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If you were to create 5,000 different websites on different domains and linked them all together (in an natural way...not every site links to every other site, etc.) BUT those 5,000 sites have zero incoming links from anywhere else...would these sites have PageRank or even get indexed in Google for that matter?
The point I'm getting as is whether or not every site in Googles index can be traced back to every other site by following links....or are there "islands" of sites, if you will, that have no links with other "islands" of sites.
Of course, with 5000 sites, I'd imagine someone would link to them one day, and that's the end of your experiment.
But why do you think 5000 is a good number. Surely one site is adequate to test your hypothesis? People think PageRank is SiteRank.
I'd have thought one site with a dozen pages would tell you all you wanted to know, and more easily set up too!
Cumulatively, in theory, you should be able to get to some visible with no incoming links to the island.