First, the reference I promised. The alternative to UCA that has been considered is called "convergent evolution", and it still seems to be an active area of research. Quite a few sources on it are readily available, but this is the one I was thinking of:
"Convergent evolution of gene circuits"
Conant and Wagner
Nature Genetics 34 (2003), 264-266.
Ah, I see the source of the confusion then. No, it is not the paper you are citing. It is simply your misunderstanding of what convergent evolution is.
Convergent evolution is the phenomenon of species who are not closely related to one another but nevertheless have astounding similarities to one another because they have adapted in similar ways to a similar environment.
A basic example is the streamlined form of teleost fish, mosasaurs and cetaceans. All responded to a marine environment with adaptations that were effectively dynamic in that environment. But none is a direct ancestor or closely related to the others in such a way that the adaptation could have been inherited one from the other.
However, "not closely related" does not equate to "not related at all". For example, although mosasaurs and cetaceans are on different branches of the amniote tree, they are both amniotes and so more closely related to each other than either is to fish. And fish, of course, are vertebrates, so more closely related to the other two than any of the three are to arthropods such as lobsters or beetles. IOW, convergent evolution takes place within an overall framework of universal common ancestry.
Also, I'm going to be referencing a paper by Theobald (and its critique) in my reply to you:
"A formal test of the theory of universal common ancestry"
Douglas L. Theobald
Nature 465:13 (May 2010), 219-222.
"The common ancestry of life"
Eugene V Koonin, Yuri I Wolf
Koonin and Wolf Biology Direct 2010, 5:64.
Yes, I remember reading both of these.
First, I'm going to nitpick on what you said. I don't doubt that evolutionary biologists have a high confidence level and give little if any consideration to some issues. But most professionals I have known steer away from calling it a fact. Ever since Popper, saying science has "proven" something is considered bad form. Rather, the statement would probably go something like:
The general consensus among biologists is that evolution has not been falsified.
Not quite. Your final statement would apply to the theory of evolution, not to observed evolutionary change. Observed evolutionary change (such as a shift of 3% in the alleles of a continuously reproducing population) is a fact.
But what drives this process of change? That is where the theory of evolution comes in. And that is where one would correctly state that the theory of evolution has not been falsified. Similarly, universal common ancestry is an inference from the theory, not a directly observed fact. So one would also correctly say of UCA that it has not been falsified.
In addition, Popper's own notions are themselves somewhat controversial. Stephen J. Gould has a great quote about the shifting lines between fact and theory especially when a theory is very well supported as evolution, natural selection and universal common ancestry are.
In science "fact" can only mean "confirmed to such a degree that it would be perverse to withhold provisional consent."
When I speak of "closed issues" in regard to evolution, I mean issues that fit his definition of "fact".
Based on the references I provided, I wouldn't think so. During the previous discussion I mentioned, I asked if anyone has ever attempted a falsification test on evolution. The answer was: Yes, Theobald has (the foregoing citation).
However, all the reviews I have found consider Theobald's attempt a failure. In fact, Koonin & Wolf (another of the foregoing citations) go so far as to suggest that the non-deterministic nature of evolution makes the construction of a good falsification test impropable ... which has been my argument for quite some time.
That is pretty much what I gleaned too. The basic problematic with very early life is that there is much more horizontal gene transfer and that tends to blur lineages and even render them meaningless. A single origin of eukaryotes is much better established. But that apparently did not occur during the first two billion years of life on earth.
And according to good scientific practice, what do we call something for which no falsification test can be designed? An assumption.
No, I wouldn't call it an assumption; a better term would be speculation.
You have to make an assumption in order to form a testable hypothesis. After all, what you are going to test is whether the assumption is probable.
One can speculate that there is a multiuniverse. But we can't test for that. So long as we recognize that we can't test for it, and therefore draw no conclusion, it remains a speculation. To conclude that there is or is not a multiverse would be an unwarranted assumption.
The case with universal common ancestry is different. We can't test for a multiverse because we have no way at all (at least not yet) to gather evidence or predict what evidence would support or falsify the concept.
But we have ample evidence that does support universal common ancestry. The concept of universal common ancestry allows scientists to make predictions about the past, present, and even to a limited extent, the future of evolutionary change and those predictions can be tested. To date, the results of such testing are overwhelmingly positive. So even if we come to the point that we have to rest with an inference for which a good definitive falsification test cannot be designed, the hypothesis of universal common ancestry is still well warranted by the evidence. Certainly to the point where it would be perverse to withhold provisional consent.