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Author
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Topic: The Evolution of the Bacterial Flagellum
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Evan
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Member # 164
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posted 13. November 2003 23:41
Thanks, Claire. I would hope that at some time Dembski and others interested in ID would respond to some of the points I made. I appreciate your comment.
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Mike Gene
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Member # 149
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posted 14. November 2003 00:06
Evan,
I'm still processing. ![[Wink]](wink.gif)
And I'm still trying to figure out if the objective of Nic’s article to come up with a proposal for how the flagellum could have evolved? Or is it a hypothesis for how the flagellum did in fact evolve?
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charlie d.
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Member # 159
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posted 14. November 2003 10:34
quote:
And I'm still trying to figure out if the objective of Nic’s article to come up with a proposal for how the flagellum could have evolved? Or is it a hypothesis for how the flagellum did in fact evolve?
The difference escapes me. A hypothesis for how the flagellum evolved is a model (a proposal) of how it could have evolved, as far as I can tell. Or am I missing something?
[ 14. November 2003, 10:34: Message edited by: charlie d. ]
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gedanken
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Member # 594
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posted 14. November 2003 10:54
This (non)distinction is important to understand. The ID enthusiasts repeatedly discuss this sort of question. It is as though that science must be required to reduce the "answer" down to only one choice ultimately, and would have failed to be useful if there were still multiple choices.
But it is especially relevant to the "explanatory filter" and arguments that seem to relate. Because this sort of question can have an effect of leading the reader into thinking that science has not provided an answer of a pathway of high probability, if it provides a multitude of such pathways that in aggregate have relatively high probability.
This could be important in rhetorical argument, because in the ID movement the notion of relevance of the explanatory filter's "inference" of "design" to the flagellum. If high probability of an ensemble of pathways to the flagellum is shown, that would counter the input to the EF that the ID enthusiasts seem to think is so important. As I see it, the distinction is to make it seem that science has not come up with an answer after all showing that there are relatively high probability pathways, because such showing counters a most favored observation's possible "inference" of ID.
This all gets down to Dr. Dembski's post on updating the inputs to the EF when new information becomes available. (He seems to think that using the EF as predictor is unreasonable, and that the EF should only be judged based on its accuracy in terms of no false positives without regard to its past performance when the information we were "ignorant of" was still unknown. Argument from "ignorance" form?)
In essence the distinction is not real--but rhetorically it is the distinction between the information still being classified as "unknown" or being "known" for purposes of input to the EF. As long as it can rhetorically be claimed to be "unknown", the facade of meaningfulness of the flagellum to ID can be maintained. (Leaving option to update the inference later when it becomes more clear—saying that the EF did not fail with a false positive because the updated information is to be used for the EF at that point.)
[ 14. November 2003, 10:57: Message edited by: gedanken ]
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Mike Gene
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Member # 149
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posted 15. November 2003 11:37
I would think the distinction is important for several reasons. For example, establishing the possibility of the flagellum’s evolution does not transfer to the historicity of the event. History, by definition, is loaded with possibilities that were never actualized, so much so that there is only one actual history, yet a near infinite number of possible histories. If one is going to propose a historical hypothesis, you don’t support it with the reduced burden of proof that is required to argue that something is merely possible.
On the other hand, if the model attempting to describe how the flagellum evolved fails, what becomes of the “could have evolved” claim?
Nevertheless, I am going to focus on the historical essence of the hypothesis to determine how well it is supported. Remember, homology, by definition, is a claim about actual history.
As for the perception that Dembski is demanding a level of mechanistic detail that is too precise, I would note this is a sword that cuts both ways. The main beef with Dembski’s reply is that he is demanding things that science cannot recover. Yet one of the most common criticisms against the hypothesis of the design of the flagellum is that design theorists have not been able to recover the identity of the designer or the methods the designer used to bring the flagellum into existence. Yet even if the flagellum was designed, I fail to see how science would recover this information.
As for Dembski’s use of the term “locus on a gene,” it is quite true that in biology, the term is used as Matt says. Yet the term locus was clearly co-opted from common language, where is simply means “the place where something is situated or occurs.”
And while Dembski’s use of the term is not common, others have used it as he did:
Allozymes are defined as different allelic forms of an enzyme that share the same catalytic activity and are produced at a single locus on a gene (Harris and Hopkinson, 1976; Acquaah, 1992).
Here
It is well-known that error processes in viral replication generate mutations of HIV-1. These can occur as point mutations at a particular locus on a gene, as hypermutations with up to 700 substitutions for each round of replication, or as recombination which usually results in about three errors per round of replication. Here
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charlie d.
