Bacteria Too Complex To Be Primitive Eukaryote Ancestors

In the search for the most primitive life forms on earth, bacteria would certainly make the list.  They are tiny, one-celled, and have small genomes.  Why, then, did Patrick Forterre and Simonetta Gribaldo of the Pasteur Institute say in PNAS,¹ “we should definitely stop thinking of bacteria in terms of simple ‘lower’ organisms”?  For the same reason that Science Daily announced about a separate finding, “Lowly bacteria are turning out to be much more complex than previously thought.”
    Some bacteria do, of course, have one of the most amazing molecular motors on earth: the flagellum.  Howard Berg’s team at Harvard recently found out that the clockwise and counter-clockwise rotations of flagella are asymmetrical.  Writing in PNAS,¹ they said, “We speculate that CCW rotation might be optimized for runs, with higher speeds increasing the ability of cells to sense spatial gradients, whereas CW rotation might be optimized for tumbles, where the object is to change cell trajectories.”  Flagellar motors are just one instance of exquisite complexity found in bacteria.  More instances are now coming to light.
    The Science Daily article reported on work at Loyola University that found a new example of “bacterial complexity” called ”protein acetylation” at work, a process once thought characteristic of the more-complex eukaryotes and rare in bacteria.  Protein acetylation is a molecular process involved in regulating genes and proteins.  “Bacteria have long been considered simple relatives of eukaryotes,” wrote Alan Wolfe for his colleagues at Loyola.  “Obviously, this misperception must be modified…. There is a whole process going on that we have been blind to.”  Has this discovery been exciting?  He said his graduate students are working around the clock, because “We’re riding the front of the wave, and that’s exhilarating.”  The headline announced that the discovery of a complex process in bacteria represents “the dawning of a new age in bacteria research.”
    Forterre and Gribaldo, writing in their PNAS Commentary,² discussed two other recent findings that promote bacteria into the ballpark of complex organisms: (1) the discovery by Fuerst that they are capable of endocytosis, in which extracellular cargo can enter the cell through wrappings of membrane, and (2) the discovery by Devos that their cell membranes contain proteins “structural analogs of eukaryotic membrane coat (MC) proteins.”  Forterre and Gribaldo explain, “In eukaryotes, MC proteins are involved in both vesicle trafficking systems and in the formation of the nuclear pore.”  But bacteria have no nucleus, do they?  Actually, many bacteria have an intracytoplasmic membrane (ICM), another analog to the eukaryotic nucleus, and their MC proteins apparently form a kind of nuclear pore to allow trafficking of RNAs between the genome and the ribosomes – just like in eukaryotes.  “The analogies between the membrane trafficking systems of PVC bacteria and Eukarya, both at the cytological and protein structure levels, are thus strikingly evident,” they exclaimed.  “It now seems impossible to ignore these data when discussing the origin of the eukaryotic nucleus.”  Far be it from an evolutionary biologist to ignore data.
    So what is the new picture of the relationship between “simple” prokaryotes and their more-evolved superiors, the eukaryotes?  For one thing, Forterre and Gribaldo revealed serious shortcomings with the popular “endosymbiosis” model – the idea that a prokaryote engulfed an archaea and gave rise to a symbiotic relationship that produced a eukaryote.  “However, symbiotic hypotheses for the origin of Eukarya remain difficult to understand in terms of known biological mechanisms,” they said.  “For example, they imply a specific association between a bacterium and an archaeon for which there are no examples in nature, and assume a very unlikely process where all of the genes of the bacterial host coding for informational proteins would have been replaced by those of the archaeal symbiont.”  So much for that idea.  Too bad it was the leading plot in many a documentary and popular evolutionary portrayal.
    Forterre and Gribaldo could only think of two approaches, both evolutionary: “A major objective of future research should now be to determine whether bacterial MC proteins are only structural analogs of eukaryotic ones (a case of convergent evolution) or whether instead they are homologous.”  With choices like that, Darwin can’t lose.  “This cannot be tested through sequence similarity (even between eukaryotic MC proteins), because these proteins evolve too rapidly at the sequence level,” they said, again assuming evolution.  “However, MC proteins have retained their core architecture during evolution….”  One wonders how they could know that.  The two unique protein domains that make up the MC proteins of prokaryotes “are strikingly similar in PVC bacteria and Eukarya.”  For this reason, they favor homology instead of convergence, but more research will be required: “Preliminary results have nevertheless already provided important information, suggesting in fact an ancient origin of these proteins in both PVC bacteria and in Eukarya, because several copies of MC proteins were probably already present in their respective last common ancestors.”
    It’s apparent that for Forterre and Gribaldo, the assumption of evolution qualifies as information about how eukaryotes evolved from prokaryotes.  “If we assume that bacterial and eukaryotic MC proteins have a common origin, how can this information be fitted with current theories on the origin of eukaryotes?”  Imagination also supplies information: “Three scenarios can be imagined,” they said.  The endosymbiosis model, as noted above, is no longer credible.  That leaves two “scenarios where modern Eukarya originated from an ancestral protoeukaryotic lineage.”  The first imagines PVC bacteria getting their MC proteins by lateral gene transfer.  They admit there’s no evidence for that.  “In the second one” (the one they favor), “MC proteins would have already been present in the last universal common ancestor (LUCA) and were inherited in Eukarya and PVC bacteria, whereas they were lost in all other bacterial phyla and in Archaea.”  How did LUCA get it?  They didn’t say.  Here’s where their story really gets convoluted, and admittedly “odd” –

