Evolutionary Tree

[SteveII]

The fact that the phylogenetic tree is not as predicted and has problems matching the data to the theory means there is still much to learn and still much to prove to get 'common ancestry' to the point where we know how it works.

Learn your philosophy of science: science is a probabilistic field, it accepts and rejects explanations for the available evidence based on probabilities, not sure fire truths. There are holes in every theory, but the fact that we can't explain gravity- and in fact, a lot of our science is demonstrably wrong regarding that particular force- does not grant you license to slyly assert that maybe gravity doesn't exist, and angels hold us all down to earth.

If we don't know how it works how can you call it a fact?

The same is true of gravity. The problem here is that you're committing the "99% = 0%" fallacy: just because we don't know everything about something does not mean that all of our observations don't pan it out anyway.

If common ancestry is not a fact and still only a theory,

Learn your basic scientific terminology: theories are not "only" theories and not facts, theories are explanatory frameworks made up of multiple facts working in concert. Does it... trouble you at all, that you don't understand even how extremely elementary scientific terms are defined?  

then the big picture of evolution (defined as end-to-end explanation of the diversity of life, common ancestry, decent with modifications) is also not a fact, but only a theory. Is that a fair assessment?

Yes, because theories are comprised of constellations of facts. They are, in reality, much much stronger than a fact could ever be.

It's your conclusion that isn't a fair assessment.

I understand the difference between fact and theory and that the word 'theory' has multiple meanings.  When I use them both in the same sentence however, my meaning is clear. So, when every third atheist tells me evolution is a fact, I should continue to remind them that only parts of it are fact. 

Regarding comparing evolution to gravity, at least we can drop the apple to be sure (deduction) that it is a fact regardless of us not knowing how it works exactly. However, in evolution, we have to infer from our observations that evolution is a fact (or not) -- and unless we figure out at least the major pieces, this inference is based on the assumption that the philosophical position of naturalism is true. I'm not saying this is wrong, just observing the distinction.  

Regarding your closing remark 'Yes, because theories are comprised of constellations of facts. They are, in reality, much much stronger than a fact could ever be.' That would only be the case if there was a constellation of facts. Evolution seems to be missing a couple of core 'facts': common ancestry, how could a biological network evolve, evolving traits with a low selection coefficient, convergent genetic evolution, and more. So...how would you characterize a theory that is comprised of a constellation of theories?