OK, can you demonstrate an algorithm to show how these will produce the desired results of the experiments.
What kind of algorithm are you looking for, exactly? As a quantitative geneticist, my immediate response would be a standard GxE model:
y = u + a(sub i) + b(sub j) + [a(sub i) * b(sub j)] + e(sub ijm)
where y is phenotype (binary or quantitative; ability to use substrate), u is the population mean, a is the effect of genotype i (users and non-users), b is the effect of environment j (low substrate and normal substrate), a*b is the interaction of the two and e is error. It doesn't seem different from any other mathematical model of GxE.
"Desired results"? I think you mean "results".
Next, since this would naturally be a superior method of evolution, can you explain why this is always not the case under the context of TOE?
?? What do you mean by "superior"? Within what range? Within what context?
Finally, can you apply your conclusions to the following.
Thanks.
http://www.genetics.org/cgi/reprint/120/4/887.pdf
Sequential mutation. Bacteria produce a shitload of individuals. Billions and billions. Probably why they've survived for so long. You'll notice that the study is about adaptation as the movement of DNA elements - translocation of segments, in other words. From page 1: "This study focuses on adaptive mutations that
result from the movement of mobile genetic elements".
A Comeback for Lamarckian Evolution?
The findings provide support for a 200-year-old theory of evolution that has been largely dismissed: Lamarckian evolution, which states that acquired characteristics can be passed on to offspring.
"The results are extremely surprising and unexpected," says Li-Huei Tsai, a neuroscientist at MIT who was not involved in the research. Indeed, one of the studies found that a boost in the brain's ability to rewire itself and a corresponding improvement in memory could be passed on. "This study is probably the first study to show there are transgenerational effects not only on behavior but on brain plasticity."
http://www.technologyreview.com/biomedicine/22061/?a=f
Yes, methylation. Reaction norms in progeny variance, and/or imprinting, depending on the stage. This is what I was saying above. There's really little opposition to non-classical heredity in biology these days. I can't think of anyone who opposes it in any real sense (except for me, with my objections to
some of the data that Pigliucci cites in defense of phenotypic plasticity). These things are explicitly in neo-Darwinian theory; I work in the same area myself. In the old days, people just consigned such effects to error among or even within subjects. Now, workers in the field - myself included - are interested in the subject. To say it's Lamarckian
might be true: now, can you demonstrate Lamarckianism in discrete stages from a tadpole to a
Triceratops, please?