May 14, 2020 | David F. Coppedge

Archive Classic: Neo-Darwinism Falsified in the Lab

This article from October 19, 2004 should be remembered because of its importance. Evolutionists ignored it.

With RNA viruses like coronavirus-SARS-2 in the news, this entry from 16 years ago deserves to be aired again, because nothing since has changed what these scientists found about neo-Darwinism. This post and yesterday’s basically pull the rug out from Darwin’s assumption that variations filtered by natural selection could produce all the beauty and diversity of life. —Ed.

Will the Spaniards be noted in history books as the ones who falsified neo-Darwinism? Not likely; no one experiment would bring down a biological paradigm with such international and historical momentum behind it. Nevertheless, looking at the results and conclusions of experiments by three evolutionary biologists at the Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia in Spain, published in PNAS this week (i.e., 10/26/2003),1 it would be hard to find any support for the central tenets of neo-Darwinian theory: namely, that evolutionary adaptations arise by natural selection acting on beneficial mutations. Instead, this paper shows experimental evidence that it doesn’t work.

Neo-Darwinism, also termed the modern synthesis of evolutionary biology, was formulated in the 1940s to rescue Darwin’s views on natural selection from growing theoretical problems (see 07/02/2004 headline). It incorporated the necessity of genetic mutations to provide the raw material for variation on which natural selection acts. This revision was necessary when the rediscovery of Mendel’s laws of inheritance ruled out ideas of blending inheritance, showing instead that inherited characters were based on discrete entities (genes) that were passed on unaltered to the offspring.

To test neo-Darwinian evolution in a microcosm, Rafael Sanjuán, Andrés Moya, and Santiago F. Elena worked with RNA viruses: organisms with a small, compact genomes that should respond quickly and noticeably to mutations. The team was looking for epistatic interactions: i.e., the effects of multiple independent (non-allelic) mutations on each other, rather than the effects of single mutations alone. These interactions can be antagonistic or synergistic: they can work against one another or with one another. Epistasis is defined as “any interaction of nonallelic genes, especially the suppression by one gene of the effect of a nonallelic gene.” Of note in this paper are the opening lines in the abstract that tell how rarely this important concept has been studied before (read: never):

The tendency for genetic architectures to exhibit epistasis among mutations plays a central role in the modern synthesis of evolutionary biology and in theoretical descriptions of many evolutionary processes. Nevertheless, few studies unquestionably show whether, and how, mutations typically interact. Beneficial mutations are especially difficult to identify because of their scarcity. Consequently, epistasis among pairs of this important class of mutations has, to our knowledge, never before been explored.   [Emphasis added in all quotes.]

Let’s picture a 2×2 grid. On the left side, label the rows “beneficial” and “deleterious.” On the top, label the columns “synergistic” and “antagonistic.” Now put two dots in each box, with the dots representing mutations that will interact with one another.

Quiz question: which box represents the only hope for evolutionary advancement? Well, the bottom and right boxes are clearly not any help. If the mutations are both deleterious and both antagonistic, at least they might turn each other off to stop the damage, like two criminals fighting each other instead of you. If the mutations are both deleterious but synergistic, they will multiply each other’s damage, like two criminals ganging up on you. If they are both beneficial but antagonistic, that won’t help, either, because it would be like two guardian angels having a squabble instead of helping you. In short, neo-Darwinism’s only hope is to find mutations in the top left box: two good mutations that work synergistically, increasing your “fitness” in the evolutionary world of competition. So how did the experiments go in the lab?

They performed two classes of experiments to measure the effects of epistasis on mutations. Continuing with the abstract, here is what they found:

Interactions among genome components should be of special relevance in compacted genomes such as those of RNA viruses. To tackle these issues, we first generated 47 genotypes of vesicular stomatitis virus carrying pairs of nucleotide substitution mutations whose separated and combined deleterious effects on fitness were determined. Several pairs exhibited significant interactions for fitness, including antagonistic and synergistic epistasis. Synthetic lethals represented 50% of the latter. In a second set of experiments, 15 genotypes carrying pairs of beneficial mutations were also created. In this case, all significant interactions were antagonistic. Our results show that the architecture of the fitness depends on complex interactions among genome components.

In other words, none of their pairs of mutations occupied the necessary box labeled “beneficial and synergistic.” Half of the synergistic (working-together) actions they measured were “synthetic lethals” – which is like the two criminals both shooting the victim simultaneously. The other 50% maybe didn’t kill the organisms but still decreased fitness overall. The second experiment was all the more depressing: given two beneficial mutations in the same organism, all significant interactions were antagonistic. This means the guardian angels were preventing each other from helping. It recalls another paper in PNAS in March 2003 (see 03/17/2003 headline) that took into account indirect genetic effects, noting that increases in fitness do not act in isolation; they often counteract one another, creating “slippage on the treadmill.”

In the current paper, the researchers found that beneficial mutations do not add up, even in the best of circumstances. Neo-Darwinian theory assumes that beneficial mutations act independently, but the team found that of the eight actual best-case scenarios (two beneficial mutations working antagonistically, since none worked synergistically) over half decreased the total fitness of the result from what would be expected if the beneficial mutations acted alone. They called this “decompensatory epistasis” if you need a new phrase to impress your friends at the water cooler.

