More than 20 years ago, Rich Lenski, then at University of California, Irvine, started a simple experiment. On a Wednesday morning, the 24 February 1988, he started the parallel evolution of 12 populations of Escherichia coli, all clonally derived from a single bacterium and competing for limited sugar in Erlenmeyer flasks. Each day, roughly half a billion new copies of the E. coli genome are made in each flask as the bacteria multiply, along with about a million mistakes, meaning that in the span of a few days, virtually all conceivable mutations in the bacteria’s five million base pair genome will have been attempted. Most of these mutations make no difference or are deleterious, but a few make the bacteria grow a little bit faster — providing up to a 10% growth advantage over their predecessors. The fastest ones are extremely rare and the population must ‘wait’ a couple of days for them to show up.
Every night, the bacteria run out of the sugar glucose and go dormant. The following day around noon, a researcher plunges a pipette in and sucks up 1% of the culture to inoculate a fresh flask. Those faster at gobbling up glucose will send more of their descendants to the following day’s pipette and, after a few weeks, descendants of the fastest one will be the only ones transferred as the mutation ‘sweeps’ to fixation.
The text is taken from a review in Nature, Evolution: Revenge of the hopeful monster, about how natural and lab experiments are changing how we think about the mutations that create the phenotypic variation that enables organisms to evolve. In Fisher's model (see yellow spheres →) a single mutation of large effect is bound to either "move" the organism in the wrong direction, away from the fitness optimum (center of spheres), or it will mostly overshoot the optimum, landing the organism on the other side, and the mutation will still be detrimental. on this basis, Fisher argued that adaptation only takes place by many small mutations. However, this assumes two things which both are unrealistic: 1) That there is only one fitness optimum. And there aren't. A model of a realistic fitness landscape would have many peaks and valleys (we call such landscapes 'rugged'), which immediately makes Fisher's model nonsensical. A large mutation may indeed take the organism further away from one optimum, but that might land the organism near another peak in the fitness landscape, and thus be beneficial anyway. 2) Adaptation occurs when the organisms are not sitting right on top of a local fitness peak, and this situation can occur when the fitness landscape changes, because the "real" environment changes. For example, in Lenski's experiment the bacteria were removed from the natural environment, and that changed the fitness landscape accordingly. If a fitness peak disappears, then the organisms may not find themselves near another peak, as Fisher's model assumes, but may be really far away. (Note that adaptation is a process that occurs for one or more traits that are no longer optimal after an environmental change, while most other traits are fine.)
That we learn new things from experiments about how evolution proceeds should be a cause for celebration, so it is with irritation that I came across this blog-post on the same article by a fellow of the Discovery Institute, Cornelius Hunter. After reading the discussion on his blog, I realize that Hunter is equating evolutionary theory with "Darwin's theory", which means that when something turns out not to be quite right with "Darwin's theory" (as is the case of gradualism, or small effect mutations, vs. mutations of large effect), then he thinks it's a problem for current evolutionary theory, to the extent that it is then falsified.
When some people have made up their mind that there is a world-wide conspiracy going on among evolutionary biologists to keep the truth from the public, and when their belief in this is motivated by their desire to prove evolution wrong because of their religious faith, then at some point all discussion becomes futile. But, one point in still arguing with them, is that hopefully the younger generations will come away with a more rational view of evolution and science.