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Member # 159
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posted 15. November 2003 12:17
quote:
Mike:
I would think the distinction is important for several reasons. For example, establishing the possibility of the flagellum’s evolution does not transfer to the historicity of the event. History, by definition, is loaded with possibilities that were never actualized, so much so that there is only one actual history, yet a near infinite number of possible histories. If one is going to propose a historical hypothesis, you don’t support it with the reduced burden of proof that is required to argue that something is merely possible.
Uhm, I thought the issue of whether the flagellum could have evolved was put to rest a while ago: even Dembski and Behe admit as much, arguing instead that the issue is that we don't have (well, didn't until Nic's article) explicit, testable and detailed proposals about how it evolved (although of course Nic's proposal is not detailed enough for Dembski). I imagine that's what the new definition of "strong" IC (vs, I gather, the more common "weak" form), recently made by Dembski is all about (here, I am not sure whether anyone spelled that difference out before). "Weak" IC, as in the flagellum, the complement system, etc, could in principle have evolved, but we don't know exactly the details yet. "Strong" IC system, of which Dembski gives no example, could not have evolved in principle.
So, again, I think whether Nic is putting out a model of how the flagellum did evolve, or could have evolved, is the same exact thing. If the model is rejected on the basis of some piece of evidence, either the model will need to be modified accordingly, or a completely different model put forward. At the same time, Nic's predictions regarding homologues and structural relationships will need to be tested to see if the model has any predictive value, compared to alternatives (assuming there are any). What else is science about?
[ 15. November 2003, 12:21: Message edited by: charlie d. ]
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Pim van Meurs
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Member # 541
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posted 15. November 2003 12:27
Mike: As for the perception that Dembski is demanding a level of mechanistic detail that is too precise, I would note this is a sword that cuts both ways. The main beef with Dembski’s reply is that he is demanding things that science cannot recover. Yet one of the most common criticisms against the hypothesis of the design of the flagellum is that design theorists have not been able to recover the identity of the designer or the methods the designer used to bring the flagellum into existence. Yet even if the flagellum was designed, I fail to see how science would recover this information
Since the issue is not the design in nature but the nature of the designer, who or what ARE the important questions. So far NO evidence of the designer(s) has been proposed beyond natural evolutionary mechanisms which does seem to place ID in an awkward position. Does the sword cut both ways? Not really since the argument is not that ID's mechanisms are not detailed enough but that they are totally lacking.
Nic's contribution is that he has shown plausible and historically defensible mechanisms to explain design in nature.
I think Mike has hit the nail on the head though that even if the flagellum were intelligently designed, the lack of theoretical foundations to detect this without resorting to motives, means, opportunity etc, results in ID being somewhat disadvantaged here. Especially when natural mechanisms and pathways can be identified. Gedanken has done a great job showing that motives are essential in a intelligent design inference
[ 15. November 2003, 12:49: Message edited by: Pim van Meurs ]
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nobody
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Member # 145
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posted 15. November 2003 14:15
Mike Gene says:
quote:
1. one of the most common criticisms against the hypothesis of the design of the flagellum is that design theorists have not been able to recover the identity of the designer or the methods the designer used to bring the flagellum into existence.
2. Yet even if the flagellum was designed, I fail to see how science would recover this information.
1. The identity of the designer, or the methods used, are irrevelant to the question of whether any particular thing has been designed or not.
2. That's why the constant demand for the identity of the designer is bogus. It's beyond the limits of science. We can state that the designer had a level of technology beyond current human capability. But that's not enough for some people because that leaves open the possibility for God to be Designer Version 1 and also for the alleged aliens, that are supposedly millions of years more advanced than humans, to be Designers Version 2. The Raelians have already chosen Designers Version 2. I expect that mainstream science will eventually adopt that position as well, because of the high level of opposition against God among some of the most vocal evolutionists.
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Pim van Meurs
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Member # 541
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posted 15. November 2003 18:32
Nobody: 1. The identity of the designer, or the methods used, are irrevelant to the question of whether any particular thing has been designed or not.
I disgree, since we can all agree that design (whether apparant or intelligentin nature exists, thus it is the nature of the designer(s) which is the real issue.
Nobody: That's why the constant demand for the identity of the designer is bogus. It's beyond the limits of science.
On the contrary, science has quite succesfully dealt in proposing designers. Evolutionary theory includes variation, selection and many other fascinating aspects.
Identifying the designer(s) IS the issue.
