Wesley R. Elsberry
Posts: 4966
Joined: May 2002
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For example, Scott Minnich, microbiologist at the University of Idaho, testified at the Dover Trial about his knockout experiments which found that the flagellum is irreducibly complex with respect to its 35 or so genes.
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Minnich did testify that he did the work:
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Q. Break down for us further this concept of mutagenesis, and I believe you have a slide --
A. Sure. All right. 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.
Q. Do you have some examples employing this particular concept of the flagella?
A. I do, in the next slide. Hopefully this will cut to the chase and show you what we're talking about. This is an organism that my students and I work on. This is a petri dish about 15 millimeters size, filled with this soft auger food source for the organism. It's soft in the sense the organisms can swim in it, but it has some rigidity that they just don't slosh around. Now, each one of these areas showing growth were inoculated with a toothpick of cells, the wild type parent here. So this is yersinia enterocolitica, a good pathogen, double bucket disease if you ingest it.
Q. That's the center?
A. Yeah, that's the center, okay? So it can swim. 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 auger, 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.
Q. I'm sorry, just so we're clear on the record, the two you're talking about on the bottom left, the first one was the bottom left and the second one was the bottom right?
A. Right.
Q. Where you took away a portion of the flagella?
A. 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.
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I don't know whether Minnich's knockout studies in particular have been published. From the testimony, it is unclear whether Minnich did knockout work on anything but Yersinia enterocolitica.
As the Matzke and Pallen review paper notes, though, there are all sorts of bacterial flagella out there, and a protein knockout in one that disables function does not necessarily do so in another, the bacteria don't all rely on the exact same proteins in their flagella, and various proteins used in flagella can be shown to be related to proteins doing other jobs in bacteria. Once you account for the ways in which a protein may not be necessary to function or able to be co-opted from other functions in the ensemble of all studied bacterial flagella, you are down to two proteins without currently known antecedents that are necessary to flagellar function. One wonders why Logan Gage isn't up on *that*.
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"You can't teach an old dogma new tricks." - Dorothy Parker
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