer. Lets focus on the real issue then for which I will retract my statement which allowed you to sidetrack to irrelevant issues and reiterate that the real issue is not the design in nature but the nature of the design(ers)
Mike: And without polling or survey data, you should refrain from asserting what “most” would accept. I think it is important that people take personal responsibility for their own claims and not try to smear them into some authority group.
Lets not get distracted by Mike's side tracking here. Motives and psychological type casting (try to smear..) are not very conducive to the discussion.
Mike: On the other hand, an ID designer might very well design life to exploit evolutionary mechanisms. In fact, certain evolutionary mechanisms themselves may be designed.
I’ve been exploring things from this angle.
Sure but in order to find evidence relevant to ID, it seems that accepting fully evolutionary mechanisms as the causes is not very helpful to the ID cause. Of course ID designers could have designed through evolutionary mechanisms, which seems indeed the most plausible explanation, the real question of course if this philosophical viewpoint has any scientific relevance. After all, I see God's beauty in the sunsets and the world around us, yet I also do accept the fully natural causes for this sunset and its majestic colors.
Mike: Now, if you insist on “comparing” “evolutionary mechanisms” with some expression of ID, feel free to outline the actual mechanisms that were behind the origin of the bacterial flagellum and the evidence that indicates they were indeed the cause behind the flagellum. We can go from there.
So far the evolutionary pathways seem to be quite a bit more prevalent than ID explanations. Perhaps Mike is willing to offer his alternatives to the recent pathways described by Nick?
Mike: If it is true that science needs independent knowledge of the designers (their methods, motives, identity) etc. before we can infer design, then science cannot, by definition, infer design without such a base of independent knowledge.
That seems to be problem for approaches which try to circumvent this. But should science be 'blamed' or the approach to infering design? I would argue that it is the latter.
Mike: Science is therefore limited to identifying only a subclass of designed things – those things whose designers can also be studied in the here and now.
Your argument seems to be too strong. What we can argue at most is that approaches which try to infer design through elimination alone seem to fail when it comes to new design.
Mike; After all, this explains a significant admission on your part (on the ARN forum): when I asked you what science would look like if ID was true, you said, “I don’t know
It is not up to me to define what ID would look like. But Mike takes this as evidence that science is somehow limited seems to be using my statement in a manner unsuitable as such. Given the strong evidence supporting natural pathways, strong enough that ID proponents seem to be more and more looking for 'front loading' approaches to ID merely runs the risk of moving ID into the realm of gaps. Is that the problem of science or the problem of the approaches chosen by ID? I would argue the latter.
Mike: Correct me if I am wrong, but you seem to be arguing that yes, science is completely dependent on knowledge about the designers in order to infer design, but no, this is not a limitation of science.
Indeed, it is a shortcoming of ID approaches which try to ignore this fact. Take for instance the eliminative approach chosen by Dembski, as Del Ratzsch and various others have pointed out it is unsuitable to infer new design.
If Mike wants to argue that the evidence of ID can be found in the lack of evidence then we have somewhat of a problem namely that Mike seems to have accepted that the evidence that would help us infer ID is absent.
If Mike suggests that these 'designers' remain elusively hidden in our inability to understand their mechanisms and pathways then it seems obvious to me that scientific alternatives which do propose mechanisms and pathways have a significant advantage.
Should science be blamed for the lack of evidence or the problematic approaches chosen to infer ID?
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Mike Gene
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posted 06. December 2003 03:19
Pim: But this shows that the appearance of design or teleology can be well understood from a Darwinian perspective. Thus ID explanations, based so far on eliminations or moving the ID relevant incident to outside our direct observations seem to be at somewhat of a disadvantage here.
Indeed. It’s a Darwinian perspective , a way of looking at things. And yes, it does have certain epistemic advantages (as I state above). But is there more?
