Thoughts on Ex parte Boyden

EDITORIAL NOTE: This article is posted anonymously at the request of the author. Not all posts from Sue D. Nym are attributable to the same author, but as you will read this author makes reference to a previous article he or she published on The author of that previous article is indeed the anonymous author on this post.


A couple months ago I commented on Ex parte Khvorova, expressing disappointment in its analysis and concern over what this might mean since it is “the first PTAB decision in molecular biology since patenting in that field got turned upside down.” To follow up on these notions, and to give credit where credit is due, I wanted to briefly comment on Ex parte Boyden, which the PTAB issued September 2, 2015.


As a quick reminder, in Ex parte Khvorova the PTAB struck down a claim to an in silico method of designing siRNA molecules. In my opinion, the ultimate outcome was probably correct but the PTAB wrote a vague decision that included several analytical missteps. At the time I worried that, as the first such PTAB decision, Khvorova might set a bad precedent both in terms of the specific erroneous dicta and the generally low analytical rigor.

Boyden Claims

The claims at issue in Ex parte Boyden are even worse than those in Khvorova. In Khvorova the claims were broad and abstract to the point that a finding of ineligibility by the PTAB was likely proper. But the Khvorova claims recited some level of detail and specificity that at least arguably rose to the level of “something more” than the abstract idea of designing siRNA molecules (e.g., “applying an algorithm to said set of candidate siRNA sequences, wherein said algorithm comprises a set of at least four variables, wherein each variable has a value that is determined by a binary condition that is defined by the presence or absence of a base at a position within the sense sequence, and within said algorithm each variable is multiplied by a coefficient”).

The claims in Boyden, on the other hand, appear to be directed to what must be the broadest conception of an abstract idea:

1. A method comprising:

determining at least one amino acid sequence alteration of an amino acid sequence of a disease associated polypeptide, relative to an amino acid sequence of a corresponding nondisease associated polypeptide;

identifying a sub-sequence in the amino acid sequence of the disease associated polypeptide in which the amino acid sequence alteration occurs;

relating the sub-sequence in the amino acid sequence of the disease associated polypeptide to a corresponding subsequence of the amino acid sequence of the corresponding non-disease associated polypeptide; and

determining a treatment characteristic, based on the relating.

Generalizing a patent claim is very dangerous in patent eligibility analysis as it often all but dooms the claim due to the tendency, in summarizing what is “essentially claimed,” to read important details out of the claim language. In this case, however, it is hardly possible (or necessary) to generalize further than the claim already does. The claim recites (1) analyzing the amino acid sequence of any protein associated with any disease (2) to find any alteration relative to the amino acid sequence of the non-disease associated counterpart protein and (3) making any treatment decision based on “the relating” (which, vague as it is, I interpret as the comparison between disease-associated and non-disease associated sequences to detect a difference).


112, § 102 and § 103

This case is interesting on one level in that it shows all the “substantive” provisions of the Patent Act at issue together with § 101. Completely aside from eligibility, there are serious enablement / written description / indefiniteness issues here. One comment to my post on Khvorova rightly noted the unfortunate and often confusing interplay between § 101 and § 112 these days. In fact, the examiner in this case gave § 112 rejections, with the PTAB affirming on indefiniteness and reversing on written description (apparently based on deficiencies in the examiner’s rejection rather than a substantive finding of adequate description).

It is also hard for me to believe this method, claimed as broadly and abstractly as it is, could have been novel (let alone non-obvious) as late as 2007. Sure enough, the examiner gave a § 102 and § 103 rejection in this case, with the PTAB affirming the obviousness rejection and reversing the anticipation rejection (again apparently due to a poorly worded/reasoned rejection).

PTAB Eligibility Decision

When it turns to eligibility, the PTAB panel does a good job of methodically analyzing the claim and applying governing law (at least a much better job than in Khvorova).

The Board starts well by clearly stating the “judicial exception” at play in the case as a “mental process or abstract idea” (Boyden, p.8):

Our initial question with regard to the claim 1 process is whether a person would also be capable of performing the acts of the claimed method as mental steps, or with the aid of pen and paper. See CyberSource Corp. v. Retail Decisions, Inc., 654 F.3d 1366, 1375 (Fed. Cir. 2011) (“That purely mental processes can be unpatentable, even when performed by a computer, was precisely the holding of the Supreme Court in Gottschalk v. Benson.”). Our reviewing court further guides that “a method that can be performed by human thought alone is merely an abstract idea and is not patent-eligible under § 101.” CyberSource, 654 F.3d at 1373.

Boyden, p.11-12.

