``Even if we do not yet understand how certain naturally occurring structures such as this develop. Is it prudent to conclude there was an intelligent designer? Doesnt this just smack of god of the gaps rationale?''
Well, I'm a bit loathe to write in defence of something that I don't really support myself, but I'll try to represent the irreducible complexity argument as best I can
Other people can do it much better.
The basis of IC is not that we don't understand how certain biological structures developed, or even that they are too complex to have arisen by Darwinian processes, but that IC structures have no simpler functional precursors. Classic neo-Darwinism requires that every biological entity have a simpler functional precursor, because non-functional structures do not contribute a selection advantage in their current generation. Structures that are alleged to be IC are not all that complex compared to, say, the cell replication machinery. They are complex in a very particular way. Of the 200 or so proteins that comprise the flagellum, it appears that every single one is essential to its proper function. The flagellum has to cross the cell wall, which means that it needs a very complex mechanism even to extrude its components through the wall. Then these components have to be assembled in a very particular way, so that about a hundred different proteins can interact in such a way as to rotate the whole structure. Take one protein away, and the whole thing falls apart (metaphically speaking).
This is a different kind of complexity than that possessed by, say, the eye. You can take any number of bits away from the mammalian eye while still maintaining something that produces some sort of selectional advantage. Even a single light-sensitive cell might provide some selectional advantage. Not much, but you don't need much. But take anything away from the flagellum, and you ain't got nothing.
There was a certain amount of rejoicing among opponents of IC (i.e., more-or-less everybody) when it was found that the genes coding for the type-III secretory system had homologies with the genes coding for the flagellum. Irritatingly, however, the balance of authority even among IC sceptics is that the TTSS devolved from the flagellum.
I think that the IC argument is quite a bit different from a classical `argument from ignorance', in that it asserts that IC structures, as a matter of principle, have no functional precursors. That may or may not be true, but either way I don't think it reduces to an argument from ignorance. It will need a lot more research to determine whether the fundamental tenet of IC is true or not, and it's difficult, time-consuming, and above all expensive research, so it will probably not get done.
The reason I don't fully buy into IC is that we don't really understand how mechanisms like cooption affect it. It could be argued that, although the flagellum has no functional precursor as a flagellum -- because it wouldn't work -- it has a functional precursor as something completely different. There's little doubt that cooption does occur, but it's not clear whether something as complicated and, above all, specialized as the flagellum can be the result of cooption. Opponents of IC, as I understand it, claim that the flagellum must result from cooption, because otherwise neo-Darwinism is wrong. Proponents claim that the burden of proof is on the opponents to show even one example of cooption of a specialized micro-structure that would serve as a template for the flagellum. That, I think, is the current stalemate.
While IC isn't a `science' in its own right, it's something that has to be accomodated within the prevailing evolutionary model, or explained in terms of it. I reserve judgement on which outcome is most likely
Until one of those two things happens, I believe it is intellectually dishonest to present the neo-Darwininan model of evolution as without any credible scientific objection. Sigh... people are going to start accusing me of being a `creationist' for even contemplating such a thing 
For all that, I can imagine few things worse than trying to teach the principle of IC in a school biology classroom. It's difficult enough to explain the most rudimentary facts of cell biology even to undergraduate medical students.
For what it's worth, although `intelligent design' proponents tend to be religious believers, there is at least one person doing research in this field (whose name escapes me) who claims that life was seeded on earth from space by a bunch of alien genetic engineers. Ironically, this is essentially the same argument that Francis Crick used to account for the insufficient length of time for which the Earth has been hospitable to DNA
Best wishes
MadBear
Well, I'm a bit loathe to write in defence of something that I don't really support myself, but I'll try to represent the irreducible complexity argument as best I can
The basis of IC is not that we don't understand how certain biological structures developed, or even that they are too complex to have arisen by Darwinian processes, but that IC structures have no simpler functional precursors. Classic neo-Darwinism requires that every biological entity have a simpler functional precursor, because non-functional structures do not contribute a selection advantage in their current generation. Structures that are alleged to be IC are not all that complex compared to, say, the cell replication machinery. They are complex in a very particular way. Of the 200 or so proteins that comprise the flagellum, it appears that every single one is essential to its proper function. The flagellum has to cross the cell wall, which means that it needs a very complex mechanism even to extrude its components through the wall. Then these components have to be assembled in a very particular way, so that about a hundred different proteins can interact in such a way as to rotate the whole structure. Take one protein away, and the whole thing falls apart (metaphically speaking).
This is a different kind of complexity than that possessed by, say, the eye. You can take any number of bits away from the mammalian eye while still maintaining something that produces some sort of selectional advantage. Even a single light-sensitive cell might provide some selectional advantage. Not much, but you don't need much. But take anything away from the flagellum, and you ain't got nothing.
There was a certain amount of rejoicing among opponents of IC (i.e., more-or-less everybody) when it was found that the genes coding for the type-III secretory system had homologies with the genes coding for the flagellum. Irritatingly, however, the balance of authority even among IC sceptics is that the TTSS devolved from the flagellum.
I think that the IC argument is quite a bit different from a classical `argument from ignorance', in that it asserts that IC structures, as a matter of principle, have no functional precursors. That may or may not be true, but either way I don't think it reduces to an argument from ignorance. It will need a lot more research to determine whether the fundamental tenet of IC is true or not, and it's difficult, time-consuming, and above all expensive research, so it will probably not get done.
The reason I don't fully buy into IC is that we don't really understand how mechanisms like cooption affect it. It could be argued that, although the flagellum has no functional precursor as a flagellum -- because it wouldn't work -- it has a functional precursor as something completely different. There's little doubt that cooption does occur, but it's not clear whether something as complicated and, above all, specialized as the flagellum can be the result of cooption. Opponents of IC, as I understand it, claim that the flagellum must result from cooption, because otherwise neo-Darwinism is wrong. Proponents claim that the burden of proof is on the opponents to show even one example of cooption of a specialized micro-structure that would serve as a template for the flagellum. That, I think, is the current stalemate.
While IC isn't a `science' in its own right, it's something that has to be accomodated within the prevailing evolutionary model, or explained in terms of it. I reserve judgement on which outcome is most likely
For all that, I can imagine few things worse than trying to teach the principle of IC in a school biology classroom. It's difficult enough to explain the most rudimentary facts of cell biology even to undergraduate medical students.
For what it's worth, although `intelligent design' proponents tend to be religious believers, there is at least one person doing research in this field (whose name escapes me) who claims that life was seeded on earth from space by a bunch of alien genetic engineers. Ironically, this is essentially the same argument that Francis Crick used to account for the insufficient length of time for which the Earth has been hospitable to DNA
Best wishes
MadBear
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