When discussing organic evolution the only point of agreement seems to be: "It happened." Thereafter, there is little consensus, which at first sight must seem rather odd. - Simon Conway Morris (palaeontologist, Department of Earth Sciences, Cambridge University, UK), "Evolution: Bringing Molecules into the Fold," Cell, Vol. 100, pp.1-11, January 7, 2000, p.11 
The origin of the [genetic] code is perhaps the most perplexing problem in evolutionary biology. The existing translational machinery is at the same time so complex, so universal, and so essential that it is hard to see how it could have come into existences or how life could have existed without it. The discovery of ribozymes has made it easier to imagine an answer to the second of these questions, but the transformation of an 'RNA world' into one in which catalysis is performed by proteins, and nucleic acids specialize in the transmission of information, remains a formidable problem. - Maynard Smith J. & Szathmary E., "The Major Transitions in Evolution," W.H. Freeman: Oxford UK, 1995, p81.
Biologists must constantly keep in mind that what they see was not designed, but rather evolved. - Francis Crick ( Nobel Prize Laureate in Physiology and Medicine), "What Mad Pursuit," 1990, p.138.
Crick is also a fervent atheistic materialist, who propounds the particle story. In his autobiography, Crick says very candidly biologists must remind themselves daily that what they study was not created, it evolved; it was not designed, it evolved. Why do they have to remind themselves of that? Because otherwise, the facts which are staring them in the face and trying to get their attention might break through. - Phillip E. Johnson, Essay: "Evolution And Christian Faith" 
If it is true that an influx of doubt and uncertainty actually marks periods of healthy growth in a science, then evolutionary biology is flourishing today as it seldom has flourished in the past. For biologists collectively are less agreed upon the details of evolutionary mechanics than they were a scant decade ago. Superficially, it seems as if we know less about evolution than we did in 1959, the centennial year of Darwin's on the Origin of Species. (Niles Eldredge, "Time Frames: The Rethinking of Darwinian Evolution and the Theory of Punctuated Equilibria," Simon & Schuster: New York NY, 1985, p14).
There are a number of problems with hypothetical schemes capable of producing rapid, large, coherent changes in phenotypes. Equally large immediate changes in the genotype might be needed, and any large change in genotype or phenotype must surely be sufficiently disruptive to be lethal. And where would a large change in a phenotype or genotype come from? Moreover, suppose an oddity were to be produced, how would a population be established and maintained? (K.S. Thomson, "The Meanings of Evolution," American Scientist, Vol. 70, September-October 1982, pp.529-531, p.530)
All scholarly subjects seem to go through cycles, from periods when most of the answers seem to be known to periods when no one is sure that even the questions are right. Such is the case for evolutionary biology. Twenty years ago Mayr, in his Animal Species and Evolution, seemed to have shown that if evolution is a jigsaw puzzle, then at least all the edge pieces were in place. But today we are less confident and the whole subject is in the most exciting ferment. Evolution is both troubled from without by the nagging insistences of antiscientists and nagged from within by the troubling complexities of genetic and developmental mechanisms and new questions about the central mystery-speciation itself. In looking over recent literature in and around the field of evolutionary theory, I am struck by the necessity to reexamine the simpler foundations of the subject, to distinguish carefully between what we know and what we merely think we know. The first and strongest of our critics to be answered should be ourselves. - K.S. Thomson, "The Meanings of Evolution," American Scientist, Vol. 70, September-October 1982, p. 529.