Francisco Ayala argues as follows:
quote:
The third proposition is that teleological explanations are necessary in order to give a full account of the attributes of living organisms, whereas they are neither necessary nor appropriate in the explanation of natural inanimate phenomena. I give a definition of teleology and clarify the matter by distinguishing between internal and external teleology, and between bounded and unbounded teleology. The human eye, so obviously constituted for seeing but resulting from a natural process, is an example of internal (or natural) teleology. A knife has external (or artificial) teleology, because it has been purposefully designed by an external agent. The development of an egg into a chicken is an example of bounded (or necessary) teleology, whereas the evolutionary origin of the mammals is a case of unbounded (or contingent) teleology, because there was nothing in the make up of the first living cells that necessitated the eventual appearance of mammals
Link
See also Ruse's lastest book "Darwin and Design", an excellent read on these issues.
[ 15. November 2003, 18:44: Message edited by: Pim van Meurs ]
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Mike Gene
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Member # 149
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posted 16. November 2003 12:19
If it is true that the ability to infer/detect design is dependent on previous knowledge about the identity, motives, and methods of the designer, then we have simply uncovered yet another limitation of science. This would mean that even if the flagellum was indeed designed, science would not be able to recover this truth. And since the human brain is quite uncomfortable with things that are left unexplained, science would be obligated to come up with an alternative explanation.
And that takes us back to the historical narrative. Historians have long noted that to one degree or another, the historical narrative is partly a function of the story teller. Thus, if we tell a story about the distant past without the ability to detect design, it stands to reason that our story will not contain design. It’s not that design is ruled out. It’s just never figured into the narrative. There is nothing inherently wrong with this. But many people overlook this simple fact that often times confuse the story with the actual past. The story may reflect the actual past. Then again, it may not. If the critics of design are correct, we have no way of knowing.
A nice illustration of this concerns the concept of homology as it relates to gene products. Homology, by definition, is a historical claim. It asserts that similarity is traced to common descent, that is, a historical lineage. Now, if we have no way of detecting design, then similarities can only be explained in the following ways: the outworking of natural law, convergent evolution, coincidence, or common descent (homology). To detect homology, we can simply rule out the three other alternatives. How do we do this? With an informal method not all that different from the EF. We intuitively rule out coincidence and natural law/convergence if the similarities are too many (specification) amidst a large complexity. Thus, for example, Nic thinks that the sequence similarity between FliI and the beta/alpha subunits of the F0F1 ATP Synthase “prove” homology. The similarities are too many to explain by coincidence and convergence and natural law is not known to channel any sequence into a specific arrangement.
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. In other words, the very analysis we need in order to detect homology without consideration of design itself fails to distinguish homology from design. None of this invalidates the homology inference, but it is important to remember this consideration when weighing homology-claims used in a context of design vs. non design (something science does not address).
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nobody
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posted 16. November 2003 12:49
Mike Gene points out:
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The logic of this would involve the notion that any designer would never reuse a design in any other form or any other context.
Correct. Except we can immediately see that the restriction you describe would be illogical for an intelligent designer.
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Mike Gene
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posted 16. November 2003 13:40
Sure, that's the point. But on the flip side, the problem with the ‘common design’ type of argument is that it is overly ripe for ad hoc use. The task for the design theorist is to come up with some form of methodological constraints for its use.
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Rex Kerr
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posted 16. November 2003 14:43
Mike Gene said:
quote:
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. In other words, the very analysis we need in order to detect homology without consideration of design itself fails to distinguish homology from design.
But this is not solely how homology is detected.
Homology makes a host of predictions: closely related species have a majority of highly related genes while distantly related species have lower homology and fewer detectable in common; when function is preserved, functionally silent residues diverge before functionally important ones; if A and B have genes thought to be homologous and C is more closely related to A than B, then it is likely that C will have the same gene, and if it does, it will be more similar to the gene in A than the one in B.
All of these predictions and more are verified routinely. It is not simply a case of homology-by-ruling-everything-else-out. Rather, in cases where homology is expected to leave a signature, we see the signature. It is overwhelmingly the method leading to similarity between genes in different species.
Unless something weird has happened, this was true in the past, but over sufficiently many generations, the signature becomes illegible. However, while this does call for a reduction in one's confidence in homology as an explanation, alternatives still need to present some pretty compelling evidence in order to be worthy of serious consideration. Horizontal gene transfer is one of those worthy of serious consideration because the signature of HGT looks sufficiently different from that of homology to be able to detect it even in (some) ancient cases. (Plus, we see modern instances of it, so we know it can happen and what it looks like when it does.)
There's something rather perverse about the ID movement's (perhaps unintentional?) focus on extremely ancient biological structures. They have picked systems where there is likely to be the least evidence of anything, due to the vast amount of time that has elapsed since the origin of the systems. It is almost as if they don't want to know the answer, and are picking those systems where anything they say will be the most difficult to refute (because it is difficult to say anything with confidence). Perhaps this is accidental; most of the protein complexes that have been studied have ancient origins, so if you pick them without regard to testability, you'd probably end up in the current situation. But as fascinating as the flagellum is, it'd be much better for ID proponents to focus on something recent, something where the signatures of evolution could be seen and shown to be lacking.
