With more recent mosaics (e.g. Tiktaalik and Pakicetus and other "missing links") in tetrapod evolution, the "overwhelming evidence" for "evolution as fact" seem to be an abductive inference based on fossil geology, comparative anatomy, and embryological similarity. And now, as then in Darwin's day, a historical evolutionary process (whatever the mechanism) is compared to what a typically atheist/deist biologist presumes an anthropomorphized cosmic designer would or wouldn't have done. This is the "one long argument" of Mr. Darwin and these theological arguments haunt science textbooks to this day.
In an era of evolutionary thought where Darwin's Tree of Life is being discussed as an outdated concept and natural selection as maybe not being a central explanatory mechanism for macro evolution, it begs the question what biologists (or anybody) mean when they assert that "Evolution is a fact." "Evolution" may be the most overloaded term in all of science. It refers to a historical "fact" and a "theory" of causation and a trivial phenomenon (microevolution) and a research program and a narrative (and a religion according to Michael Ruse).
James Shapiro, a fairly mainstream microbiologist and evolutionary biologist has written a book Evolution: A View from the 21st Century that challenges a lot of the assumptions of the mainstream Evolutionary Synthesis. He differentiates between several key aspects of evolution.
General discussions of evolution, especially in the context of the “Intelligent Design” controversy, suffer from an unfortunate conflation in the minds of the lay public (and also of scientists) of three distinct questions:When you think about, the 3rd item is all over the place right now. There is no consensus on whether natural selection is a sufficient explanation for what Darwin used it to explain--the origin of all species--and that is an understatement. The 1st item is in a similar state of disarray in terms of a coherent theory, but this is less surprising and more widely understood--and the chief reason why many theorists separate it from the Evolutionary Synthesis. Now, the 2nd item is something that many, though not all, ID theorists either agree with or at least grant for argument's sake. Many ID theorists do dispute whether the evidentiary basis for common descent is as strong and coherent as neo-Darwinists and evolutionary materialists aver, but ID is generally not in conflict with an "evolutionary process" of some kind.
•  The origin of life
•  The evidentiary basis for an evolutionary process
•  The nature of evolutionary change
The one issue that has effectively been settled in a convincing way is the evidence for a process of evolutionary change over the past three billion years. The reason the answer to this question is so solid is that every new technological development in biological investigation—from the earliest days of paleontology through light microscopy and cytogenetics up to our current molecular sequence methodologies—has told the same story: living organisms, past and present, are related to each other, share evolutionary inventions, and have changed dramatically over the history of the Earth.* [emphasis added]How much an ID theorist agrees with a common "story" depends on what he means by "related to", "share", and "history." Even a Young Earth Creationist might agree with these articles as stated, though Shapiro probably means "history" as the mainstream interpretation of the "fossil record" rather than simply as time. But the majority of ID theorists, including Steve Meyer, Michael Behe, William Dembski, and even Jonathan Wells, seem to adopt or use the mainstream view of fossil dating.
The central point of departure for Intelligent Design is whether there is a significant component of intelligence that is required for a complete explanation for the biological world. But there is a real and general way in which both ID theorists and creationists see organisms as related to each other and sharing innovations in a non-Darwinian sense, an innovative relationship between living things that has unfolded in a dramatically changing diversity over Earth's history (whether a long history or short).
And the question remains whether even the evidence for an evolutionary process, intelligent or not, is quite so strong without a prior conviction that all natural phenomenon have a strictly natural cause (where "natural" essentially means "material" or "physical"). As evolutionist par excellence Richard Lewontin said:
Our willingness to accept scientific claims that are against common sense is the key to an understanding of the real struggle between science and the supernatural. We take the side of science [defending science against "attackers"?] in spite of the patent absurdity of some of its constructs, in spite of its failure to fulfill many of its extravagant promises of health and life, in spite of the tolerance of the scientific community for unsubstantiated just-so stories, because we have a prior commitment, a commitment to materialism. It is not that the methods and institutions of science somehow compel us to accept a material explanation of the phenomenal world, but, on the contrary, that we are forced by our a priori adherence to material causes to [seek only material causes in science]. Moreover, that materialism is absolute, for we cannot allow a Divine Foot in the door. The eminent Kant scholar Lewis Beck used to say that anyone who could believe in God could believe in anything. To appeal to an omnipotent deity is to allow that at any moment the regularities of nature may be ruptured, that miracles may happen.And that, Charlie Brown, is the meaning of Slippery Slope. Somehow, this "Divine Foot in the door" didn't stop scientists like Isaac Newton, nor the many "creationist" scientists that preceded both Darwin and widespread Deism, from real, ground-breaking science. Somehow, in the absence of an "absolute" materialism, both common sense and the belief in a universe made comprehensible by a rational Designer made them expect an orderly world where miracle was exceptional but not excluded.