"The intuitive feeling that pure chance could never have achieved the degree of complexity and ingenuity so ubiquitous in nature has been a continuing source of skepticism ever since the publication of the Origin of the Species; and throughout the past century there has always existed a significant minority of first-rate biologists who have never been able to bring themselves to accept the validity of Darwinian claims ....
Perhaps in no other area of modern biology is the challenge posed by the extreme complexity and ingenuity of biological adaptations more apparent than in the fascinating new molecular world of the cell
.... To grasp the reality of life as it has been revealed by molecular biology, we must magnify a cell a thousand million times until it is twenty kilometers in diameter and resembles a giant airship large enough to cover a great city like London or New York. What we would then see would be an object of unparalleled complexity and adaptive design. On the surface of the cell we would see millions of openings, like the port holes of a vast space ship, opening and closing to allow a continual stream of materials to flow in and out. If we were to enter one of these openings we would find ourselves in a world of supreme technology and bewildering complexity...
... Is it really credible that random processes could have constructed a reality, the smallest element of which--a functional protein or gene--is complex beyond our own creative capacities, a reality which is the very antithesis of chance, which excels in every sense anything produced by the intelligence of man?"
---from Evolution: A Theory in Crisis, Michael Denton, copyright 1986, Adler and Adler
The challenge to his evolutionary framework was underlined by the fact that the only explanation Darwin was able to offer in Origin was his appeal to the 'extreme imperfection' of the fossil record. But this was largely a circular argument because the only significant evidence he was able to provide for its 'extreme imperfection' was the very absence of the intermediates that he sought to explain.
The gaps were a particularly acute problem for Darwin as he was absolutely insistent that evolution by natural selection must be a very slow gradual process:
That natural selection generally acts with extreme slowness I fully admit...I do believe that natural selection will generally act very slowly, only at long intervals of time...Slow though the process of selection may be. As natural selection acts solely by accumulating slight, successive, favourable variations, it can produce no great of sudden modifications; it can act only by short and slow steps.Such a slow gradual mechanism of evolution necessitated innumerable transitional forms and this was acknowledged freely by Darwin on many occasions in the Origin.
Denton, concludes, "The absence of intermediary forms essentially emptied all Darwin's macroevolutionary claims of any empirical basis." (Denton, pp. 56-57)
The assumption back in Darwin's day was that we had not sufficiently examined and explored the fossil record, that transitional forms would be uncovered in abundance--one day. But here we are in the 21st century, and are no closer to finding confirming fossil transitional forms that support gradualism. What we see is stasis and saltations or jumps to very different forms that cannot be the result of gradual macro evolution.