Hi! Author here. You're right — but two things to consider here.

First, that quote is referring to human-made systems, not natural ones (as is the rest of the essay!) and I think our views align on whether human systems regularly work.

Second, natural systems (and all complex-enough systems) are always running in some degraded fashion. So what "working" means is ambiguous: they are broken, yet accomplishing the goal. The quote from the essay refers to "working" in the "free of faults" sense, in which I again think our views align.

"they are broken, yet accomplishing the goal."

Are they really either of those two things? Natural systems have no "goal", they just are. If they change, they change. If they stay the same, they stay the same. Because there is no goal, there is no "broken". It is only we who assign some sort of meaning to them and characterize them as "working", either because they meet our needs, or just because we are inherently impressed by complex systems.

If you follow through on there being no goal, there is no working or not-working state, in which case it bears no relevancy on the question of whether "Working" is not the natural state in a complex world!

Or rather, you could say TFA is made more correct, by virtue of “working” not being a natural state in the first place.

But if we allow room to anthropomorphize, we can basically state that the natural goal of a natural system is to keep doing what it do, at least in regards to the larger outcomes. And for some strange reason, these systems are shockingly difficult to influence at meaningful scale in ways that are rarely true for the systems we design. In one sense, they continue to operate despite continuous minor and possibly major (but not catastrophically so, by definition) perturbations to their state

You need to burn ridiculous quantities of dino juice to influence the weather system. You need to look at windows a little funny to bring it to a complete halt. You need to bully only few substations to bring down the electrical grid.

I’ve read recently about natural systems in the book Antifragile. It’s interesting how those systems can become better.

holy unrelated discussion, batman! it sure yaps