Close Call at the BPAI - Near-Precedential Decision Sinks Computer Claim Under Utility Requirement

Ex Parte Nehls et al., Appeal 2007-1823, Decided: January 28, 2008

After a busy Summer in 2007, the BPAI has been (ominously?) quiet as of late, issuing no precedential opinions since Ex Parte Catan in July 2007, and only issuing 4 informative opinions during the same time.

In Ex Parte Nehls, the BPAI came close to breaking their silence, where Chief Administrative Judge Fleming, along with Administrative Patent Judges Adams, Grimes, Green, Linck, Prats and Fredman decided a controversial case over an application that claimed a computer-based system for comparing nucleic acid sequences:

13. A computer-based system for identifying nucleic acid fragments of the human genome of commercial importance comprising the following elements:

a) a data storage means comprising the sense or antisense sequence of at least 18 contiguous nucleotides of any one of SEQ ID NOS:9-1,008;

b) search means for comparing a target sequence to each of the sequences of the data storage means of step a) to identify homologous sequence(s); and

c) retrieval means for obtaining said homologous sequence(s) of step (b).

The claims were rejected by the Examiner under 35 U.S.C. §§ 101 and 112, first paragraph, on the basis that the Specification did not disclose a patentable utility for the claimed computer system comprising SEQ ID NO: 9 in its data storage means.

Under the CAFC's decision in In re Fisher, § 101 requires a utility that is both "substantial" and "specific." The court held that a substantial utility requires showing that “an invention is useful to the public as disclosed in its current form, not that it may prove useful at some future date after further research. Simply put, to satisfy the ‘substantial’ utility requirement, an asserted use must show that that claimed invention has a significant and presently available benefit to the public.”

Turning to the claims, the BPAI summed up the issue this way:

Here, the claimed computer system is disclosed to be useful for identifying nucleic acids that are similar to SEQ ID NOs 9-1008 . . . The utility of the claimed computer system therefore depends on the utility of the nucleic acids of SEQ ID NOs 9-1008: if the disclosed nucleic acids lack utility, so do nucleic acids similar to them and a computer system for identifying such similar nucleic acids.

Finding that the gene trapped sequences (GTSs) (SEQ ID NOs 9-1008) were mere "research intermediaries", the majority decided that such a disclosure lacked utility:

The uses asserted in the Specification for the disclosed nucleic acids . . . are not “substantial” or “specific,” as those terms were defined by the Fisher court. They are not substantial because . . . the GTSs represented by SEQ ID NOs 9-1008 are “no more than research intermediates that may help scientists to isolate the particular underlying protein-encoding genes and conduct further experimentation on those genes.” . . . Accordingly, the GTSs represented by SEQ ID NOs 9-1008 are merely “objects upon which scientific research could be performed with no assurance that anything useful will be discovered in the end.” The uses asserted for the GTSs represented by SEQ ID NOs 9-1008 therefore do not meet the standard for a substantial utility under § 101.

Nor are they specific utilities, because they could be asserted for any partial cDNA transcribed from any gene in the human genome. Because nothing about Appellants’ asserted utilities sets the nucleic acids of SEQ ID NOs 9-1008 apart from any other human cDNA fragment, Appellants have only disclosed general uses for the disclosed GTSs, not specific ones that satisfy § 101.

Now, here's the rub - in deciding an obviousness issue on the same claim, the majority ruled that "the particular sequence data recited in claim 13 is nonfunctional descriptive material and does not distinguish the claimed computer-based system from the prior art system that is the same except for its sequence data" (emphasis added). Adds the opinion:

Here, the descriptive material (SEQ ID NOs) recited in the claims is not functional material like the data structures in Lowry. There is no evidence that SEQ ID NOs 9-1008 functionally affect the process of comparing a target sequence to a database by changing the efficiency or accuracy or any other characteristic of the comparison. Rather, the SEQ ID NOs are merely information being manipulated by a computer; the SEQ ID NOs are inputs used by a computer program that calculates the degree of similarity between a target sequence and each of the sequences in a database. The specific SEQ ID NOs recited in the claims do not affect how the method of the prior art is performed – the method is carried out the same way regardless of which specific sequences are included in the database.

APJ GREEN, dissenting-in-part:

The position of the Majority is inconsistent. It is unfair to Appellants to rely primarily on the sequence data to find that the claims do not meet the utility requirement of 35 U.S.C. § 101, and then state that the sequence data are only nonfunctional descriptive material that does not contribute to the patentability of the claim under 35 U.S.C. § 103(a). Which is it?

I agree with the Majority’s analysis under 35 U.S.C. § 101 that the claimed SEQ ID NOs do not have patentable utility, and thus concur in the result. I do not agree, however, that the SEQ IDs are nonfunctional, descriptive subject matter, which should not be considered in the obviousness analysis. I thus respectfully dissent as to the Majority’s opinion as to the obviousness analysis.

APJ ADAMS, dissenting-in-part:

Along the way the majority engages in a metaphysical discussion of the difference between nucleic acid molecules and SEQ ID NOS . . . Cutting through the chaff, there is no doubt that SEQ ID NOS per se are data, and if Appellants had simply claimed SEQ ID NOS per se, the claims would properly be rejected under 35 U.S.C. § 101 as directed to patent ineligible subject matter. This is, however, not what Appellants have claimed, and a rejection of the claims as drawn to patent ineligible subject matter under 35 U.S.C. § 101 is not before this panel for review.

Nevertheless, the majority blends the concept of patent eligible subject matter under 35 U.S.C. § 101 with the “printed matter” doctrine under 35 U.S.C. § 103 to arrive at their conclusion that the claimed invention is obvious over a prior art reference that does not teach the SEQ ID NOS recited in Appellants’ claims.

Accordingly, I cannot join with the majority’s analysis of the record.

View/download the 53-page opinion here (link)

- Some interesting remarks from the footnotes in this case:

Footnote 3: "The Lowry [CAFC] court did not consider whether, and under what circumstances, computer-readable information that is analogous to printed matter can distinguish a claimed invention from the prior art."

Footnote 4: "a claim to a computerized system for searching a phonebook placed in a database would not be patentable, absent some novel and nonobvious characteristic of the computer hardware or search tools."

Footnote 5: "MP3 files encoding different songs will cause a computer’s speaker to output different music, but music is a paradigmatic nonfunctional descriptive material. Descriptive material is not functional merely because it results in different outputs when acted on by a computer program."