PJ said:
That is, until it is observed to be possible in the laboratory, the idea that evolution is fact in the same sense that the laws of motion, or the chemical basis for gunpowder explosions is spurious.
The exact kinds of change we describe as "Darwinian evolution" have been observed in the laboratory and in the field. It is only the extension to long times or large scales that remains unobserved.
The same is true for extensions of other theories to long times or large scales. And the same uncertainty is involved. As it turns out, Newtons Laws do not extend to long times and large scales - and the failure to so extend was noticed and investigated as soon as technology allowed.
No such failure has been observed for Darwinian Theory as yet. Certainly the family and genus levels of organization, involving a few million years or so, have fallen neatly into Darwinian predictions.
There is a recognised opening for a serious modification of the theory in the failure of some genetic lineages to produce adaptations common in others. The possibility that certain arrangements of the DNA code or its expression cannot with resaonable probability evolve in certain "directions" due to the path in modification space they have already traveled - a sort of QWERTY phenomenon writ deep - is known and is being considered. But it requires accepting the basic theory as a given, for even consideration.
PJ said:
For instance, it is well known that many genetic studies have shaked up the "tree of life". Animals thought to be related closely have been shown to not be so.
Not quite. The relative distance of various animals from each other has been affected, but normally in areas in which argument already existed, and as far as I know no carefully and uncontroversially described "close" animals have been found to be genetically "distant" on any absolute scale.
In plants, which are less well known, some surprises have turned up where there had been little attention paid. And in fungi, which are poorly known, many surprises still await us no doubt. But this marks ignorance and inattention, not disagreement with the well known and accepted.
PJ said:
Should we not then expect to satisfy a similar requirement to affirm the validity of evolutionary processes being able to account for the diversity of life as we know it?
We have met those expectations, producing at a small scale and in short times exactly the changes whose extension to large scale and long times - as with the stellar reactions and the volcano chemistry studied small and quick in the lab - our theory demands.