Regarding why Neo-Darwinians are so tied to theories that are actually disproved by the evidence, Gould (who was himself an anti-theist) noted in his famous essay "Darwinian Fundamentalism" the distressing fact that Neo-Darwinianism had been transformed from a Scientific theory into the new unshakable faith of the present age. He and his colleagues criticized the willingness of educational establishments to continue teaching portions of Darwinian evolution that had long since been scrapped, as well as their unwillingness to embrace modern theories such as the "wonderful monster" concept of change via simultaneous rapid mutations (Punctuated Equilibrium). In fact, although he held creationists in utter contempt, he too was embarassed by the tendency of text-book publishers to print pictures of hypothetical "transitional life forms" that no fossil evidence has ever uncovered and which are biologically untenable.

For instance, Gould and many other paleontologists were only too well aware that a structure in-between an arm and a wing that was actually neither, made for a life-form that even under the concept of "survival of the fitest" would be "deleted." As most modern paleontologists point out, we have fossil arms and we have fossil wings, we have fossil arms and fossil flippers, but no transitional forms in between. They've generally given up on searching for biologically untenable "links" and because design and creation are immediately ruled out (materialism is after all the ruling philosophy in the academy) as possibilities, they have generated a series of increasingly bizarre and unlikely theories such as punctuated equilibrium which speculates that at some point a lizard gave birth to a bird, and said bird found another similar mutant and the bird species began. At some point you have to step back and scratch your head and say, "and we Christians are the kooks because we believe God made birds and lizards?"

So the fossil record far from proving Neo-Darwinianism actually does the opposite. Darwinians always assumed they would find "transitional life forms" showing the development of one species into another. They haven't, and in fact, recent digs particularly in the Cambrian strata in China are showing that the classic Darwinian tree, which went from a single common ancestor to an increasing diversity of life is actually upside-down. As we've mentioned there was a sudden "explosion" of life in the Cambrian period, and much less diversity afterwards, in other words, there are fewer and fewer lifeforms as one goes up the tree, not more and more. The fossil record tells us that species became extinct, but it doesn't tell us new ones evolved from the existing ones. All the assumptions, taken on faith, by Darwinian scientists in the 19th century have failed to pan out in the fossil record.

But even more damaging to the Neo-Darwinian faith are the advances in DNA research and Biochemistry, areas that Darwin had no knowledge of and which are proving antithetical to his theories. The discoveries in these fields are showing to the chagrin of Darwinians that there is no natural mechanism for ADDING information to the DNA sequence that would allow, for instance, for a change of species. What this means is that while we can tinker with DNA in a lab, "nature" simply doesn't have a mechanism for changing DNA in the way that would allow for Flatworms to become Field Mice. It simply can't be done, and it doesn't matter how much time or mutation one posits.

Proteins are made up of long complex chains of organic chemicals called "amino acids", various proteins are brought together to form structures within cells each of which has a highly complex role to play - they are in essence the "engines" of the cell, the composition of these amino acid chains is determined by the information contained in DNA. It is the DNA code that instructs the cellular machines that put together the Amino acid chains in what order they are to go. Nothing in Darwin's theory can account for the creation of the information in DNA or, most importantly, how amino acids were assembled in the correct order to form proteins prior to the creation of DNA. Proteins cannot precede the DNA necessary to construct them and inorganic chemicals cannot create information.

Also, natural selection cannot occur without the driving force of life and death and thus "genetic favoritism" and gradual change. What this means is that prior to the existence of life-forms Neo-Darwinianism lacks an engine to drive it. Natural selection actually presumes the existence of at least cellular life-forms before it can operate. So it cannot explain the combination of organic chemicals or even their creation.