I cannot speak for ID proponents but I would argue that the issue is NOT the appearance of design in nature which you yourself claim can be due to Darwinian processes but the nature of the designer. Lets focus on the real issue then for which I will retract my statement which allowed you to sidetrack to irrelevant issues and reiterate that the real issue is not the design in nature but the nature of the design(ers)
I’m more than pleased to shift major focus on the nature of the designers. In time.
Lets not get distracted by Mike's side tracking here. Motives and psychological type casting (try to smear..) are not very conducive to the discussion.
It’s not very conducive to a discussion to present one’s personal views as if they represent consensus or objective reality.
Sure but in order to find evidence relevant to ID, it seems that accepting fully evolutionary mechanisms as the causes is not very helpful to the ID cause.
I’m not concerned about any ID “cause,” so there is no need to be concerned for me. As far as your own opinions go here, I haven’t the foggiest idea of what you would consider “evidence relevant to ID.” Thus, I’m not sure I can help you here.
Of course ID designers could have designed through evolutionary mechanisms, which seems indeed the most plausible explanation, the real question of course if this philosophical viewpoint has any scientific relevance. After all, I see God's beauty in the sunsets and the world around us, yet I also do accept the fully natural causes for this sunset and its majestic colors.
At least we can reach agreement on the plausibility of designing through evolution. I’ve explained the logic of this position several times. Does it have scientific relevance? I have found it to be so. It provides a frame of reference that sparks inquiry (for example, the closer look at cytosine deamination in relationship to the genetic code and side chain hydrophobicity). The frame of reference is subtle and is easy to overlook if one is demanding a sensational proof of design.
So far the evolutionary pathways seem to be quite a bit more prevalent than ID explanations. Perhaps Mike is willing to offer his alternatives to the recent pathways described by Nick?
You didn’t answer my question. Were those real evolutionary pathways? Are you saying the F0F1 ATP synthetase is indeed homologous to the TTS machinery?
That seems to be problem for approaches which try to circumvent this. But should science be 'blamed' or the approach to infering design? I would argue that it is the latter.
You are the only one inserting the words “blame,” “failure,” “problem” into the exchange. I don’t consider a limitation of science to be a failure in need of something to blame. A limitation is just that – a limitation. Science already has limitations and I am pointing out that the assertions of the ID critic entail yet another limitation.
Your argument seems to be too strong. What we can argue at most is that approaches which try to infer design through elimination alone seem to fail when it comes to new design.
The argument is not too strong – it follows logically from the position of the ID critic. If science depends on independent knowledge of the designers to infer design, then science can only detect certain types of design – designs that happen to detectably coexist with their designers. Say the bacterial flagellum is indeed designed. If the critics are correct, the only way science could ever detect this truth is if it first uncovered data about the flagellum’s designers.
It is not up to me to define what ID would look like. But Mike takes this as evidence that science is somehow limited seems to be using my statement in a manner unsuitable as such. Given the strong evidence supporting natural pathways, strong enough that ID proponents seem to be more and more looking for 'front loading' approaches to ID merely runs the risk of moving ID into the realm of gaps. Is that the problem of science or the problem of the approaches chosen by ID? I would argue the latter.
I’m simply pointing out that you have no idea what science would look like if ID were true. Aside from the fact that this severely weakens your ability to constructively critique an ID hypothesis, it is understandable given the manner in which you strongly link your (potential) ID thinking to designer-centric demands.
Indeed, it is a shortcoming of ID approaches which try to ignore this fact. Take for instance the eliminative approach chosen by Dembski, as Del Ratzsch and various others have pointed out it is unsuitable to infer new design.
I’m not sure what this had to do with my point - you seem to be arguing that yes, science is completely dependent on knowledge about the designers in order to infer design, but no, this is not a limitation of science. If it is a fact that a design inference depends on independent knowledge of the designers, then this is another limitation of science.
If Mike wants to argue that the evidence of ID can be found in the lack of evidence then we have somewhat of a problem namely that Mike seems to have accepted that the evidence that would help us infer ID is absent.
This has nothing to do with my posting.