Mercifully avoiding the potentially harmful dicta scattered throughout Khvorova, the Board then proceeds to succinctly analyze claim 1, the broadest method claim. As to Alice step 1, the Board notes:

Claim 1 is directed to a method that could be conducted in the mind of one of skill in the art while reading a scientific paper that identifies amino acid sequence alterations in a disease associated polypeptide as compared to the normal or non-disease associated polypeptide. As recognized by the Examiner (Ans. 14), claim 1 does not require the step of sequencing a protein, but rather requires determining at least one amino acid sequence alteration in an amino acid sequence relative to another amino acid sequence. [T]hus claim 1 is broad enough to include performing the steps mentally, which falls within the judicial exception of an abstract idea.

Boyden, p.12. Depending on the type of sequence analysis to be performed, comparing in the mind one amino acid sequence to another can range from impossible to quite manageable. The claim’s breathtaking breadth did not exclude very simple analysis that could, as the Board noted, be readily performed in a researcher’s mind.

The Board’s analysis under Alice step 2 is more cursory:

In this case, the recited elements, and the particular order of the elements, i.e., determining amino acid sequences and then comparing them to identify altered sequences in disease associated polypeptides, are all conventional in the art, and Appellants’ claim 1 contains no inventive concept. Thus, we agree with the Examiner that claim 1 is directed to an unpatentable abstract idea.

Boyden, p.12-13. It may have been helpful for the Board to elaborate a little on how or why it concluded these things were conventional in the art. That said, they are in fact so clearly conventional that it’s almost difficult to point to any specific reference showing this. These are fundamental activities molecular biologists have engaged in for decades.

Difficult Alice Hair-Splitting

Moving to the computer-implemented versions of this method, the Board applies the core of Alice and, like the curious little girl of that same name, falls down a bewildering rabbit hole. While “[t]he other independent claims[…] are directed to computer-environment implementations of the process of claim 1[,] limiting an abstract idea to a computer environment does not make an invention patent-eligible.Boyden, p.13 (citing Alice, 134 S. Ct. at 2359; CyberSource, 654 F.3d at 1375; SmartGene, Inc. v. Advanced Biological Labs., SA, 555 F. App’x 950, 951, 954 (Fed. Cir. 2014)). Because in the Board’s view these claims “merely limit the process of claim 1 to a computer environment,” they were held ineligible.

This part of the decision gets more difficult and the Board’s simplistic analysis may be wrong. Alice suggests that the fact an invention relates to an inherently technical activity, rather than a mere way of organizing human activity like in Bilski, weighs heavily in favor of eligibility. Here there can be no argument that the claimed invention relates to a technical endeavor (protein sequence analysis). A contrary rule may require, as some have noted as one of the primary criticisms of the Ariosa decision, that a patentee show two independent inventions in order to have eligible subject matter—i.e., the alleged judicial exception as well as an independently patentable improvement to, e.g., computer technology.

On the other hand, this case may illustrate why Alice’s “technical field” suggestion should not be applied too formalistically. Given the abstractness and breadth of the underlying method claim, allowing another claim that simply requires the method to be performed on a computer rather than in the mind is hard to swallow. A review of the claim language suggests that perhaps the better basis for a finding of ineligibility is the fact that, even though the claim recites and relates to technical activities, there is still no discernible technical advance. These claims recite what was truly routine in the art (i.e., the method of claim 1) and simply say to map it over to computers.

While claim 1 is clearly ineligible, the computer-implemented claims are a closer call and the Board’s holding of ineligibility, while potentially worrisome if carried too far, may be palatable in the limited context of this specific case. As we have so often seen, strict logic and rigorous analysis often give way to “I know it when I see it” conclusions in the Wonderland of § 101.


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Join the Discussion

2 comments so far.

  • [Avatar for Night Writer]
    Night Writer
    October 14, 2015 01:29 pm

    >>Our reviewing court further guides that “a method that can be performed by human thought alone is merely an abstract idea and is not patent-eligible under § 101.”

    This, of course, is coming from ignorance and anti-innovation judges. Can you image any rational person saying that a machine that can do their thinking for them shouldn’t be eligible? Huh? So, if I build a machine to dig for me it is OK, but if I build a machine to think for me it is not? That is thinking that does understand that information processing is a physical process.

    So, the judges are saying that a machine that can do their job of deciding cases is ineligible under 101 because the judges can do it? That doesn’t sound like promoting innovation to me and sounds more like the logic that is used at witch trials in 1200.

  • [Avatar for Itzik]
    October 7, 2015 06:52 am

    Dear Sue,
    You say that you find it hard to believe the claimed method was novel, not to mention non-obvious, and indeed the Examiner seems to retrieve prior art that shows this. But I wonder, if the claim was to a completely new and inventive idea: if it was filed in days where making treatment decisions based on such comparisons was a striking breakthrough in human thinking on utilizing human knowledge of amino acid sequences, would you also find it patent ineligible?