If the LUCA already harbored MC proteins, it was probably compartmentalized.  This idea can appear odd to many biologists who use [sic] to think of the LUCA and all its contemporaries as very primitive entities.  However, the formation of vesicles and membrane manipulation may be very ancient features of life… suggesting, by analogy, that even ancient cells with RNA genomes could have had such capacity and therefore already be compartmentalized.  If MC proteins were already around at the time of the LUCA, the ancient biosphere might have been more diversified than usually suspected, with various lineages of compartmentalized cells, some of them with nuclei (which could be named synkaryotes) and others without (akaryotes), thriving in various environments.  Endocytosis of proteins might well be an ancient trait that was lost in bacteria with rigid cell walls.  Although PVC bacteria are bona fide members of the bacterial domain, they might therefore have conserved some ancestral features in terms of cellular structure and function that open up new avenues of thinking about the nature of our cellular ancestors.  Further exploration of microbial diversity will most likely bring surprises.  Other compartmentalized cells could in fact exist among the vast numbers of still uncultivated archaeal and bacterial lineages.

One detects a suggestion that the above paragraph might have a lot of could-be’s and may-be’s in it, perhaps.  There’s a lot of complexity to explain.  Now, the reader understands the context for that line with which this entry opened: “In any case, the results of Fuerst and Devos and colleagues remind us that we should definitely stop thinking of bacteria in terms of simple ‘lower’ organisms.”

1.  Yuan, Fahrner, Turner, and Berg, “Asymmetry in the clockwise and counterclockwise rotation of the bacterial flagellar motor,” Proceedings of the National Academy of Sciences, published online before print July 6, 2010, doi: 10.1073/pnas.1007333107.
2.  Patrick Forterre and Simonetta Gribaldo, “Bacteria with a eukaryotic touch: A glimpse of ancient evolution?”, Proceedings of the National Academy of Sciences, published online before print July 12, 2010, doi: 10.1073/pnas.1007720107.

Readers must be aghast at this entry: astonished at the complexity of bacteria, and utterly appalled at the shameless, incorrigible tenacity of Darwinian faith in their naturalistic tale.  “If we assume that bacterial and eukaryotic MC proteins have a common origin….”  That sentence reveals the cardinal sin of the Darwin Scientific Method, abbreviated MAD (Multiply Assumptions of Darwin): namely, (1) Assume evolution, (2) Observe a fact, (3) Make up a story to tell how the fact evolved.  These blind leaders of the blind are so blind they cannot see that they just called their assumption “information.”  They said, “how can this information be fitted with current theories on the origin of eukaryotes?”  That’s not information – that’s incantation.  It’s conjuring up images in their own heads.  It’s also reasoning in a circle.  They just said, in short, “Assuming evolution, how would that assumption fit with current theories of assumed evolution?”  It’s the can opener joke: “Assume a can opener.  How would that assumption fit with theories of how having a can opener would help open the tuna can?”  Show us the can opener!  Then we’ll all open the can and have lunch, instead of dreaming up “scenarios” where can openers “originate” in some uncanny common ancestor.
    Assuming on, from amusing leap to leap, they employed the second cardinal sin of the MAD method: imagination.  “It’s not hard to imagine…” they said a couple of times.  It’s not hard when they get a lot of practice every day.  What’s hard is following rigorous science that is observable, testable, and repeatable.
    Despite their posturing, they just disarmed their idol, Charlie, and squeezed him against the wall.  They robbed him of the most popular explanation for the origin of eukaryotes (endosymbiosis), and put all the complexity back into a mythical “last universal common ancestor” (LUCA).  So now, they have to assume LUCA with LUCK will produce LUCY, given time and chance.  No evidence required.  Folks, this is not science.  Assuming one’s own imagination without evidence is the seedplot of mythology.  Got science?  The data show supercomputing in a pinhead processor, complex regulation in software, and fast, accurate image processing.  That’s not MAD, that’s MADE – Multiple Affirmations of Design Excellence.  Yes, gentlemen, it is “impossible to ignore these data when discussing the origin” of things that are MADE (Romans 1:20).