If Mike suggests that these 'designers' remain elusively hidden in our inability to understand their mechanisms and pathways then it seems obvious to me that scientific alternatives which do propose mechanisms and pathways have a significant advantage.
I already spoke of the epistemic advantages. But what does this really mean?
Should science be blamed for the lack of evidence or the problematic approaches chosen to infer ID?
Who said anything about “blame?”
[ 06. December 2003, 03:20: Message edited by: Mike Gene ]
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Mike Gene
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posted 06. December 2003 03:39
Rex: But this is something of a tangent, because when I said "So you really need competing hypotheses right away, or you learn nothing." it was intended with the implicit acknowledgement that design can explain absolutely any data whatsoever. Everyone has to compete with the "everything is designed by the whimsy of an omnipotent being" hypothesis.
This is not much of a problem. I simply take these options off the table. That is, whim and omnipotence are to be excluded from the explanation. I have long stated that I envision a human-like designer.
So, again, I think you do need competing hypotheses right at the start.
That depends on the competing hypotheses. I have found good old “if, then” reasoning to be quite adequate to the task. In time, as things fall into place, perhaps competition with the main show may be in order.
And then there is this.
Fair enough. But the question remains: is it possible to distinguish design from evolution in these ancient systems even in principle, or is the data too scant? If the data is too scant for now, it doesn't matter that these systems are the most important, interesting, and likely to be designed: we still won't be able to answer the question. I fear the data is too scant.
Maybe it is. Before Nic wrote his 70 page article on the flagellum, he told me many times this system was too ancient to explore. If the concern is about the antiquity of the event, perhaps someone should tell us what the cut-off is. Just how old is too old to be worthy of investigation?
This is why I advocate studying more recent systems. Not because they're the most interesting, but because they're the easiest to study.
Of course it would be easier. But without reason to suspect ID in recent times, what’s easiest to study may be completely irrelevant. I suspect intelligent intervention behind the origin of life. I don’t suspect intelligent intervention behind the origin of humans. I can just repeat what I said before:
Now, there is nothing perverse about me focusing on ancient systems. My hypothesis is that life itself was engineered and used to seed this planet (a modest extension of the Crick/Orgel hypothesis of Directed Panspermy) and the engineering entailed front-loading (my own take). This raises the very real possibility that design, in the form of intelligent intervention, was restricted to the first life forms.
Where else should one look? You yourself admitted you don’t have a good suggestion. If I’m to neglect this area (because of my limited time and energy) and cherry pick something else simply because it is more recent, why think design was there in the first place? I don’t envision intelligent design as a regularity. It is not like a natural law that will express itself ubiquitously. If the designer acted like a law of nature, we might treat it with more traditional approaches and focus on more recent events (where there is more information).
Without a more rigorous model of where to expect design, I’m likely to be led off on a wild goose chase. My focus near the origin of life (the site of the proposed design event), coupled to front-loading, allows me to gradually envision such a model and think about design in a positive manner.
Attempting to approach the topic in a modest, systematic, and positive fashion hardly seems perverse to me.
PS: Oops. Just noted I'm past my self-imposed 50 posting rule. You guys can have the last word here.
[ 06. December 2003, 03:47: Message edited by: Mike Gene ]
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Rex Kerr
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posted 06. December 2003 18:35
Mike says he takes omnipotent and whimsical designers off the table, in favor of human-like designers. This is fine, but I would suggest that if one can make the assumption of human-like designers, one needn't be restricted to the very general tools available in, say, the explanatory filter.
Also, I would like to stress again that I don't think that the flagellum is unworthy of study. I simply think that it is unwise to study the system with the hope of detecting design, especially if one is thinking of human-like designers who would, due to cognitive limitations, probably be forced to design in large part by evolution with "unnatural selection". Unwise because we may well not have enough information to distinguish between, say, natural evolution on Earth; evolution on another planet followed by accidental seeding of Earth (panspermia); seeding by human-like designers; and seeding by essentially omniscient/omnipotent designers.
