I've been spending quite a bit of time debunking ID (Intelligent Design) arguments on various other blogs. This blog is for storing some of my longer arguments. I prefer to call ID 'Imagination Deficit' as I feel that better describes it.

Tuesday, June 20, 2006

Responding to Mike Gene

It's always a shame when someone closes an argument without allowing you to respond, as Mike Gene has done to this discussion at Telic Thoughts.

Mike seems to think I've been misrepresenting his arguments. I don't believe I have. But going round and round those claims again is not going to get us very far, so I'm going to stick to the actual claims that Mike is making for the science.

Mike said:

"Fine. You seem unaware of the context where I have been debating this issue for years, and a common argument was that the homology between the TTSS and flagellum suggested that the TTSS predated the flagellum (a point that you will ironically make below). If you think it important to distinguish between “a TTSS” and the TTSS that we observe and study, you should spell out their differences and why they are important."

Actually the point I am making is the same as the one made by Mike himself here (emphasis added by me):

"There is no evidence that anything like the type III system predated the flagellum."

Now, ignoring for a moment Mike's claim that there is no evidence, the key point in this sentence I would like to highlight is 'anything like'. To quote Mike again (same quote as above):

"If you think it important to distinguish between “a TTSS” and the TTSS that we observe and study, you should spell out their differences and why they are important."

Yes, this is vitally important. Because the claim being made by the scientists is that 'something like' the modern TTSS was involved in the evolution of the flagellum. Let's call it a simple, ancestral secretory system. So we have at least three structures we are interested in:

- a simple ancestral TTSS, which was precursor to both the flagellum and eventually the modern TTSS
- the modern flagellum which is probably a precursor to the modern TTSS
- the modern TTSS

And making a clear distinction between the known modern TTSS and the speculation of a simpler precursor system is extremely important to understanding how the evolutionary explanation works.

We revisit this exact point later on in Mike's reply, Mike quotes me as saying (emphaisis added by me here):

"Because, as is mentioned in your paper, "several proteins of the flagellum's basal body are homologous to the secretory machinery of this export system". This is evidence that something like the type III system predated the flagellum. It's not conclusive - but it's still evidence."

To which Mike replied:

"See? You want to claim that the homologies are evidence that “the type III system predated the flagellum,” yet the evolution of the TTSS from the flagellum also accounts for the homologies."

Mike has got my claim wrong. I am claiming that the homologs - certainly some of them - are evidence that something like the type III system predated the flagellum.

Mike is bundling all the homologies into one group. There are multiple homologies between the modern TTSS and the modern flagellum. Some of the homologies suggest a distant ancestor precursor secretory system which is something like the modern one. Others amonst the homologies suggest that the modern flagellum predates the modern TTSS. By overgeneralising and bundling all the homologies into one the disctinction is being lost.

So there is in fact evidence that something like the modern TTSS predates both the flagellum and the modern TTSS. This can be seen from some of the homologies between the two modern systems. Other homologies suggest the order in which the two modern systems have arisen.

"If you think it important to distinguish between “a TTSS” and the TTSS that we observe and study, you should spell out their differences and why they are important."

I hope I have at least partly answered this. Nick Matzke's entire model rests on this distinction.

This next bit is my opinion and has nothing to do with any claims MikeGene may be making (just to make it clear!).

When we are trying to piece together the evolution of a complex structure that probably occurred many millions if not billions of years ago. When we are doing this we are obviously having to hypothesise tentative models. The whole point is that - having coming up with such a hypothesis - we can now test parts of it to see if it actually works. We have a starting point for more investigation. And if - or more likely when - we find some evidence that contradicts this hypothesis (after all, it's extremely tentantive at this stage) then we will be able to revise it, come up with some new predictions from the revised hypothesis and test it again.

And this is exactly how scientific investigations work. It can be that we will never fully model all of the steps in the evolution of the flagellum to our satisfaction, which won't stop us from trying to.

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