(2017-12-12, 02:09 AM)Paul C. Anagnostopoulos Wrote: [ -> ]This is all very nice, but aren't we getting ahead of ourselves? Can you name an irreducibly complex biological mechanism that we can focus on?
The flagellum is not IC. Again, can we pick something that is?
Not according to Scott Minnich’s genetic knockout experiments on the E. coli flagellum. These experiments have shown that it fails to assemble or function properly if any one of its approximately 35 structural parts are missing.
Excerpts from Minnich's sworn testimony at the Dover trial (
article):
"I work on the bacterial flagellum, understanding the function of the bacterial flagellum for example by exposing cells to mutagenic compounds or agents, and then scoring for cells that have attenuated or lost motility. This is our phenotype. The cells can swim or they can’t. We mutagenize the cells, if we hit a gene that’s involved in function of the flagellum, they can’t swim, which is a scorable phenotype that we use. Reverse engineering is then employed to identify all these genes. We couple this with biochemistry to essentially rebuild the structure and understand what the function of each individual part is. Summary, it is the process more akin to design that propelled biology from a mere descriptive science to an experimental science in terms of employing these techniques.
[…]
So it was inoculated right here, and over about twelve hours it’s radiated out from that point of inoculant. Here is this same derived from that same parental clone, but we have a transposon, a jumping gene inserted into a rod protein, part of the drive shaft for the flagellum. It can’t swim. It’s stuck, all right? This one is a mutation in the U joint. Same phenotype. So we collect cells that have been mutagenized, we stick them in soft agar, we can screen a couple of thousand very easily with a few undergraduates, you know, in a day and look for whether or not they can swim.
[…]
We have a mutation in a drive shaft protein or the U joint, and they can’t swim. Now, to confirm that that’s the only part that we’ve affected, you know, is that we can identify this mutation, clone the gene from the wild type and reintroduce it by mechanism of genetic complementation. So this is, these cells up here are derived from this mutant where we have complemented with a good copy of the gene. One mutation, one part knock out, it can’t swim. Put that single gene back in we restore motility. Same thing over here. We put, knock out one part, put a good copy of the gene back in, and they can swim. By definition the system is irreducibly complex. We’ve done that with all 35 components of the flagellum, and we get the same effect."
(Kitzmiller Transcript of Testimony of Scott Minnich pgs. 99-108, Nov. 3, 2005)
During this testimony, Scott Minnich showed slides in the courtroom documenting his own research experiments, which performed knockout experiments on the flagellum, and experimentally found that the flagellum is irreducibly complex.
Quote:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1943423/
This 2007 paper you cited documented research that investigated a number of alternate forms of flagella in different bacteria. It hardly refutes the irreducible complexity of the flagellum. They found a conserved core of flagellar proteins and corresponding basic structural components. They incorrectly claim that received opinion in the profession is that flagella arose from an early ancestral T3SS secretory system.
Pallen and Matkze in their contemporaneous research paper (
https://pdfs.semanticscholar.org/2a95/2f...6c3ee3.pdf) admit that
“all (bacterial) flagella share a conserved core set of proteins,” numbering around 20 proteins, and they further concede that there is a common core of subsystems found in known bacterial flagella (See
this article):
"Three modular molecular devices are at the heart of the bacterial flagellum: the rotor-stator that powers flagellar rotation, the chemotaxis apparatus that mediates changes in the direction of motion and the T3SS that mediates export of the axial components of the flagellum."
Despite all the apparent diversity of flagella they admit that all bacterial flagella share a conserved core of about 20 proteins, and a common core (what could be called an irreducible core) of subsystems: a motor, a chemotaxis mechanism, and a secretion apparatus. It seems like the many diverse types of flagella are variations on a common thematic archetype.
After claiming that the flagellar system initially evolved from an ancestral T3SS system (untenable because it almost certainly came at least a billion years after the flagellum) they concede that the flagellar apparatus in the various different bacteria still had a barrier to gradual evolution that they claim will ultimately be explained by exaptation. We're still waiting for the detailed testable model.
And we know this core is irreducibly complex (per Behe's definition) through Scott Minnich's research.
Quote:I won't worry about the rest of your post until we have picked an IC mechanism. But I will come back to it.
Also, could we decide on which definition of IC we're using? For example, is an IC mechanism one which, when reduced, does not maintain its original function or does not have any function? Here are four definitions:
http://www.asa3.org/ASA/education/origins/ic-cr.htm
"Demonstration that a system is irreducibly complex is not a proof that there is absolutely no gradual route to its production. Although an irreducibly complex system can't be produced directly, one can't definitively rule out the possibility of an indirect, circuitous route."
---Behe, 1996
~~ Paul
Michael Behe's original definition of irreducible complexity, in Darwin's Black Box, page 39, 1996: An irreducibly complex biological system is "...a single system which is composed of several well-matched, interacting parts that contribute to the basic function, and where the removal of any one of the parts causes the system to effectively cease functioning." Perhaps this could be called functional irreducible complexity. However, as you noted, Behe conceded that even if a system is irreducibly complex in this way and thus could not have been produced directly except by a miracle, one cannot definitively rule out the possibility of an indirect, circuitous route of many steps using conceptual mechanisms like scaffolding, coevolution and co-option or exaptation. There is no strictly logical barrier against this. It's a matter of plausibility. As the complexity of an interacting system increases, the likelihood of such an indirect route drops precipitously.
The bacterial flagellum was identified by Behe as such a system.