Past that, the nanotubes just have to get locked into the matrix of the silk in the right orientation... which could just happen to anything of the right dimensionality in the silk as it anneals into shape.
This reminds me of a story of dolphins, who apparently suffer a lot from mercury poisoning, mostly caused by the smog of unfiltered coal plants entering their ecosystem. One issue of mercury poisoning is that the body has no way to get rid of it - it gets stored in the fats, IIRC. Unless you're a mammalian mom. Then the body gets rid of mercury through your milk. Mercury is most lethal at the infant age. So in short, most dolphin mothers' firstborns die [0].
Anyway, perhaps the carbon fibers are actually toxic, and the only way the spiders can get rid of the material is through their silk?
[0] http://www.takepart.com/article/2015/02/11/revealing-cove-do...
Except for not being a dog, such a spider is anticipated in Goethe's little poem «Annonce» (Advertisement):
A little dog is sought
that never barked nor bit
takes broken glass as feed
leaves diamonds as - -
Ein Hündchen wird gesucht,
Das weder murrt, noch beißt,
Zerbrochene Gläser frißt
Und Diamanten scheißt.chuckles to self
A lot of people? The carbon has to end up somewhere. I don't see this as surprising at all, any more than it's surprising that if you, a human, eat a lot of arsenic, you'll add some of it to your hair. Growing hair and growing silk are not fundamentally different activities.
Yet despite the bargain bin trappings, the results are so incredibly cool! The spiders just... incorporated carbon nanotubes and graphene into their silk-spinning process? What?! What's the mechanism?! No one knows! Who would have guessed this would work? It sounds like a joke experiment they cooked up while waiting for the glassware to bake!
Hopefully a more rigorous study replicating and expanding on these results will appear. But it just blew my mind the way this particular science appeared.