However, since it isn't my time and effort being spent to study it, and there are certainly worse hobbies one could have, I can't really complain if people decide to study the flagellum in the hopes of answering design-or-not questions.
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gedanken
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posted 07. December 2003 12:16
Yes, the problem is what are the limitations on "human-like" designers. Are they limited to being present and having access to the events that occurred? Or are they allowed to have technology far beyond anything we have ever seen in order to implement their "designs".
This is an area of possible conflation--in which Mike makes us believe that he has limited the field to "designers" that are realistic, like humnans who were physically present, while in fact the limitation is only of a very insubstantial nature of some limited areas of constraints of how they behave, with no constraints on their technology to achieve their "goals".
Without any limitations on that technology, there is no difference in terms of the unconstrained and unknown nature of the prior joint probabilities of the designer effecting the event--thus there is no way to pinpoint the reliability of an "explanatory filter" like inference. If you allow for "human like" designers to swoop in at arbitrary times with their space ships, how have you limited the prior probabilities in any way based on knowledge? Any fantastic technology is allowed, just as in omnipitent designers any fantastic way of being all knowing and all causing is allowed. There are no constraints, even though the wording makes it sound like reasonable constraints are being offered.
quote:
That depends on what you think the competing hypothesis is supposed to be. Consider any police investigation. If Jones is the murder suspect, it doesn’t mean we can’t investigate the suspect unless we also come up with another competing suspect. The only hypothesis that needs to compete against Jones being the suspect is the hypothesis that Jones is not the suspect. If we turn to origins, it should be clear that the non-teleological explanations have never really competed against teleological explanations.
But Mike, police work is based in large part in establishing motive, means, and opportunity. Miss out on any one of the three, and one has not drawn any reasonable inference. Your methods concentrate on motive, and leave means and opportunity as free variables, inelligible for study. Study them and problems occur with your methods. (By "motive" I mean in a more generic way that you look at "design" per se as something that humans do, without also looking at the fact that they have to be on location necessary to effect their acts, and at the time of their personal component of the actions. Mike studies "design" as an abstract "motivation" in what he sees in the flagellum, without allowing the factors of presence of the designer and opportunity to do such design to enter into consideration. It is a particular aspect of human behavior, to achieve "design" that I am relating to motive, because other aspects of motive are missing as well, like motive for making a flagellum in the larger step of such a fantastic sequence of extraterrestrial manipulation of Earth's history.)
I agree in a sense with Mike's statement, in that the issue is not strictly the "competing hypothesis". My analysis shows that Dr. Dembski was correct that having competing hypotheses is not sufficient. What is essential is having theory of how the event occurred with sufficient detail to eliminate or substantially reduce the effects of coincidence. Without theory of some sort to limit all of motive, means, and opportunity in police work, one would detain suspects on whim.
And there is an issue as well on just what "investigation" means. Mike might say that he is only "investigating" the design of flagellum. But what becomes serious investigation? When President Kennedy was shot, did all Republicans become suspects? Certainly not! Did we say, "Oh, there could have been space ships delivering shooters to the grassy knowl"? No, in police work we limited the investigation to people who existed, at least in "theory".
quote:
Attempting to approach the topic in a modest, systematic, and positive fashion hardly seems perverse to me.
Yes, I am waiting for the modest, systematic, and positive presentation of the means, motive, and opportuntiy for human-like intelligence to design the flagellum.
[ 07. December 2003, 13:15: Message edited by: gedanken ]
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Nel
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posted 07. December 2003 13:56
Ged
Without any limitations on that technology, there is no difference in terms of the unconstrained and unknown nature of the prior joint probabilities of the designer effecting the event--thus there is no way to pinpoint the reliability of an "explanatory filter" like inference. If you allow for "human like" designers to swoop in at arbitrary times with their space ships, how have you limited the prior probabilities in any way based on knowledge? Any fantastic technology is allowed, just as in omnipitent designers any fantastic way of being all knowing and all causing is allowed. There are no constraints, even though the wording makes it sound like reasonable constraints are being offered.
