I don’t know what Swamidass is suggesting, but I suggest that you read the relevant papers about evolution of flagella (plural). You see, there are two with different “designs.”
The use of the singular article is an easy tipoff that the user has never gone beyond Behe.
Have you looked for yourself? Behe doesn’t even tell you that there are two different flagella.
There are far more than just 2 @mercer, far more.
Could you provide references?
To what? The answer, also, is “no”, unless there is a good reason too. Why is it material? It is also easy to find them with Google searches.
The simpler flagella and the intermediate steps between TTSS and those flagella.
Not till we deal with this:
Oh c’mon. I supplied all the articles to Moran/Behe and Miller/Behe.
Flagellum1 is composed of 20 different proteins.
Flagellum 2 is composed of 19 different proteins, but none of the 19 are the same as any of the 20 proteins in Flagellum 1.
Flagellum 3 is composed of 19 different proteins, and all of them are the same as the 20 proteins in Flagellum 1, except for the 1 missing protein.
If (2),then Flagellum 1 may or may not be IC.
If (3), then Flagellum 1 is not IC.
May I have the references now?
Not yet, not till you recognize that you have left the IC1 definition, because it is not serviceable. Look what you wrote…
Notice, that in the IC1 definition, there is NO consideration of intermediates. The total number of parts also is not relevant, but the IC core. We would remove parts from these flagellum, to determine the minimum number of parts that still had some function in moving the cell. That mininum number is the degree of IC.
At no point does IC1 consider intermediate states.
At no point does IC1 consider other functions.
As soon as you want to take these into account, we are no longer dealing with IC1. If you think it is possible a valid objection can arise from this, then you have to also admit that IC1 is not a valid argument against evolvability. As Behe put it, it is merely a non-rigorous way of explaining things to the public.
Until we agree that IC1 is invalid, there is no point in moving on to the next point. It is too bad really if that is the case. There is a beautiful example of a 7 part movement mechanism, which might have an IC1 degree of just 2 or 3. That would be fun to show you! I hope we can get there.
For me the tip-off that these arguments are wrong was very simple; I noted that the Likelihood Ratio for the model I happen to be working on was far smaller than the Borel Limit or Universal Probability Bound claimed to be “Impossible”. Either I encounter the impossible on a regular basis, or someone is doing their math wrong.
I like this paper on the topic:
From The Origin of Species to the origin of bacterial flagella
https://www.nature.com/articles/nrmicro1493
In particular, Table 1: Homologies of flagellar proteins, lists the proteins in the flagellum, which can be removed without destroying the motility function, homologies to other proteins within the cell, and references to source materials.
The Nature copy is paywalled. Here is an open access copy from U. Cal Berkeley, Nick Matzke’s alma mater.
From The Origin of Species to the origin of bacterial flagella
Thanks! Sometimes I don’t remember to check for the paywall.
Dr. Swamidass, I’m afraid I don’t follow your point. If there is a flagellum of 19 proteins, then the flagellum of 20 proteins (19 of which are the same) is not IC. If we can remove parts from the 19 protein flagellum and it still functions, then the 19 protein flagellum is not IC.
But I don’t understand why you think this is at all relevant to the question of whether or not there is a plausible evolutionary pathway to the bacterial flagellum. And I don’t understand why you want to withhold information.
You say there is a 7 part system that has movement. Great. Do you think it was a precursor to the bacterial flagellum?
Hmmm. What is the definition of IC1 are you using? Do you know what an IC-core is?
I’m using the same definition that Behe uses. An IC-core would be the parts that are necessary for the functioning of a system.
I’m beginning to suspect that the problem is that you don’t think Behe allows for exaptation. If so, that is not the case. Behe made it very clear in DBB that IC systems could evolve indirectly from other systems - in other words, exaptation.
So let’s apply that to the idea of a 20 part flagellum. Suppose we already had a 19 part system that performed an entirely different function. But those 19 parts, when combined with a 20th part were the exact ones needed to form a flagellum. Since Behe already allows that organisms can evolve one or two functionless proteins, this would be well within what he considers to be the limits of Darwinian evolution.
Of course, there might be other problems. From what I understand, flagella do not form by diffusion. There is a very ordered, step-wise process used to build a flagellum, where many other parts are needed. But perhaps one could say that the original flagellum was formed by diffusion and the process for building it evolved later.
And perhaps one could argue that all the parts for a flagellum exist in a cell, though they are found in numerous other systems, but through diffusion the original flagellum was able to form and provide a selective advantage.
So I think there may be ways plausible ways of explaining the random evolution of the flagellum, through exaptation. But if a minimum of 20 parts is needed for the flagellum to function, then I don’t think there would be a “direct” way to evolve it from a simpler flagellum.
Now you are changing his definition. He has written it out and explained it many times. The first two flagella both have an IC degree of less than 19. We do not know precisely how much because in your thought experiment we didn’t try subtracting parts. Why do you think the larger one is not IC? Of course it is. We do not look at homology when determining IC1.
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