Philosopher's stone

Modern evolutionary theory posits descent with modification. Moreover, genetic modification occurs through various mechanisms - natural selection, mutation, gene flow, genetic drift. Most of this could be more or less acceptable to critics of neo-Darwinism like the ID theorists.

However, neo-Darwinists add universal common descent and all it entails (e.g. speciation). Many scientists and other relevant scholars would dissent from this. Indeed, what's often presented to the public about evolution doesn't match what's in the academic literature and discussed among experts. To the public, evolution is presented essentially as established fact rather than theory. Scientists "all agree," if there are disagreements they are over minor issues, etc. But among fellow evolutionists in academic circles and publishing in the academic literature (to say nothing of outside critics like the ID guys), there are significant doubts over various significant aspects of evolutionary theory. This includes heated debate over whether we should try to plug the leaky holes in the sinking ship, or start all over with a new paradigm. A theory doesn't get any more precarious or unstable than that, I don't think.

Scientific critics (to varying degrees) would include Eva Jablonka, Stuart Kauffman, Marion J. Lamb, Lynn Margulis, Gerd Müller, Stuart Newman, Denis Noble, James Shapiro, Craig Venter. If I'm not mistaken, secular philosohpers like David Berlinski, Jerry Fodor, Massimo Piattelli-Palmarini, and David Stove would likewise fit the bill. This is hardly an exhaustive list.

Take Pierre-Paul Grassé. He was a French scientist who passed away decades ago. One of the things Grassé did was to ask what are the boundaries between microevolution and macroevolution. How can we go from the micro to the macro. How are large-scale morphological changes or changes in body plans - which presumes, among other things, a certain amount of novel genetic information - the result of natural selection, mutation, gene flow, and/or genetic drift?

Grassé worked on fruit flies. An advantage with fruit flies is thousands of generations of fruit flies can be produced in a relatively short amount of time. Plus, scientists can tweak or otherwise effect various mutations in fruit flies. Which is part of what Grassé did. Nevertheless, the fruit flies didn't evolve, not in a macroevolutionary sense. Rather, they remained fruit flies.

Grassé's fruit flies aren't the only example. Another example is the bacteria E. coli. We could likewise cite other microorganisms, insects, etc.

Of course, evolutionists point out antibiotic resistance. Not to mention Richard Lenski's famous long-term experiment. But most of what's pointed out is evidence of microevolution, not macroevolution. (BTW, some atheists allege the terms "microevolution" and "macroevolution" are terms only creationists would use. But the fact is these terms are used by secular scientists in the scientific literature. Just search a scientific database like PubMed or Web of Knowledge or the like for the terms, and observe their usage.)

In addition, there are serious limitations and flaws in the studies. Take what Michael Behe recently said:

Still, the important question to ask is, what exactly has this venerable project shown us about evolution? The study has addressed some narrow points of peculiar interest to evolutionary population geneticists, but for proponents of intelligent design the bottom line is that the great majority of even beneficial mutations have turned out to be due to the breaking, degrading, or minor tweaking of pre-existing genes or regulatory regions (Behe 2010). There have been no mutations or series of mutations identified that appear to be on their way to constructing elegant new molecular machinery of the kind that fills every cell. For example, the genes making the bacterial flagellum are consistently turned off by a beneficial mutation (apparently it saves cells energy used in constructing flagella). The suite of genes used to make the sugar ribose is the uniform target of a destructive mutation, which somehow helps the bacterium grow more quickly in the laboratory. Degrading a host of other genes leads to beneficial effects, too.

The Science story references a new paper from Lenski's lab (Wiser et al. 2013) showing that the bacterial strain continues to improve its growth rate. The chief talking point of the paper is that the rate of improvement follows a curve that will not max out -- improvements would continue indefinitely, although at an ever-slowing rate. The natures of the newer beneficial mutations, however, are not reported -- whether they, too, are degradative changes, or minor, sideways changes, or truly constructive changes. (I know which way I'll bet....)

In one supplementary figure the authors show that the increasing growth rate is built on some previously known, beneficial-yet-degradative mutations. Earlier this year Lenski's lab (Wielgoss et al. 2013) identified a mutation that built on a previous mutation, too, which may prefigure what kind of changes the unidentified mutations in the current paper will turn out to be. Over the course of the project several of the dozen separate strains developed what is called a "mutator" phenotype. In English, that means that the cell's ability to faithfully copy its DNA is degraded, and its mutation rate has increased some 150-fold. As Lenski's work showed, that's due to a mutation (dubbed mutT) that degrades an enzyme that rids the cell of damaged guanine nucleotides, preventing their misincorporation into DNA. Loss of function of a second enzyme (MutY), which removes mispaired bases from DNA, also increases the mutation rate when it occurs by itself. However, when the two mutations, mutT and mutY, occur together, the mutation rate decreases by half of what it is in the presence of mutT alone -- that is, it is 75-fold greater than the unmutated case.

Lenski is an optimistic man, and always accentuates the positive. In the paper on mutT and mutY, the stress is on how the bacterium has improved with the second mutation. Heavily unemphasized is the ominous fact that one loss of function mutation is "improved" by another loss of function mutation -- by degrading a second gene. Anyone who is interested in long-term evolution should see this as a baleful portent for any theory of evolution that relies exclusively on blind, undirected processes.

(Source)

At any rate, given the considerable and considerably extensive cracks in the evolutionary edifice, it's possible neo-Darwinism is about to crumble and fall. If it does it would take down much of modern biology as well since much of modern biology is built squarely on neo-Darwinism.

It's possible modern biology is at a similar point in history that chemistry was in when it transitioned from alchemy to a modern science. If so, then people like Jerry Coyne and Richard Dawkins are the old guards, like those ancient Medieval alchemists with their convoluted and arcane language, still searching for the philosopher's stone to turn non-life into life, yet scoffing at anyone else who so much as would question phlogiston theory. Perhaps we await the likes of a Robert Boyle or Antoine Lavoisier for biology.