In my recent analysis of the Alice decision, I wrote the following:

In Benson, the Court believed (wrongly it turned about, but that’s beside the point) that the claims covered the basic algorithm for converting binary coded decimal to binary, something that appeared “fundamental” to the domain of computer science and mathematics. Similarly, in Mayo, the Court believed (again, wrongly, but again that’s beside the point) that Prometheus’s claim covered a so-called “law of nature,” something “fundamental” to the domain of medicine and biology. (It’s ok that the Court was wrong on the facts in Benson and Mayo, because what really matters for the future application of § 101 is the methodology and underlying theory, not the specific facts.)

Michael Risch, Professor Law at Villanova School of Law, responding to the last sentence commented that:

This can't be right. Being wrong on the facts of what is abstract or natural half the time is the core of the problem! This is where lower courts will screw up!

Michael is of course right that being wrong on the facts in patent cases, including patent eligiblity is the core problem, and that the lower courts are likely to decide an eligiblity question incorrectly if they "screw up" the facts.

When I said that "what really matters for the future application of § 101 is the methodology and underlying theory, not the specific facts" I was referring to the "specific facts "of Benson and Mayo, and how the Supreme Court will never acknowledge that it got the facts wrong in those cases.  

As we argued in our amicus brief for Ronald Benrey, the Supreme Court was entirely wrong on the facts of Benson.  First, the Court incorrectly believed that Benson's claim was on the basic algorithm for converting binary-coded-decimal to binary.  But Benson clearly stated in his file history that the BCD-binary conversion algorithm was known and that his invention was a specific way of performing the algorithm using a fewer number of operations and digital logic elements than known in the art.  Second, the Court incorrectly believed that computers perform calcluations "by actually doing arithmetic in much the same way a person would by hand."   Finally, the Court assumed, again incorrectly that all mathematical algorithms are scientific truths.  

As to Mayo, there the Court erred in believing that Prometheus' claim recited a law of nature.  Under no modern scientific or philosophical theory does Prometheus' claim qualify as a law of nature.  At best, it is simply a biological fact, an "accidental generalization," no different in kind than saying "adult male Chihuahuas are smaller than adult male Great Danes."

But the Supreme Court will not acknowledge, at least openly, that it got the facts of these cases wrong. In our exchange, Michael correctly noted that

"But lower courts will not see them as wrong. That's the problem."

Indeed, that is the problem.  This is because a court will typically analogize a give claim to the claim in Benson or Diehr or Flook or Mayo, or now Alice as a way of deciding whether is it patent eligible, just like the Court did in Mayo, "The claim before us presents a case for patentability that is weaker than the (patent-eligible) claim in Diehr and no stronger than the (unpatentable) claim in Flook." 132 S. Ct. 1289, 1299.  I call this the "Diehr-Flook Proximity Test."  Court resort to this approach because reasoning by analogy is genetic in the law.   It works sometimes but not always.  By definition a patent claim is a unique thing, and so needs to be treated as such, but courts are so used to “this is like that,” that it is difficult to get them to see things from a different ‘first principles’ perspective, which is often needed in patent eligibility questions.

When a patent eligibility question comes before a lower court, the facts matter tremedously.  While patent eligibility is said to be a question of law, deciding it without understanding the facts of the technology and the facts of the scope of the claim in terms of what it really "preempts" will almost certainly lead to the wrong decision.  That is why we argued in our ABL amicus brief for an objective approach to patent eligibility based the use of the concept of POSITA: whether a POSITA would consider the actual claim limitations to wholly preempt all practical applications of the abstract intellectual idea, law of nature, or natural phenomenon in the real world.  This is because it is the POSITA who would implement a practical application of the idea in the real world. The POSITA would recognize as meaningful limitations that a lay person would consider trivial or insignificant.  

Facts do matter in patent eligiblity.  We can only hope that courts and patent examiners remember that.