Some of the proponents of neo-darwinism have cited the type 3 secretory system as the aboriginal system from which the entire flagellum might have arisen through a gradual evolutionary process. The reason they cite the type 3 secretory system as a possible ancestor to the flagellum is that the structure of this roughly 10-part secretory apparatus does play a part in the flagellum itself during the assembly of the flagellum and it ends up also hanging around as part of the structure of the flagellum. To build a flagellum, you need a lot more than a type 3 secretory system or anything similar to it, but people have suggested that this is the ancestral form upon which all the other parts were added to build a full flagellum. They’ve suggested “The flagellum is not irreducibly complex. There was a simpler precursor system from which larger system eventually evolved.”
There are several different ideas about the evolutionary relationships that obtain between the flagellum as a whole system and the type 3 secretory system. One is that the type 3 secretory system is the aboriginal form – the ancestral form – from which the flagellum as a whole evolved.
Another closely related idea is that the flagellum and the type 3 secretory system co-evolved from some simpler common ancestor. Both of these would represent challenges to the Michael Behe thesis that the flagellum is irreducibly complex and did not arise through a series of gradual evolutionary steps in the standard Darwinian way. But there are two other possibilities. One is that the flagellar motor is the aboriginal system or the flagellum as a whole is the aboriginal system from which the type 3 system is a degenerative by-product. This would be the hypothesis of degenerative evolution where essentially what’s envisioned is that the flagellar system would have been there with its in his full glory its full 30 parts and its biosynthetic pathways and all of that but that some of the parts in some systems in some bacteria would have been lost such that the the secretory system would then perform this limited function of being a secretory device and it would have lost parts and lost the expression of genetic information.Another idea is that the two are completely independent, they had independent origins. So those are the four possibilities. The latter two possibilities – the idea of degenerative evolution or separate origins – are consistent with Behe’s theory of intelligent design in his claim that the flagellum as a system could not have arisen through a series of gradual evolutionary steps. Those are the four different hypotheses and the four possibilities for explaining the relationship between these two systems that we find in bacteria of many different varieties.
The interesting thing about this debate between Behe and his interlocutors who are advancing co-option is that the two different hypotheses generate different testable predictions and those predictions are helping us to decide whether Behe is right or whether his critics are right. For example, if the co-option idea is right and the flagella system is derived, if it has evolved from a simpler aboriginal system – in particular the type 3 secretory system – then when we find the type 3 secretory system in isolation, the genes that are responsible for building that system should be older than the genes that are responsible for building the flagellum as a whole. There are different ways of testing the relative ages of genes and these different methods are surprisingly yielding a conclusion that confirms Behe’s thesis rather than the co-option thesis. In particular, they’re showing that the genes for building the type 3 secretory system, when it occurs in isolation, are younger than the genes for building the flagella system as a whole, not older, which suggests that the flagella system was the aboriginal system and the type three secretory system is the derived system or the devolutionary byproduct of that aboriginal system.
One of the ways that we can measure the relative ages of genes or different sets of genes is by comparing the mutational density in those different sets of genes. These mutation density experiments will measure the degree of variation of homologous genes in different sets of genes. If there’s a lot of variation, it’s assumed that there were a lot of mutations, which would imply a lot more time had elapsed since the aboriginal genes were established. If the number of mutations is fewer, if the gene density is lower, then that would imply less age, less time has elapsed since those original genes were established. In the case of the flagellum and the type 3 secretory system, mutation density experiments have shown that the mutation density in the genes required for building the type 3 secretory system in isolation are much younger than the genes that are required for building the flagellum as a whole. Therefore we can conclude from that that the flagellum is a much older system and that the type 3 secretory system is to either derived from that or simply arose independently long after the fact. But in no case do those mutation density experiments suggest that the type 3 secretory system is the aboriginal system because the genes for building that type 3 secretory system are younger than those of the genes that are required for building the flagellum as a whole.
There’s another fascinating way that evolutionary biologists can assign a relative age to these two very distinct systems – the type 3 secretory system and the flagellum as a whole. That is by evaluating their phylogenetic distribution among various bacterial species. It turns out that the type 3 secretory system is only found in a very small subset of gram-negative bacteria. It’s not found in the gram-positive bacteria and it’s not found in all gram-negative bacteria. That suggests that it hasn’t been around very long, it’s only distributed very narrowly in the phylogenetic tree of bacteria. Conversely, the flagellum is found distributed much more widely across many different groups or species of bacteria and that suggests that it has an origin deeper in the phylogenetic tree of bacterial species because there’s simply been a longer time for that distribution to occur across those different species. That would again suggest that the flagellum and the genes that made it are older than the type 3 secretory system and the genes that made it.
There’s another fascinating discovery that’s enabled us to assess the relative ages of the type 3 secretory system versus the flagellum as a whole and that is that the genes for building the type 3 secretory system, when it occurs in isolation, are found on little mobile genetic units called plasmids. We know that plasmids and other kinds of mobile genetic units are transferred from bacterium to bacterium, that they move around, but these genes for building the type 3 secretory system are not found in the core circular bacterial chromosome. This suggests that the aboriginal system, the genes for building the system as a whole were in place first and then these mobile units likely were added later and provided this capacity for building the type 3 secretory system in isolation from the function of the flagellum as a whole. That’s another indicator that suggests again that the flagellum is the aboriginal system and the type 3 secretory system is something that either came later or is derived from that aboriginal system.
There’s one more indicator of relative age. It turns out that these type 3 secretory systems are used by bacteria to inject toxins in eukaryotic organisms so that they can ingest the contents of the eukaryotic organism. Eukaryotes come on the scene billions of years after the first bacteria are already on the planet. If you think about the functional requirements of a bacterial cell, they will need a flagella motor much sooner in their evolutionary history then they will need a secretory device to allow them to act as a predator vs. a eukaryotic cell or organism. That suggests that the flagella motor was on the scene first. It confers a basic functional requirement of all bacteria irrespective of whether or not eukaryotes are on the scene. The function is motility, it allows the bacterial cell to move around and find its food but this specialized innovation for secreting toxins into eukaryotes is only going to be useful once eukaryotes are on the scene and they come on the scene long after bacteria have first emerged therefore suggesting that the flagellum is again the first thing on the scene and the type 3 secretory system comes along after. It’s not its ancestor and therefore the flagellum could not have evolved through an evolutionary process of co-option as envisioned by some of Behe’s critics.
Various results that suggest that the genes that are necessary to build the flagellum are older than the genes that are involved in building the type 3 secretory system not only count against the hypothesis that the type 3 secretory system is the aboriginal system from which the the flagellum evolved, but they also count against the hypothesis that the two evolved in tandem, at roughly the same rate such that they are commonly derived byproducts of some common ancestor. Because on that thesis, you would expect the genes in each of the two systems to be roughly the same age and yet through several different indicators we find that there’s a clear asymmetry such that the flagella motor and the genes necessary to build it are older, not younger than the genes necessary to build the type 3 secretory system. These indicators of relative age in each case disconfirm not just one, but both, of the evolutionary ideas about how the flagellum as a whole would have arisen from something simpler.