No. I meant dead as in dead wrong, which implies any peer-reviewed literature supporting it is also dead wrong.

That’s still pretty funny - You wouldn’t happen to have any evidence of evolution being incorrect would you? But the Gaps, you say? LOL

Anyway, your Darwin and Futuyma quotes are quite correct. Natural selection is the primary, but not the only mechanism by which evolution occurs. That most genes are not actively being selected for or against is nothing more than proof for punctuated equilibrium - take Junco evolution for instance - this little sparrow has many, many genes and many traits for which those genes code - yet only a couple of them (size and white in the tail) are changing (at least as far as we can tell). Presumably, change in all other genes/traits could be occuring as well, but not by selection, by molecular drift as neutral theory describes it.

In short, I see no reason why both might not be acting at the same time (when looking at the overall gene pool of a species), in different regions of the genome.

Statements like…

“modern sythesis is ill-defined and will change it’s definition so long as it can assert “Anything But Design.”"

“…that neutralist and selectionist theories continue to identify fatal flaws in each others theories, leading to the inviting possiblity that neither viewpoints of organic evolution are right, but are both are wrong.”

Dan said:

If by “dead,” you mean there’s a better theory with supporting evidence (peer-reviewed evidence, etc.),

No. I meant dead as in dead wrong, which implies any peer-reviewed literature supporting it is also dead wrong.

But regarding the issue of neo-Darwinism and neutral theory.

I am convinced that natural selection has been the main, but not the exclusive means of modification

–Charles Darwin

or how about Futuyma 1986:

The major tenets of the evolutionary synthesis, then, were that populations contain genetic variation that arises by random (ie. not adaptively directed) mutation and recombination; that populations evolve by changes in gene frequency brought about by random genetic drift, gene flow, and especially natural selection

So if natural selection is the main means of modification, the implication is that most changes ought to have a selective influence with respect to immediate fitness. But here is what the neutralists brilliantly demonstrated:

This gives a rate of nucleotide substitution per generation of at least 20, making the contrast still greater with Haldane’s (1957) estimate of 1/300 per generation as the standard rate of gene substitution in evolution. Considering the amount of selective elimination that accompanies the process of gene substitution (substitutional load, see Chapter 5), the most natural interpretation is, we believe, that the majority of molecular mutations that participate in evolution are almost neutral in natural selection.

Theoretical Aspects of Population Genetics by
Kimuara and Ohta

and Dan wrote:

And as for the neutral theory of molecular evolution that Kimura developed, it absolutely fits with the modern evolutionary synthesis

In neo-Darwinism Natural Selection was the main means of modification, and Kimura made a devastating argument to the contrary. Thus the assertion that neutral theory absolutely fits with modern synthesis is an admission that modern synthesis is ill-defined and will change it’s definition so long as it can assert “Anything But Design” (ABD).

But even with Kimura’s fine and devastating critique of selectionist evolution, neutral theory does not account for the formation of large scale biological innovation. Stochastic processes which are at the root of neutral theory can not account for large scale specified or irreducibly complex structures any more than a noise generator (also a stochastic process) can make a Rachmaninoff Concerto.

And finally, design advocates should take note, as did Geneticist Michael Denton, that neutralist and selectionist theories continue to identify fatal flaws in each others theories, leading to the inviting possibility that neither viewpoints of organic evolution are right, but are both are wrong.

And thanks for taking a Lynn Margulis quote out of context. Her endosymbiosis theory has been suggested to be in opposition to the modern evolutionary synthesis, but if you look at them more closely, the two theories are not incompatible and the truth is likelier to be that natural selection works on many levels (genetic up to the ecosystem) and variation is introduced both at the genetic and the cellular level.

And as for the neutral theory of molecular evolution that Kimura developed, it absolutely fits with the modern evolutionary synthesis - think of it as the molecular basis for genetic drift.

“The neo-Darwinist population-genetics tradition is reminiscent of phrenology, I think, and is a kind of science that can expect exactly the same fate. It will look ridiculous in retrospect, because it is ridiculous.” Lynn Margulis

Oh, and in regard to having better theories, the willingness to say one is wrong before having a replacement makes sense. If Kepler or everyone else continued to believed Ptolemaic epicycles were adequate and good enough, who knows where we’d be today. Skepticism is to be welcomed by science not rejected by it. Davidson and Margulis have reasonable doubts, and last but not least Pigliucci knows a neo-Darwinism is crying out to get fixed (if such a thing is even possible).

And regarding peer-reviewed evidence for evolutionary biology, don’ t you mean peer-sanctioned opinions?

And just out of curiosity, do you consider Kimura-Ohta-Jukes-King’s theories Darwinian?

If by “dead,” you mean there’s a better theory with supporting evidence (peer-reviewed evidence, etc.), you’ve got to be kidding.

Is Gravity “dead” too?

Sorry in advance for the smart-ass comments, but STC’s just askin’ for it. ;-)

Furthermore, the neo-Darwinian variety of Darwinism is dead.

The statement “Darwinism is one of the best theories in the history of science,” is pure rubbish. It has made no significant predictions that have been fulfilled. It makes almost no predictions that are testable.

Behe claimed under oath in in his Kitzmiller testimony that

…I regard my paper with Professor David Snoke as to be arguing for the irreducible complexity of things such as complex protein binding sites.
The Behe and Snoke paper explicitly (badly) modeled exactly the same sort of structure as the Bridgham, et al. paper. It sure seems relevant to IC given Behe’s sworn testimony.

At first I had to say I sympathized with RBH’s and Musgrave’s position, and so it is understandable that they interpreted Behe’s remarks regarding Bridgham as a rejection soley on the basis of a protein-ligand system, when the rejection was based on the lack of SEVERAL parts. I pointed out 2 amino acids are quite a stretch to be arguing for SEVERAL. Behe and snokes papers helped quantify what SEVERAL should mean in a context of single protein binding sites.

Over on Panda’s Thumb PvM reaches some interesting conclusions from Prof. Psiaki’s guest post of 4/6. He seems particularly drawn to Psiaki’s final sentence:
The principle of irreducible complexity does not give one all of biology,…