avocationist
Posts: 173
Joined: Feb. 2006
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This is a sort of run-on commentary:
Miller – The Flagellum Unspun
*Uses personal incredulity argument. Calls it sentiment. One demerit.
*Elevates imagination. Says that when a person cannot imagine something, it is a personal statement about their limitations. So lack of imagination is a personal failing. I’m going to agree that imagination can be important – for example Einstein’s theories of relativity – but imagination needs to lead to hard evidence. And there is more than one kind of imagination. Yes, imagination is a wonderful thing, but why does this branch of science seem so dependent upon it?
*States that the ID designer must act outside the laws of nature. This is not necessarily true and in fact I consider such notions absurd. Yet Miller’s God does do so occasionally.
*Miller states the flagellum is not IC because the Type III secretory system, which exists in other bacteria, contains similar proteins to those found in the base of the flagellum, and was probably co-opted to form the flagellum.
This really is the sum of his argument right here. The flagellum has 30-40 proteins, of which 10 are homologous with the type III system. (Unfortunately, that argument is now obsolete, being largely abandoned in favor of the idea that the Type III system is actually devolved from the flagellum instead. Mike Gene’s reasons why the Type III is not a precursor was removed for brevity but is available) However, the real problem with Miller’s argument is that he thought the Type III system was ever much of a refutation in the first place.
*Next, Miller states evolution is opportunistic and able to mix and match proteins. This is something I don’t understand and I invite enlightenment. My question basically revolves around: how does the information get into the genome to code at the right time and place for some sort of widget that is in use elsewhere. As Behe shows, in the cell everything is tightly controlled. Things aren’t out of place and hanging out looking for work. Just because various pieces are lying around in the garage, to make a functional system out of them requires insight, especially if 3 or more are to be put together at once. But even if we add only one new piece to an existing structure, how does this occur? Sure, the piece itself is available, and somewhere in the genome is the code to create it, but that still leaves the question of rearranging it to a new place. And it must fit exactly or be modified to do so. From Dembski’s response, quoting Bracht, “Old interfaces and binding sites must be removed and new ones must be created.”
*Then he says that because the Type 3 exists, and since that involved use of 10 proteins, and since it is itself functional, this disproves Behe’s contention that no parts of the flagellum can be removed without loss of function. Say what? Is he mixing up arguments here? The type 3 system is functional as a type 3 system and is also similar to the base of the flagellum, but if you remove that base, the flagellum is indeed nonfunctional. But Miller argues that if you remove a component – the Type 3 – and since it has a function of its own (which is arguably not true since the two are only homologous) that this disproves the IC of the flagellum.
I.e., the existence of the Type 3 disproves that the flagellum must be fully assembled before any part can be functional. To me, this completely misses the point and is a hollow victory. If this is important to Behe’s thesis, I am unaware of it. The main point of IC is that the parts all are necessary to the flagellum.
He thinks he has accounted for a subset of the flagellum (the type 3 unit) but that tells us exactly nothing about how the entire flagellar system got together with its 30-40 proteins. So Miller has 10 accounted for and that apparently works for him.
*He says for one IC system to contain another is contra the IC argument. He says if the flagellum contains smaller functional units it is by definition not IC.
It seems to me that it doesn’t matter, although IC is meant to meet Darwin’s challenge that if a system could be found which could not be built upon “numerous, slight, successive” modifications then Darwinism is refuted. However, I see no reason why one of those slight modifications couldn’t be a functional set from another system. And if it can’t, this is not against ID, but against Darwinism.
So right here we have 3 problems:
1.The Type 3 system probably is not a prior component that got co-opted.
2.Even if it was, Miller makes not even an effort to account for the other 20 or more proteins, and does not worry about it, apparently being satisfied with a semantic victory.
3.It certainly doesn’t strengthen Darwin’s argument for slight and successive modifications to insist that IC systems can have been cobbled together from units that originally served other purposes. In any case, it is improbable for them to get together whether by direct or indirect routes.
Behe and Dembski both argue that it is unlikely for evolution to cobble together an IC system, whether each protein component is added one by one, or if some additions consist of an entire group of proteins which are co-opted, such as the Type 3 system.
Of course, since we have no picture at all of the history of the flagellum, we cannot really know what sort of steps might have led to it, and whether it started out with its first components doing something else entirely, and at what point in the step-by-step process motility became the function. Were there 30 steps? 12? Did it become a motility device after 5 reincarnations? 10? The final step only?
If it was a step by step process toward motility, as per fish eyes paper ideal, and if at one point the Type 3 was taken in as a whole, I see no problem with that. On the other hand, if there were, say, 10 steps, and in each step a novel use was made by adding a widget and each time the growing-toward-flagellum had a completely different function until finally it became a flagellum – well! Wouldn’t that be something. And what I want to know is if a part gets co-opted, does that part also continue to function in the old way? I mean, it would still be needed for whatever it used to do right? So does production of that widget get doubled in the genome and built at two different places?
*Next, Miller states that Dembski has exaggerated the difficulties of the components coming together by dividing the process up into origination, localization (getting them together in the cell) and configuration (assembly). He points out that once you have a protein sequence, it self-assembles. There is some truth to this, but the problems of matching interfaces and incorporating the co-options into the blueprints are real. I am not sure if all proteins self-assemble, but at any rate the putting together of some systems require much chaperoning, and the assembly of the flagellum is one such. According to Mike Gene (and I'll look this up if anyone is intersted) the assembly of the flagellum may itself be an IC process.
*Now, Miller states that Dembski’s probability calculations regarding the likelihood of 30 or more proteins spontaneiously assembling themselves is too low because no one really thinks a flagellum has to be gotten together that way. He says that Dembski has ignored that the type 3 system contains nearly one third of the needed proteins.
It is surprising, however, that Miller finds this to be of more than small help. And keep in mind that the Type 3 system is now largely abandoned as a hopeful precursor. He has no other argument for how the entire thing would get together other than to say that Demski has followed a faulty reasoning by assuming that he can analyze the likelihood of the flagellum assembling itself since he has not taken into account that there might be unthought-of ways for it to do so. Actually, Dembski does acknowledge that very thing, but certainly this is an argument from ignorance! Also, it is an appeal for patience.
Miller is saying that although we indeed have absolutely no idea how it could get together, we should still assume that it could do so somehow, because if we are skeptical of that, then we are operating from a priori assumptions (that it can't). This argument, to me, goes both ways. It is great to keep in mind how surprising new knowledge can be, but at the same time, it is an appeal not to use the tols we now have to make coherent sense of the world. It is to say we really have no tools to evaluate how nature works, how natural law works, how chance and probability work, how intelligence interacts with reality.
*Next he mentions the complex Krebs cycle, which apparently is made up of proteins that also exist elsewhere in the cell. He quotes a paper which states it is a clear case of opportunism. In fact, in support of opportunism he quotes someone named Jacob as saying that evolution does not produce novelties from scratch but works with what already exists. Now here we have a problem. For somewhere, sometime, novelty must occur. And we really don’t know how it does. And Jacob also assures us that the Krebs cycle is the best chemically possible design.
*Miller now cites Dolittle’s refutation of the blood clotting cascade, but I have read the response to it and I am convinced that Dolittle has done little.
The take home lesson here is that there is way too much that we don't know about how life really works.
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