Legal analogies for rights to self-replicating intellectual property

We finally got around to watching Food, Inc. last night, and while most of it wasn't new to us, it was definitely worth viewing.  I'd recommend it.  One of the subjects discussed was Monsanto's role in the genetically modified seed industry and the farmers that it has successfully driven to ruin.  Much as in the chicken industry, farmers who opt-in to business with Monsanto soon become trapped by restrictions and costs.  Because the genetic modifications of Monsanto seeds are patented, farmers are unable to save seeds from one season to the next, and must re-buy every year.  Most of this portion of Food, Inc. discusses the farmers and seed cleaners actively hunted down and sued by Monsanto lawyers.

The idea of farmers not being able to save their own grown seeds is ridiculous on the face of it, but after watching the documentary I was wondering what legal analogies might be drawn elsewhere in order to make some progress with more fair patent regulations.  The obvious analogue seems to be self-replicating nanotechnology.  Forget about existential threats like grey goo- the question of who should own later generations of these technologies is vexing enough by itself.  It's sensible enough to say that if Monsanto creates a genetic modification, they have some exercisable rights concerning its use.  But is it reasonable to tether farmers who fairly buy these products for generations on end?  A living seed (or even a self-perpetuating machine) is an inherently generative thing.  It doesn't make sense to create this sort of product and then pretend that it only has one shelf life.

...actually (maybe the reference to "shelf" led me here?) it just struck me that similar analogies could be drawn for ownership rights of e-resources in libraries.  As e-books become more mainstream and libraries purchase them for patron use, some publishers have threatened limited ownership rights, so that libraries would lose access to an e-book after so many check-outs (and I believe the proposed number is absurdly low... like two dozen check-outs or so) and have to repurchase it.  The argument of the publishers has been that e-books don't wear out like printed books, and it's unfair to publishers to sell away titles that won't ever deteriorate and need replacing.

At least in this case each individual check-out isn't construed as a reproduction of the publisher's intellectual property as in the above biotech/nanotech instances.  But similar questions apply.  And the basic one is this: when a fair purchase is made on a product for which proliferation of use is understood as inherent to the properties of the product (future generations for seeds or nanobots, future loans for a book), on what basis can the IP owner really claim the right to regulate later usage?

On the bright side, farmers and seed producers have recently sued Monsanto in an effort to avoid being punished when other peoples' Monsanto crops contaminate their own.  This hardly begins to approach proper recompense for these farmers, but keeping a multinational juggernaut from suing its victims into the ground is at least a start in the right direction.