As detailed in this (paywalled) article, the public comments responding to the U.S. Patent and Trademark Office's "2015 Update on Subject Matter Eligibility" have two overriding themes. First, the USPTO's Section 101 examination "Guidance" lacks consistency and clarity to allow practitioners to predict whether claims will be rejected under 35 U.S.C. § 101. Second, even assuming that the USPTO's Guidance was clear, USPTO practice under Alice and Mayo is inconsistent and unpredictable. Different examiners and different art units apply the Guidance in different ways. Some examiners fail to explain the bases of their patent-eligibility rejections; others set forth bases (e.g., the machine-or-transformation test) that are unsupported by the law.
In short, everyone agrees that the USPTO's implementation of examination for patent-eligible subject matter is a mess. The various players enjoy scant agreement, however, concerning how to clean up that mess.
On the one end of the spectrum, the Biotechnology Industry Organization believes that "the addition of steps or elements that optimize or perfect the conventional method for some specific purpose should always be patent-eligible," and that the USPTO "should consider providing examples of claims to nature-based products where otherwise 'well-understood, routine and conventional' activity has been specified with enough detail to render the claim patent-eligible.” The biotech industry submission goes to lengths to emphasize the factual findings that examiners must make to support Section 101 rejections, and quarrels with the Guidance's permission for examiner's to state a prima facie Section 101 rejection with conclusory statements and Official Notice.
On the other hand, the Electronic Frontier Foundation urges that "[g]iven the ongoing flux and uncertainty with regard to subject matter eligibility, USPTO examiners should exercise caution in . . . assessments of patent applications, and the path of caution weighs toward finding ineligibility in situations of doubt." The EFF then quarrels with examples in the Guidance that suggest patent-eligibility of certain subject matter, and raises examples of recently-issued patents that it believes should have been rejected under Alice.
Further complicating the political picture is that the high tech industry includes an array of views within these two extremes. BSA | The Software Alliance (with high profile members such as Adobe, IBM, Microsoft, and Oracle) sticks up for some business methods, stating that it is wrong to comclude that under Alice "all inventions that have the effect of improving the organization of human activities are not patentable subject matter." Google, on the other hand, wants the USPTO to emphasize to examiners "that an inventive concept generally requires a technical solution to a technical problem rather than recitation of conventional or generic claim elements," which Google believes would "increase consistency and predictability in examinations."
I stick by my earlier recommendation for practitioners to review and use the USPTO's patent-eligibility Guidance where appropriate. But as these recent public comments demonstrate, the law of patent-eligibility is an unpredictable and roiling ocean of disparate interests and views that is unlikely to settle down any time soon.