What does this mean to neo-Darwinian theory? “Indeed, when epistasis is decompensatory, both beneficial alleles involved in the interaction cannot spread to fixation in the population, because the double mutant is less fit than each single mutant.” This drastically undercuts any hope for evolutionary progress. Beneficial mutations are “scarce” to begin with, but more is not better – it’s worse. Like adding hot sauce to ice cream, the benefits of each counteract one another when combined. “As a consequence,” they continue, describing the only hope left, “lineages bearing alternative beneficial mutations should compete with each other on their way to fixation and, as a consequence of asexuality and clonal interference, only the best competitor will eventually become fixed in the population.” That is, only one beneficial mutation can become fixed at a time, even in the best case scenario.

The discussion of results in the paper by Sanjuán et al. hammers neo-Darwinian theory with additional gentle, but effective, blows. First, they restate the basic finding: “Among pairs of deleterious mutations, although both synergistic and antagonistic epistases have been detected, interactions were predominantly antagonistic, such that their combined effect is significantly smaller than expected under a multiplicative model.” And in the best-case scenario of artificially-induced beneficial mutations, “antagonistic epistasis represents the most abundant type of interaction among beneficial mutations, with several cases showing decompensatory epistasis.”

How should these experiments impact evolutionary theory, including the “queen of evolutionary problems,” the origin of sex? (see 04/14/2003 headline…. link to be fixed later). Neo-Darwinists may well wish to run and hide:

The results reported here have two important implications for theories seeking explanations for the evolutionary advantage of recombination and sexual reproduction. First, according to the Fisher–Muller argument, sex and recombination are advantageous because they combine into a common genotype beneficial mutations that arose in different ones, speeding up the rate of adaptation. However, if the genetic architecture of RNA viruses determines that, in general, antagonistic epistasis and, in particular, decompensatory epistasis among beneficial mutations is the norm, then recombination would not necessarily imply a benefit in terms of adaptive evolution. Second, sex might still be beneficial for RNA viruses as an efficient mechanism for purging deleterious mutations. However, according with the Mutational Deterministic Hypothesis [i.e., the suggestion that sex enables a population to purge deleterious mutations from the genome], if this is the case, an excess of synergistic epistasis among deleterious mutations is required to compensate the 2-fold advantage of clonal reproduction [i.e., asexual reproduction]. Our first data set shows that synergistic interactions among random mutations are neither stronger nor more common than antagonistic interactions. Indeed, the existence of variability among loci in the sign and strength of epistasis, and especially the dominance of antagonistic epistasis, decreases the parameter space over which sex may evolve.

Since the parameter space was small to begin with, their words sound euphemistic, as if to cheer up a prisoner facing a hanging at dawn that maybe someone will find an alibi: “Like who?  Like what?” the prisoner asks. “I dunno; just supposin’,” the friend replies. How sex may evolve: that’s somebody else’s problem.

Also, they note, their results “impose a strong burden” on the “often invoked limitless adaptability of RNA viruses.” Citing another paper, they quote, “RNA viruses might be more at the mercy of their mutation rates than we think.” If decompensatory epistasis and antagonistic interactions are the general rules for mutations in all organisms, any hope for variability and adaptability due to mutation and selection has been severely limited, if not falsified, by these experiments. On the contrary, they say their experiments demonstrate a mechanism for stability of the genome: “In this sense, because it involves masking the interaction among deleterious alleles, antagonistic epistasis might be seen as a sort of genetic mutational robustness.” (See 09/22/2004 headline on robustness as a design constraint in the living cell.)

In conclusion, they caution evolutionary modelers to realize that they can no longer merely assume fitness gains (if any) add up. Mercifully, they use the words hint and suggest: “Finally, we would like to hint that the above findings prompt the necessity of considering nonmultiplicative fitness effects in mathematical descriptions of viral evolution.” Indeed, “the results we present here suggest that more realistic models must incorporate variance in the type and strength of epistasis among mutations.” But did they themselves find any synergistic, beneficial epistatic effects by experiment? None. Maybe neo-Darwinism is like the businessman who lost money on every sale but thought he could make it up in volume.

1Rafael Sanjuán, Andrés Moya, and Santiago F. Elena, “Evolution: The contribution of epistasis to the architecture of fitness in an RNA virus,” Proceedings of the National Academy of Sciences USA, 10.1073/pnas.0404125101, Published online before print October 18, 2004.

Any scientific hypothesis must be testable and subject to falsification by experiment. It is not enough to tell just-so stories, and describe things in glittering generalities with armchair scenarios. Neo-Darwinian theory, the idea that natural selection acting on “scarce” beneficial mutations can produce all the diversity of life, from diving cormorants to catapulting chameleon tongues to sponge fiber optics to high-tech fruit fly aircraft to supersonic high-jumping froghoppers to efficient penguin, whale and dolphin flippers to fish physics students to glass-sculpturing diatoms to self-propelled motors, must be testable if it is to be declared scientific.

So there. These scientists finally put neo-Darwinism to the test in a microcosm that should have shown, if the principles were correct, a clear case of fitness increasing as a result of natural selection acting on beneficial mutations. It failed. It failed miserably. Not only were no instances of synergistic beneficial mutations detected, the beneficial mutations that were artificially inserted worked against each other! Neo-Darwinism is falsified! And it was falsified not by creationists, but by evolutionary biologists working in the lab at an institute for the study of biological evolution!

Now all we need to do is get the word out. Stop the propaganda machine, stop the NCSE and ACLU threats at the school boards, stop the PBS NOVA programs and the media spin doctors. Rearrange the museums, gather up the pro-Darwin displays and national park signs and toss them, along with neo-Darwinian theory itself, and by implication all of Charlie’s baggage that was already obsolete before 1940, onto the dumpster of discredited ideas. Darwin’s Century is now a mere footnote of history, an unfortunate detour that killed 100 million people, but at least now we know better.

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