At Why Evolution Is True, Jerry Coyne pictures a newly rediscovered and rather unhandsome fly native to a particular rock in Kenya (and nowhere else) where it sports about in the bat guano deposited in a cleft in the rock. The fly has only vestigial wings — “evidence for evolution, of course,” notes Dr. Coyne. Isn’t it interesting how “evidence for evolution” tends to be, as in this example, evidence not for the building up of new functionality but for its loss, where the loss has some adaptive advantage? Losing information is one thing — like accidentally erasing a computer file (say, an embarrassing diplomatic cable) where, it turns out in retrospect, you’re better off now that’s it not there anymore. Gaining information, building it up slowly from nothing, is quite another and more impressive feat. Yet it’s not the loss of function, and the required underlying information, but its gain that Darwinian evolution is primarily challenged to account for.
That’s the paradox highlighted in Michael Behe’s new review essay in Quarterly Review of Biology (“Experimental Evolution, Loss-of-Function Mutations, and “The First Rule of Adaptive Evolution“). It’s one of those peer-reviewed, Darwin-doubting biology journal essays that, as we’re confidently assured by the likes of the aforesaid Jerry Coyne, don’t actually exist. Casey Luskin has been doing an excellent job in this space of detailing Michael Behe’s conclusions. Reviewing the expansive literature dealing with investigations of viral and bacterial evolution, Dr. Behe shows that adaptive instances of the “diminishment or elimination” of Functional Coding ElemenTs (FCTs) in the genome overwhelmingly outnumber “gain-of-FCT events.” Seemingly, under Darwinian assumptions, even as functionality is being painstakingly built up that’s of use to an organism in promoting survival, the same creature should, much faster, be impoverished of function to the point of being driven out of existence. Jerry Coyne’s Kenyan fly may then be the opposite of “evidence for evolution” of the kind that Darwinists really need.
So far the masters of evolutionary apologetics have ignored Behe’s damaging article. [Update: Coyne has now done so. More anon.] Trying to imagine what they would or will say if they can ever carve out the time from a busy schedule to read it, I posed a few questions to Dr. Ann Gauger, developmental biologist and senior research scientist at Biologic Institute.
Q. What does Behe’s article mean for the larger debate about Darwinian evolution?
A. Mike’s paper is an extension of his thesis introduced in his The Edge of Evolution, namely that it is much easier to reduce, modify or eliminate existing functions than to build new ones. He documents from the scientific literature that most adaptations to new environments or challenges are due to loss or modification of existing functions, and that gain of function mutations are very rare.
Indeed, my recent paper with Ralph Seelke in BIO-Complexity (“Reductive Evolution Can Prevent Populations from Taking Simple Adaptive Paths to High Fitness,” Vol. 2010) demonstrates Mike’s thesis completely. When challenged to grow in medium with very little tryptophan, 14 different populations of cells reduced or eliminated genes for making tryptophan, rather than fixing the broken tryptophan-making gene they carried. (Fixing the gene would have required cells to revert two specific mutations, with each reversion itself conferring a growth advantage.)
Because reducing or eliminating expression of the broken gene was “adaptive,” i.e. it allowed them to reproduce faster than cells still expressing the broken gene, and because there are many more ways to reduce or eliminate gene expression than to fix the gene, the populations always chose to reduce or eliminate gene function.
Mike’s paper is making plain what should have been obvious, given what we know about the nature of genetic events and the way natural selection works. Yet most evolutionary biologists still appear to believe that, given enough time and population, nature can work wonders. Our work at Biologic and Mike’s work is intended to demonstrate that such confidence is misplaced.
Q. Let’s explore that last point you made a bit more. Won’t Darwin defenders still say Behe’s observations are not only obvious but trivial? I can hear it now: Common sense suggests that of course it’s easier to reduce, modify or eliminate functions than to build new ones. No one would doubt that. But given vast resources of time, we can expect the “harder” task of building new functions to be accomplished often enough to “work wonders.” In your own research with Dr. Seelke, you found that cells chose to “reduce or eliminate function.” But with vastly bigger populations and vastly more time, wouldn’t we be justified in expecting gene fixes too, even if far fewer in number?
Also, what do you make of the point that seemingly over the long haul, adaptations that “reduce, modify or eliminate” would be so overwhelming in number compared to hypothetical new functions that the organism would simply become non-viable by attrition before it had a chance to do much with its sparse added functionality — in which case, game over?
A. Here’s the thing. It’s only “trivial” if it comes from Mike Behe. Many of the papers he reviews were published in big name journals. For example the paper about loss of mating function in yeast was published in PNAS, the virus work was published in Genetics and Science among other places, and Lenski’s work has also been widely published. I doubt the authors Behe reviews would appreciate having their work categorized as trivial.
For most organisms in the wild, the environment is constantly changing. Organisms rarely encounter prolonged and uniform selection in one direction. In turn, changing selection prevents most genetic variants from getting fixed in the population. In addition, most mutations that accumulate in populations are neutral or weakly deleterious, and most beneficial mutations are only weakly beneficial. This means that it takes a very long time, if ever, for a weakly beneficial mutation to spread throughout the population, or for harmful mutations to be eliminated. If more than one mutation is required to get a new function, the problem quickly becomes beyond reach. Evolutionary biologists have begun to realize the problem of getting complex adaptations, and are trying to find answers.
The problem is the level of complexity that is required, from the earliest stages of life. For example, just to modify one protein to perform a new function or interact with a new partner can require multiple mutations. Yet many specialized proteins, adapted to work together with specialized RNAs, are required to build a ribosome. And until you have ribosomes, you cannot translate genes into proteins. We haven’t a clue how this ability evolved.
As for the problem of gene loss, in the wild organisms typically encounter a variety of environments, so varying selection usually prevents those populations from suffering irreversible loss of genetic information. There are two exceptions, however. Extreme population bottlenecks can lead to loss of genetic variation, and the sudden fixation of harmful (or extremely lucky beneficial) mutations in the population. Since most mutations are neutral or harmful, conservation biologists know this and that is why they try to keep as much genetic diversity as possible in endangered species.
Second, some organisms have adopted a parasitic or otherwise limited lifestyle, and as a result have streamlined their genomes to eliminate unnecessary functions. This is a dead end for these organisms. Once genes are eliminated, they are gone. There is no going back. And as Behe points out, smaller genomes have fewer resources for adapting to new challenges.