• Lynn Margulis (1938- ): cell mergers/symbiogenesis as a source of evolutionary novelty
It seems all of these scientific mechanisms do not fit into a Darwinian framework.
False. Not long ago I reviewed a recent college text on zoology which covers Margulis' work in a chapter on evolution. It all fits together, like pieces of a jigsaw puzzle, not as a "square pin in the round hole" controversy as you and ID folks imagine.
Margulis explained how primitive cells evolved organelles, thus extending the reach of Darwin's theory into the dawn of life itself. Since the days of Lynn Margulis, Darwin's principles have been shown to reach back into the prebiotic period.
Your cites do not discredit Darwin's theory as you think. This is just manufactured controversy. All your sources are saying is that there are more ways for variation to occur than by mutation alone. Here's your flaw: no one is claiming mutation alone accounts for variation.
If you remove that bogus assumption, Shapiro and the rest of your sources are perfectly in tune with Darwin.
One of the things I notice about people who attack Darwin is that they seem to know little about him or what he actually said. For example, few people even know the name of his book, the one that fired the shot heard 'round the world. Here it is:
On the origin of species by means of natural selection, or the preservation of favoured races in the struggle for life
Just from the title alone, he gives you a pretty good idea of what natural selection is.
Instead of claiming what Darwin did or did not say about variation, why don't we just go to the source and find out what the problem is? Here he is at the opening of Chapter V (The Laws of Variation):
I HAVE hitherto sometimes spoken as if the variations—so common and multiform in organic beings under domestication, and in a lesser degree in those in a state of nature—had been due to chance. This, of course, is a wholly incorrect expression, but it serves to acknowledge plainly our ignorance of the cause of each particular variation.
after which he goes into an exhaustive treatment of the subject, by referencing the various laws known to influence variation. After that, he concludes (p. 170):
Whatever the cause may be of each slight difference in the offspring from their parents—and a cause for each must exist—it is the steady accumulation, through natural selection, of such differences, when beneficial to the individual, that gives rise to all the more important modifications of structure, by which the innumerable beings on the face of this earth are enabled to struggle with each other, and the best adapted to survive.
Notice, none of your sources have any problem with Darwin's conclusions about variation.
That's because no such controversy exists.