In their new book What Darwin Got Wrong Jerry Fodor and Massimo Piattelli-Palmarini argue that twentieth century evolutionary theory--the result of the forced marriage between Mendelian genetics and Darwinism--is substantially flawed. Peter Forbes's candid review of the book is worth a look. Forbes explains the crux (or at least one of the cruxes) of the problem:
The problem is that the source of novelty is so dammed elusive. Most genes don't change very much at all, even the body-plan genes seem to be very similar in the mouse and blue whale. Or, to compare even less similar creatures: a mouse gene essential for building the eye can be inserted into the fruit fly to produce a fly eye! This refutes a key prediction of Neo-Darwinism, Ernst's Mayr's statement that it would be futile to look for similar genes in different creatures. Neo-Darwinism predicted that random mutations would pile up until the genes of mice and men were as different as, say, the Finno-Ugric and the English languages.
The best bet at the moment seems to lie in the altered timing of processes involving cascades of many genes. And what alters the timing? Well, now we're at the frontline of research, and there are candidates but no certainties. One of the most dramatic possibilities is that elements of DNA have entered the germline from viruses. Putting this together with Margulis's ideas on the evolution of the ancestral single cell, we can see that viruses and bacteria are starting to loom very large in the picture of evolution.
False predictions, absence of a credible mechanism, and unfounded speculation--these well sum up evolutionary theory. Evolutionists, however, can take solace that this is a friendly attack. Fodor and Piattelli-Palmarini are not questioning the ultimate truth of evolution. Evolution may be all wrong, but it is still true. That we know. As Forbes explains:
Given the provocative title, it's important to stress what Fodor and Piattelli-Palmarini's polemic is not. From the outset, they assert that they have no quarrel with the course of evolution and its timescale, only its mechanism. Furthermore, they affirm that they are "outright, card-carrying, signed-up, dyed-in-the-wool, no-holds-barred atheists." For that small relief, much thanks.
Evolution may make no sense, but it will always be true. It must be, for god would never make this world. So evolution will flit from nonsensical idea to nonsensical idea in its never ending attempt to make sense. Who knows what the theory of origins will be in the future, but it will be called evolution. And it will be true. Religion drives science and it matters.