I don't have a suggestion for which system this should be. Blood clotting would be a natural choice, but Dembski seems to be backing off from blood clotting as an irreducibly complex system. Perhaps developmental factors esp. those leading to the differentiation of the mammalian brain could be studied?
In any case, I do actually agree with Mike Gene. The analysis we need to detect homology in extremely ancient systems may well fail to distinguish homology from design. This is not a good way to advance a competing hypothesis--apply it in cases where it cannot be distinguished from the dominant hypothesis on the basis of the evidence!
[ 16. November 2003, 14:45: Message edited by: Rex Kerr ]
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Pim van Meurs
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posted 16. November 2003 15:03
Mike: If it is true that the ability to infer/detect design is dependent on previous knowledge about the identity, motives, and methods of the designer, then we have simply uncovered yet another limitation of science. This would mean that even if the flagellum was indeed designed, science would not be able to recover this truth. And since the human brain is quite uncomfortable with things that are left unexplained, science would be obligated to come up with an alternative explanation.
That is an interesting description of an eliminative approach. However science has the advantage that it does not have to rely on this, instead it can propose plausible designers. Is Mike arguing that the present ID approach may be wanting scientifically since it cannot deal with issues of designers? It seems to me that Mike is repeating the observation by Del Ratzsch that the design inference is incapable of inferring new design. But rather than seeing this as a limitation of science it seems to be a limitation of the approach.
quote:
So typically, patterns that are likely candidates for design are first identified as such by some unspecified ("mysterious") means, then with the pattern in hand S picks out side information identified (by unspecified means) as releavant to the particular pattern, then sees whether the pattern in question is among the various patterns that could have been constructed from that side information.
What this means, of course, is that Dembski's design inferene will not be particularly useful either in initial recognition or identification of design
p. 159 Del Ratzsch Nature design and science
In fact the flagellum being designed is not the issue, its the nature of the designers which are of interest to science. In fact science has, despite claims by Mike that it could not uncover the truth, done much to explain the design of the flagellum. If Mike believes that there exists a better design explanation then I am looking forward to a discussion of such. But if I am not mistaken, Mike does accept the regularity/chance pathways as the designer(s) of the flagellum? Instead Mike proposes that there may have been some front loading in the distant past?
In other words, Mike's argument that science has no way of detecting design is wrong on many levels. Science is quite capable of detecting design and even instances of intelligent design quite well. Nic has proposed a very interesting scenario, perhaps Mike would like to propose a similar scenario which would help us compare an intelligent designed hypothesis versus Nic's?
Mike: The logic of this would involve the notion that any designer would never reuse a design in any other form or any other context.
In fact for an evolutionary designer, the reuse of design seems to make sense but among intelligent designers we often see a reluctance to reuse elements in another form or context. Which is evidenced for instance by the existence of degeneracy in biology and redundancy in engineering. Not that I am arguing that a designer COULD not reuse design but that issue seems to deal with motives...
Rex Kerr states: "In any case, I do actually agree with Mike Gene. The analysis we need to detect homology in extremely ancient systems may well fail to distinguish homology from design.This is not a good way to advance a competing hypothesis--apply it in cases where it cannot be distinguished from the dominant hypothesis on the basis of the evidence!"
Which is one of my basic objections to such ideas as front loading since it merely displaces the issue to an instant perhaps beyond our reach.
Mike: If the critics of design are correct, we have no way of knowing.
I think the critics of (intelligent) design rightly point out that an intelligent design inference requires something more than plausibility for it to be able to compete as a scientific hypothesis. Intelligent design is not ruled out because it is implausible, but because of the lack of evidence to allow it to be tested as a scientific hypothesis. Is Mike suggesting that the absence of such evidence is inherent to an intelligent design inference? I would disagree strongly with Mike if that were his position.
[ 16. November 2003, 15:19: Message edited by: Pim van Meurs ]
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charlie d.
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posted 16. November 2003 16:59
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nobody:
Mike Gene points out:
-------------------------------------------------The logic of this would involve the notion that any designer would never reuse a design in any other form or any other context.
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Correct. Except we can immediately see that the restriction you describe would be illogical for an intelligent designer.
but since the designer for some reason seems indeed extremely reluctant to reuse the same design in distantly related organisms (eg, very differently designed flagella for motility of bacteria, archea and eukaryotes; different antifreeze proteins in arctic fish species, different crystallin proteins, etc etc - dozens of similar examples), the lack of logic of it all does indeed raise quite a conundrum.
[ 16. November 2003, 16:59: Message edited by: charlie d. ]
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