Jim Manzi likes to type a lot (and now so do I), so when he wrote this, he makes some curious statements and mistakes.
"No matter how far science advances, an explanation of ultimate origins seems always to remain a non-scientific question."
Does it? I notice science keeps pushing it back, further and further into the realm of the unknowable. This leaves those who would invoke god as an explanation less and less to do. Might it be conceivable they then eventually be left with nothing to do after all? (At least as far as explaining the natural world is concerned.)
"Evolution in nature is more complicated — but the complications don’t mean that the process is goalless, just that determining this goal would be so incomprehensibly hard that in practice it falls into the realm of philosophy rather than science."
Or this is wrong, and evolution in nature is, in fact, goalless.
"The combination of a constantly changing fitness landscape and an extraordinarily large number of possible genomes means that scientists appropriately proceed as if evolution were goalless, but from a philosophical perspective a goal may remain present in principle."
Possibly. But why burden an explanation with unnecessary multiplicity?
"Science can not tell us whether or not evolution through natural selection has some final cause or not; if we believe, for some non-scientific reason, that evolution has a goal, then science can not, as of now, tell what that goal might be."
If you posit the existence of goals--of the existence of something which science can't disprove exists--then why submit that they exist at all, especially if they are completely superfluous?
We can imagine goals because we see primarily the successes of evolution (even extinct organisms are, for their time, outrageously successful), we don't see the failures, and yet there were always far far far more failures than successes. If we saw both in volume and proportion, would designists still suggest evolution had goals after all? Possibly they might, but would it still seem reasonable to do so?
"The theory of evolution, then, has not eliminated the problems of ultimate origins and ultimate purpose with respect to the development of organisms; it has ignored them."
Inasmuch as there is nothing to ignore (Evolution does not, for instance, strictly address abiogenesis. That's still a different department, and it makes no sense to fault evolution for not addressing it), but this, too, is wrong. Goals were often suggested as evidence for the reproductive success for some lineages over others by plenty of early workers and naturalists. It took time to dispense with this imaginary baggage, because it gradually became apparent that success was not a target of natural selection, but a result; one where indifference rules. Goals can still be imagined, but this is only possible by ignoring all of the failures, something science is certainly not doing.
"These problems are defined as non-scientific questions, not because we don’t care about the answers, but because attempting to solve them would impede practical progress."
Practicality doesn't prevent physical cosmologists from working on problems. And can Manzi really say no progress has been made? Practicality also poses no obstacle to mathematics (even before when practical uses for crypto were found last century).
"Accepting evolution, therefore, requires neither the denial of a Creator nor the loss of the idea of ultimate purpose. It resolves neither issue for us one way or the other. The field of philosophical speculation that does not contradict any valid scientific findings is much wider open to Wright than Coyne is willing to accept."
I think it's interesting that Manzi is constrained by his argument within the limits of the physical world and the information it generates, things which we only know about and benefit from by way of science, rather than any other kind of philosophy.
But he's not wrong. I do think his conclusion is correct (even if the reasoning behind it is plain wrong); science cannot address the existence or nonexistence of God; both views are therefore compatible (so long as religious philosophy chooses to not contradict reality).