"The normal notion of a patent is that the patent covers the creation of something, but not its use."
Quoting from http://www.nolo.com/legal-encyclopedia/improvement-patents-n... :
> New Uses for Existing Inventions
> You can also get an improvement patent for an innovation that provides a new use for an existing invention. For example, in 2000, the Federal Circuit allowed a patent for the idea of using Bag Balm -- an ointment normally used to soothe irritated cow udders -- to treat human baldness. The court found it patentable, because it's a new use of a known composition.
Quoting from http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3146086/ :
> In addition to patent protection for the original compound and method of use, patents directed to new uses and treatment indications can be obtained. Developing new methods of use for identified compounds can be a successful strategy for maximizing research dollars and for increasing the commercial life.
Those sound like it's possible to patent use, in addition to the 'creation of something.'
There are several types of patents listed at http://www.uspto.gov/web/offices/ac/ido/oeip/taf/patdesc.htm . One is a patent on new varieties of plants (see https://en.wikipedia.org/wiki/Plant_Patent_Act_of_1930 ). I don't think that counts as "instructions or the specifications for the creation of some object."
You wrote: "Otherwise, you would need to sign a contract for buying a hammer (assuming it was patented) outlining the allowed uses."
I believe this is almost exactly what's at issue in the NYT article, replacing hammer with ink cartridge.