The same is true in origin of life theories. And even in some areas of evolution. As is often pointed out, the argument is not whether it occurred, it's how it occurred.
For many in these fields, it doesn't really matter that all the details are known as to how the actual event occurred. What matters is how things look like.
For some scientists the DNA looks like rubbish, the work of a sloppy tinkerer and so a sloppy beginning seems to be a good explanation for it, even if they have no idea how it happened. For other scientists DNA looks like a miracle, a work of perfection. More so some designs look very much like human craftmanship: 
although far more advanced. And so design seems to be a good explanation for it, even if we have no idea exactly how it happened. It's just something you're accepting for the moment to see where it leads.
[ 07. December 2003, 14:10: Message edited by: Nelson-Alonso ]
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Rex Kerr
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posted 07. December 2003 14:17
A pine cone looks like a hand grenade from the outside. Even if you found a pair of pictures of a human-made motor and bacterial flagellum that actually looked quite similar to each other (I have trouble seeing it in these two), what are we supposed to infer?
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Nel
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posted 07. December 2003 14:22
A pine cone doesn't explode when you pull something from it.
What I infer from these two pictures (not necessarily just their appearance, but the functionality) is exactly what an expert in the field (not suprisingly) indicated, that it looks like it was designed by a human.
[ 07. December 2003, 17:18: Message edited by: Nelson-Alonso ]
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gedanken
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posted 07. December 2003 14:35
quote:
... There are no constraints, even though the wording makes it sound like reasonable constraints are being offered.
The same is true in origin of life theories. And even in some areas of evolution. As is often pointed out, the argument is not whether it occurred, it's how it occurred.
Hi, Alonso,
But I see that you avoided my question by changing the subject.
you said that "The same is true in origin of life theories", but this is not at all the case. I think you may have missed some subtle aspects of my point about "theories", and how they avoid the problem of coincidences in the explanatory filter.
You see that the explanatory filter must control for coincidences. This is why Dr. Dembski introduced the "ProbRes" factors. Without those factors, reducing the "alpha" cutoff probability, then an inference of "design" would occur with coincidental combination of just picking a seemingly related topic from all of human knowledge, and of picking one of many possible choices of features to compare that humanly related topic to. If the number of choices of those two aspects are high, then there are many opportunities to pick a coincidence (such as seeing a face in clouds), so the "ProbRes" factors are needed to control for those coincidences.
But the EF amplifies any unknown distributions just as much as it amplifies the known "chance" distributions by the factor of M*N from "ProbRes" factors. That is why Dr. Dembski is correct in NLF page 103, where he shows that simply finding the "best explanation" in a purely Bayesean sense is not sufficient. (Shown with an urn example, in which comprares two unlikely causes, but where some third explanation is surely much more reasonable, yet the "best explanation" comparison of only those two causes favors one of those two unlikely causes).
The only way ouf of this problem, however, is to pose actual theory of events, so as to control for coincidence. By posing actual theory, one reduces the "ProbRes" factors M and N, rather than just leaving them around causing amplification of unknown as well as known distributions. Because only with theory do we have any way to mitigate the possibility that we have simply chosen aspects to compare out of thin air.
As to OOL research, that is entirely about theory of how different sequences of events could relate. Of course I have no way to compare the probability of space ships coming down to deposit first life, and relationships being researched in OOL theory. I don't know if that is high, or low probability, so I have no way to make a comparision. So I have no way to find out if the EF would be a reliable inference procedure in that case. As such, it is inherently unreliable, since it cannot be shown to be based on reliable input factors. The opportunities for coincidence, of picking the electric motor's picture from all of human knowledge, and a particular view of the details of how the flagellum rotates--these are entirely subject to coincidence for which "ProbRes" factors must be applied.
I am waiting for the modest, systematic, and positive presentation of the means, motive, and opportuntiy for human-like intelligence to design the flagellum.
[ 07. December 2003, 14:44: Message edited by: gedanken ]
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