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I was wondering why lawsuits are not raising the subject matter eligibility under Section 101?

For e.g. at the recent news: http://www.law360.com/articles/643635/abbott-wins-another-round-in-20-year-protein-patent-fight why can't the losing party raise the issue of patent eligibility?

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    I am not sure this is answerable, as it is basically asking "what are these parties thinking". However, I can guess at one compelling reason. Most disputes are between parties which each have a suite of patents in the same field. If one party alleged that the subject matter of one patent was unpatentable and so the opponent's patents in that space were invalid, then they would be implicitly admitting that their own patents in that space are invalid. That would be a Pyrrhic victory. – Maca Mar 13 '16 at 11:41
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In general, a person can patent a wide variety of inventions as described in 35 U.S.C. § 101. But one exception to this rule is that a person cannot obtain a patent to a "product of nature." But the scope of a "product of nature" is limited; even a human made microorganism is patentable. The Myriad decision you refer to in your question relates to this narrow "product of nature" exception to patentability, and holds that:

A naturally occurring DNA segment is a product of nature and not patent eligible merely because it has been isolated, but cDNA is patent eligible because it is not naturally occurring.

The simple answer to your question about pharmaceutical patent litigation is that most pharma cases deal with human-made small molecules or biologics. They are not naturally occurring. The are not isolated DNA. So the Myriad case simply does not apply.

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