Ken Miller’s Misleading Promotion of Ohno’s Work

Presented below is the misleading passage from Ken Miller’s book which gives a misleading account of facts regarding Ohno’s speculation.  Comments will be provided after the quotation to show the misleading nature of Miller’s claims.

From Ken Miller’s Book,  Only a Theory: Evolution and the Battle for America’s Soul. Penguin, June 12, 2008.]
In the 1970s, however, a number of Japanese scientists made a most unusual observation. Industrial plants engaged in nylon manufacture produce chemical waste products from the synthetic reaction and often discharge these wastes into holding pools around the factories. Containing, as they did, only water and nylon waste compounds, nothing should have grown in these ponds. But something was growing, in fact: scummy mats of bacteria, apparently thriving on the artificial, synthetic polymer. To their very great surprise, the researchers discovered that these bacteria possessed an enzyme capable of breaking down, or hydrolyzing, nylon. They had evolved “nylonase.”
Where did this new enzyme come from? Studies in the California laboratory of Susumu Ohno found the answer in 1984. The nylonase enzyme in these bacteria was derived by duplicating a gene that controlled another, quite different function, and then inserting a single extra base into its DNA code.
BEFORE OUR VERY EYES
But the process can in fact be observed directly, and under controlled conditions. The evolution of nylonase is precisely such an example. Intrigued by the unavoidable conclusion that this new enzyme had evolved naturally by means of gene duplication and mutation, about ten years ago a group of researchers at Osaka University decided to see if this remarkable process could be reproduced in the lab.  They took a culture of Pseudomonas bacteria that had no ability at all to metabolize nylon compounds and grew it on a medium containing small fragments of the nylon molecules as the sole source of food.
After just nine days they found colonies of “hypergrowing” bacteria that had begun to master the trick of using nylon fragments as food. They then transferred these bacteria to a medium containing another nylon compound, and within three months they found that some of the bacteria had evolved the ability to grow on this compound as well. As the researchers summarized their results: “In the present study, it was shown that microorganisms can acquire an entirely new ability to metabolize xenobiotic compounds such as a by-product of nylon manufacture through the process of adaptation. ” In short, they evolve the ability right before our very eyes.
Prior to this experiment one might have asked if we could really be certain that evolution had produced this capability. Maybe those nylon-digesting genes had already been present and were just waiting for Wallace Carothers to cook up his new compound. That turns out not to have been a possible explanation for the Pseudomonas experiments, in which the inability of the bacteria to metabolize nylon was carefully documented before the study began. As it went on, though, week after week, evolution ran its course, and the new capability developed under direct human observation.
However we look at it, the information for this entirely new capability came about without a designer, without a plan, and from the sheer opportunism of living organisms generating new variations in the face of selective pressure. And the source of the information, in a way, is nylon itself. By introducing nylon into the environment, we provided trillions of bacteria with a puzzle for which the solution promised a great reward. Come up with an enzyme that lets you break down nylon, even if it’s just a quick and dirty modification of an existing one that doesn’t really work very well, and you’ll be given a free lunch. Under such circumstances the information needed for the solution is found in the selective process  itself, just as Schneider’s program tells us. Evolution works in the real world, even when we’re watching!

Miller give the misleading impression that Ohno deduced his speculation from actual laboratory experiments.  First, it is clear from Ohno’s own paper that Ohno was just speculating on data provided by Okada’s paper in 1983. In fact Ohno made some embarrassing errors in his own paper. So this Ohno’s frame shift hypothesis was more the result of Ohno’s imagination than any lab work that compared bacteria before and after a supposed evolutionary event.

So Miller represents Ohno’s lab work inaccurately, and represents Ohno’s speculation as an actual fact. The following claim by Miller is thus misleading.

Where did this new enzyme come from? Studies in the California laboratory of Susumu Ohno found the answer in 1984. The nylonase enzyme in these bacteria was derived by duplicating a gene that controlled another, quite different function, and then inserting a single extra base into its DNA code.

Secondly, the 1995 experiment at Osaka University on hypergrowing bacteria did not do a comparison of gene sequences before nor after the evolutionary event. Given Kanagawa’s 1993 research showing nylB genes already present in Pseudomonas strains without any mention of the nylB evolving under lab conditions, it is more likely if such a comparison were done, it would have falsified Ohno’s claims.

The 1995 Osaka University experiment involved a different bacteria, Pseodomonas, than what Ohno studied, Flavobacterium/Arthrobacteria KI72. Thus, as a matter of principle, the Osaka experiments could not likely have confirmed Ohno’s claims because Kanagawa showed the genes involved in similar strains of Pseudomonas were substantially different (65% different in amino acids) than  the Flavobacteria/Arthrobacteria KI72 studied by Ohno. The frame-shift mutation that Ohno speculated will only work for the KI72 nylB gene if at all, not the Pseodomonas nylB gene.  It was entirely possible given Kato’s 1991 experiment, a few residue changes, rather than the 400 Ohno claimed, was the cause of that particular strain of Pseudomonas being able to digest nylon.

Furthermore, Kanagawa argues the nylB genes of Pseudomonas nylB and Flavobacteria/Arthrobacteria KI72 descended from a common ancestor, and given the similarity is only 53% similar in DNA sequence, emergence of nylB in Flavobacteria/Arthrobacteria KI72 was long before 1935, contrary to Ohno’s speculation.

Miller also fails to acknowledge bacteria, Bacilus cereus, in the Indian Ocean which harbor nylB genes dissimilar in sequence to the gene Ohno studied were discovered in 2007 to be able to digest nylon. Given that the Indian Ocean is not nylon rich as the wastewater ponds which Ohno speculated induced nylonase nylB evolution, and given that the genes of Bacilus cereus are different than the genes in Flavobacteria/Arthrobacteria KI72 (which Ohno studied), this strongly suggests the pre-existence of NylB nylonases prior to 1935 which did not evolve in response to the presence of nylon in the environment. It is astronomically improbable a random sequence resulting from frame shift mutation that creates 400+ residue changes, as Ohno suggested, could converge on a functional NylB protein structure found in other organisms.

Miller claims:

Maybe those nylon-digesting genes had already been present and were just waiting for Wallace Carothers to cook up his new compound. That turns out not to have been a possible explanation for the Pseudomonas experiments.

Actually Miller’s claim is falsified by the fact nylB genes with dissimilar sequences are spread across the globe and in different organisms and environments far removed from nylon.  Not to mention, Miller fails to point out evidence of the pre-existence of nylB in from Kanagawa’s 1993 research.  As mentioned on the homepage, Ebata and Morita’s experiments show nylonases existed before 1935.

And a minor point, the nylon which NylB acts on was not the nylon-6,6 that was discovered by Carothers, but the nylon-6 discovered by Paul Schlack. So even on minor points of history, Miller is inaccurate.